Bio-Rad Profinity eXact Purification Resin User Manual

For Technical Support, call your local Bio-Rad office, or in the U.S.,

call 1-800-4BIORAD (1-800-424-6723).

Profinity eXact

™

Protein

Purification System

Instruction Manual

Table of Contents

Section 1 Introduction............................................................1

1.1 Introduction ......................................................................1

Section 2 Product Description ..............................................3

2.1 Profinity eXact System Components ................................3

2.2 Profinity eXact Expression Technology ............................4

2.3 Profinity eXact Purification Technology ............................4

2.4 Resin Characteristics ......................................................6

2.5 Chemical Compatibility ....................................................6

Section 3 Profinity eXact System Strategies ......................10

Section 4 Cloning and Expression Procedures..................12

4.1 pPAL7 Expression Vector ..............................................12

4.2

E. coli

C-Max5a Cloning Host Cell ................................12

4.3

E. coli

BL21(DE3) Expression Host Cell ........................12

4.4 Cloning Region Sequence ............................................14

4.5 General Cloning Guidelines ..........................................14

4.6 Cloning with the Linearized, RIC-Ready pPAL7 Vector ..15

4.6.1

RIC Cloning

........................................................15

4.6.2

Restriction Enzyme Digestion Cloning

................18

4.7 Cloning with the Supercoiled pPAL7 Vector ..................20

Section 5 Protein Expression and Lysate Preparation ......22

5.1 Protein Expression ........................................................22

5.2 Quick Solubility Screening Protocol................................23

5.3 Lysate Preparation ........................................................25

5.3.1

Lysis/Cell Resuspension Buffer Selection
(NaCI, Tris-HCI, and pH)

....................................25

5.3.2

Nucleases and MgCI

2

........................................26

5.3.3

Protease Inhibitors

..............................................26

5.3.4

Urea and Guanidine-HCI

....................................26

5.3.5

Profinity eXact MBP Control Lysate

....................27

5.3.6

Lysis Protocol

......................................................27

Section 6 Purification Procedures ......................................28

6.1 General Guidelines ........................................................28

6.1.1

Wash Buffer Selection

........................................28

6.1.2

Lysate Loading

....................................................29

6.1.3

Profinity eXact MBP Control Lysate

....................29

6.1.4

Cleavage and Elution

..........................................30

6.1.5

Cleaning and Regeneration

................................30

6.2 Profinity eXact Mini Spin Column Kit Purifications ..........30

6.3 Bio-Scale Mini Cartridge Purifications With

LC Instrumentation ........................................................32

6.4 Bio-Scale Mini Cartridge Purifications With Syringe........34

6.5 Gravity Column Purifications ..........................................36

Appendix A N-terminal Target Protein Structure and

Cleavage Kinetics ..............................................38

Appendix B Intrinsic Cleavage Rates....................................41

Appendix C Triggered Cleavage Rates ................................42

Appendix D Comprehensive Chemical Compatibility List ..44

Appendix E Troubleshooting Guide......................................47

Appendix F References ........................................................49

Appendix G Ordering Information ........................................51

Appendix H Legal Information ..............................................52

Section 1
Introduction

Fig. 1. One-step tag cleavage and elution: Pure and simple.

1.1 Introduction

Affinity tags are commonly used to facilitate the purification of
recombinant proteins. Once purified, these proteins are often studied to
further elucidate the protein’s structure, function, and interaction with other
molecules. However, just as a protein’s intermolecular relationship with
other proteins is complex, so is the intramolecular dynamic between a
fusion protein’s affinity tag and the target protein. An affinity tag or protease
recognition sequence may negatively interfere with the protein’s natural
biochemical properties or characteristics (1, 2, 4, 5, 7–12, 15, 16, 18),
yielding ambiguous experimental results. Consequently, researchers have
utilized a variety of methods to remove the affinity tag from a purified protein.

The current technology for tag removal is tedious and time consuming,
requiring a number of steps. After initial purification, the eluted tagged
protein is exposed to a cleavage enzyme, which hydrolyzes the tag from
the protein fusion. A subsequent step is then needed to isolate the protein
from the tag and the protease, which can result in significant loss of product,
additional investment of labor, and increased cost to the overall purification.

The Profinity eXact™(exact affinity cleavage technology) protein purification
system offers a novel alternative to existing affinity purification and cleavage
tools (Figure 1). The system utilizes an immobilized, extensively engineered
protease that both recognizes and avidly binds (KD< 100 pM) to the small
N-terminal co-expressed affinity tag in the protein fusion. Subsequent to
column washing, the protease performs a specific, controlled cleavage and
removal of the tag from the fusion directly on the column, resulting in the

1

2

release of highly purified recombinant protein with a native N-terminus.
During elution, the cleaved Profinity eXact tag remains tightly associated with
the resin’s immobilized protease, eliminating the need for additional steps to
remove the protease and the tag. Addressing a key dissatisfaction with
recombinant tag technology, the Profinity eXact system improves the efficiency
of tag removal by generating a highly purified protein containing only its native
amino acid sequence—all with one simple elution step (see Figure 2). The
tag-free protein’s crystal structure, protein function, and interactions with other
proteins may be studied without concern for an interfering affinity tag.
Additionally, this purification system is well suited for the expression of peptides,
whose small size often complicates expression and purification.

.

Fig. 2. Profinity eXact affinity-tagged maltose binding protein (MBP) purified with a 1 ml
Bio-Scale Mini™Profinity eXact cartridge on a Biologic Duoflow™system. Samples

were run on a 4–12% Criterion™Bis-Tris gel. Lanes 1 and 6, Precision Plus Protein™standards;
lane 2, crude

E. coli

extract; lane 3, host protein contaminants in the flow-through fraction;
lane 4, host protein contaminants washed from the cartridge by Profinity eXact bind/wash
buffer; and lane 5, eluted tag-free MBP.

Section 2
Product Description

2.1 Profinity eXact™ System Components

Table 1. Profinity eXact System Components and Storage Conditions.

CClloonniinngg aanndd EExxpprreessssiioonn SSttaarrtteerr KKiitt,, 2200 rreeaaccttiioonnss CCaattaalloogg NNoo.. 115566--33000000
pPAL7 RIC-ready vector 0.5 µg –20°C

pPAL7 supercoiled vector 10 µg –20°C
SOC medium 2 × 10 ml Ambient/–70°C

E. coli

BL21(DE3) chemical competent expression cells 10 × 50 µl –70°C

E. coli

C-Max5a chemical competent cloning cells 10 × 50 µl –70°C

pUC19 control (10 ng/µl) 10 µl –70°C
RRIICC--RReeaaddyy EExxpprreessssiioonn VVeeccttoorr,, 2200 rreeaaccttiioonnss CCaattaalloogg NNoo.. 115566--33000011
pPAL7 RIC-ready vector 0.5 µg –20°C
SSuuppeerrccooiilleedd EExxpprreessssiioonn VVeeccttoorr,, 2200 rreeaaccttiioonnss CCaattaalloogg NNoo.. 115566--33000022
pPAL7 Supercoiled vector 10 µg –20°C

EE.. ccoollii

BBLL2211((DDEE33)) EExxpprreessssiioonn CCoommppeetteenntt CCeellllss KKiitt,, 1100 rreeaaccttiioonnss CCaattaalloogg NNoo.. 115566--33000033
BL21(DE3) expression cells 10 × 50 µl –70°C
pUC19 control (10 ng/µl) 10 µl –20°C /–70°C
SOC medium 1 × 10 ml Ambient/–70°C

MMoonnoocclloonnaall AAnnttiibbooddyy CCaattaalloogg NNoo.. 115566--33000044
Profinity eXact affinity-tagged antibody 1 vial –20°C
BBoottttlleedd RReessiinn CCaattaalloogg NNoo.. 115566--33000055
Profinity eXact resin 10 ml 4°C
MMiinnii PPuurriiffiiccaattiioonn SSttaarrtteerr KKiitt,, 1100 ppaacckk CCaattaalloogg NNoo.. 115566--33000066

Profinity eXact mini spin columns 10 each 4°C
2 mL capped collection tubes 50 each
Lyophilized Profinity eXact MBP control lysate 1 vial 4°C
Bacterial lysis and extraction reagent 10 ml ambient
Binding/washing buffer 50 ml 4°C/ambient
Elution buffer 20 ml 4°C/ambient

MMiinnii SSppiinn CCoolluummnnss,, 1100 ppaacckk CCaattaalloogg NNoo.. 115566--33000077
Profinity eXact mini spin columns 10 pack 4°C
2ml capped collection tubes 50 pack

PPuurriiffiiccaattiioonn CCaarrttrriiddggeess,, 22 ppaacckk oorr 44 ppaacckk CCaattaalloogg NNooss.. 773322--44664466

&& 773322--44664477
Profinity eXact cartridges, 1 ml 2 or 4 4°C
PPuurriiffiiccaattiioonn CCaarrttrriiddggee,, 11 ×× 55 mmll CCaattaalloogg NNoo.. 773322--44664488
Profinity eXact cartridges, 5 ml 1 4°C
EExxpprreessssiioonn aanndd PPuurriiffiiccaattiioonn SSttaarrtteerr KKiitt CCaattaalloogg NNooss.. 115566--33000000

&& 115566--33000066
Cloning and expression starter kit 20 reactions –70°C
Mini purification starter kit 10 each 4°C

3

2.2 Profinity eXact Expression Technology

Fusion proteins with an N-terminal Profinity eXact tag are expressed with
the pPAL7 expression vector (5.9 kb). This inducible expression vector
utilizes the strong, tightly regulated T7 lac promoter (6). The pPAL7 plasmid
confers ampicillin resistance, constitutively expresses the lacI repressor,
and has been designed to facilitate cloning of a target gene through several
different methods.

Precise fusions—in which the resultant purified product does not contain
any additional amino acids at the N-terminus—may be constructed using
the HindIII restriction site and an appropriate restriction site in the multiple
cloning site (MCS) or by cloning with the prepared restriction-independent
cloning (RIC) vector. Use of the linearized, RIC-ready vector facilitates
high-throughput cloning of DNA sequences, regardless of the restriction
sites that may be present within a target gene.

Some proteins exhibit significant N-terminal structure that may affect
binding to the resin (Appendix A: N-terminal Target Protein Structure and
Cleavage Kinetics), or their first two amino acids result in non-ideal cleavage
kinetics (Appendix B: Intrinsic Cleavage Rates and Appendix C: Triggered
Cleavage Rates). The challenges presented by these proteins are easily
addressed at the cloning stage by utilizing a two amino acid linker (such as
the recommended Thr-Ser linker) between the Profinity eXact tag and the
target protein—generating an

imprecise fusion

. A Thr-Ser spacer between
the Profinity eXact tag and the target protein ensures optimal cleavage
kinetics and purification, regardless of the target protein. These imprecise
fusion proteins, once purified, retain the Thr-Ser linker at the N-terminus.

2.3 Profinity eXact Purification Technology

The Profinity eXact purification resin utilizes Superflow™crosslinked
agarose coupled to a unique subtilisin mutant. The Superflow support
matrix exhibits low nonspecific protein binding while providing the high
mechanical stability and flow dynamics desired for medium pressure liquid
chromatography applications (see Table 2).

Mutant subtilisin protease—S189, the functional ligand immobilized to the
support matrix—has been precisely engineered for affinity chromatography
(3, 14). S189 subtilisin is extremely stable and efficiently refolds

in vitro

.

The recombinant protease also is designed to specifically recognize and

4

cleave at the C-terminus of a nine amino acid sequence (EEDKLFKAL).
Through a third set of mutations, this cleavage reaction has been changed
from a self-initiating digestion to one that is triggered by 100 mM potassium
fluoride; complete cleavage is most often achieved within 30 min, at room
temperature.

The subtilisin exhibits extremely high binding affinity to the 8 kD Profinity
eXact tag (KD< 100 pM). The Profinity eXact tag is a form of the wild-type
subtilisin BPN' prodomain—genetically engineered for high stability and to
contain the distinct cleavage recognition sequence of the subtilisin mutant.
Additionally, the subtilisin prodomain serves as an exo-recognition
sequence for the immobilized subtilisin, which significantly increases the
system’s binding affinity and cleavage specificity to the tag.

Once it has been captured by the Profinity eXact purification resin—and the
cleavage reaction has been triggered with a sodium fluoride-containing
buffer—the affinity tag is precisely cleaved at the C-terminus of the cleavage
recognition sequence. The result is a quickly purified protein product that
lacks any amino acid residues derived from the Profinity eXact tag.

5

2.4 Resin Characteristics

The resin attributes are summarized in Table 2.

Table 2. Characteristics of Profinity eXact Purification Resin.

Functional ligand Mutant subtilisin, S189

Base bead Superflow agarose (6% crosslinked)

Format Spin column: 600 µl 17% suspension

(100 µl settled resin)

Bottled: 50% suspension

Cartridge: 1 or 5 ml packed resin

Storage buffer: 100 mM sodium phosphate,

0.02% sodium azide, pH 7.2

Particle size 60–160 µm

Molecular exclusion limit 6,000 kD

Recommended linear flow rate <1,000 cm/hr at 25°C*

pH stability 2–13

Chemical compatibility See Table 4 and Appendix D: Comprehensive

Chemical Compatibility List

Storage 4°C

Shelf life in storage buffer When unopened, 1 year from receipt; store at 4°C

Operational temperature 4–40°C

* Recommended linear flow rate determined by the following factors:

The flow rate of 100 mM sodium phosphate, pH 7.2 was incrementally increased through a Bio-Scale Mini Profinity eXact
1 ml cartridge packed with a 20% compression factor. The pressure-flow curve for the Profinity eXact purification resin
became nonlinear at linear velocities above 1,000 cm/hr.

2.5 Chemical Compatibility

The Profinity eXact purification system is compatible with a broad range of
additives commonly used to purify proteins. Extensive information is listed
in Appendix D: Comprehensive Chemical Compatibility List.

Highest purification yields are achieved by eliminating Cl–ions from
all lysis and wash buffers. The chloride ions from additives like NaCl,

KCl, and Tris-HCl act as slower cleavage/elution-triggering anions (see
Table 3). NaCl or KCl salt is commonly added to lysis and wash buffers to
reduce electrostatic interactions between background proteins (or DNA)
with a chromatographic support. When using the Profinity eXact purification
resin, sodium acetate (NaOAc) and potassium acetate (KOAc) are

6

!

recommended substitutes for NaCl or KCl. If using the 0.1 M sodium
phosphate Profinity eXact bind/wash buffer, a higher sodium phosphate
concentration (e.g. 0.3–1.0 M, pH 7.2) may also be used to raise the ionic
concentration of the lysis and wash buffers.

Table 3. Triggering Anions.

Triggering Compound Concentration for Concentration for

Anion Fast Cleavage Moderate Cleavage

F

–

NaF, KF 100 mM 5 mM

N

3

–

NaN

3

10 mM 1 mM

NO

2

–

NaNO

2

5 mM 1 mM

HCO

2

–

NaHCO

2

1,000 mM 25 mM

Cl

–

NaCl, KCl >1,000 mM 75 mM

Although the wild-type subtilisin BPN' is a serine protease, the
purification resin is unaffected by most serine protease inhibitors due to
the Profinity eXact subtilisin’s active site mutations. The protease cocktails
tested include combinations of the following inhibitors: AEBSF, aprotinin,
benzamidine, E-64, EDTA, leupeptin, pepstatin A, phenanthroline, and
PMSF. See Table 4 for additional information regarding the compatibility
of protease inhibitors, common additives, and solutions typically used in
affinity chromatography methods.

7

Table 4. Chemical Compatibility (Partial List—See Appendix A for
Complete List)

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Triggering Ions F–, Cl–, N

3

–

, NO

2

–

, HCO

2

–

Triggers cleavage of fusion Remove from all

llyyssiiss aanndd wwaasshh
and elution of target buffers for highest yields
protein See

TTaabbllee

3 for ionic concentrations

to use as trigger in elution buffer

Salts Sodium acetate Reduces non-specific protein £3 M (an excellent substitute for NaCl

binding due to ionic interactions in lysis and wash buffers)

NNaaCCll oorr KKCCll

Triggers cleavage of fusion Remove from all

llyyssiiss aanndd wwaasshh
and elution of target protein buffers—use sodium acetate or

sodium phosphate instead to reduce
electrostatic interactions

Buffers Tris-HCl Cl

–

in lysis and wash buffers Substitute with Tris-acetate or
triggers cleavage of fusion Tris-phosphate and adjust pH with
and elution of target protein acetic or phosphoric acid

Tris-acetate 50 mM tested
Tris-phosphate 50 mM tested

Acids HCl Cl

–

in lysis and wash buffers Avoid use of HCl for highest yields;
triggers cleavage of fusion instead, use acids such as
and elution of target protein phosphoric or acetic acid

Detergents Non-ionic (NP-40, Triton

®

Solubilize proteins £5% (v/v)

X-100, Tween

®

-20)

Zwitterionic (CHAPS, Solubilize proteins £5% (v/v or w/v)
CHAPSO, Dodecyl-b,
D-maltoside,
Octylthioglucoside)

Ionic (CTAB, Sarkosyl, Significantly lower yields Remove from all buffers
SDS)

Protease PMSF F

–

triggers cleavage of fusion 0.5 mM; no adverse effects when

Inhibitors and elution of target protein incubated with resin for up to 3 hr

TLCK 100 µM
TPCK 100 µM

Pharmingen™ Protease F

–

may lower yield slightly 2×

Inhibitor Cocktail

Calbiochem

®

Protease 1×

Inhibitor Cocktail Set I

8

!

!

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Roche cOmplete Protease F–may lower yield slightly 1×
Inhibitor Cocktail Tablet

Lysis Solutions Bacterial Lysis and 1×

Extraction (Bio-Rad)

B-PER

®

in phosphate 1×

buffer (Pierce)

B-PER

®

(Pierce) Cl–from Tris-HCl results in 1×

slightly lower yield

ReadyPreps

™

Lysis Do not use

solutions (Epicentre)

BugBuster

®

(EMD) 1×

FastBreak

™

Cell Lysis 1×

(Promega)

CelLytic

™

Express Do not use

(Sigma)

Denaturants Guanidine•HCl Cl

-

triggers cleavage of fusion Remove from all

llyyssiiss

and

wwaasshh

during load and wash steps buffers

Urea Solubilizes proteins £2 M; with 4 M, ~30% reduced

control MBP binding capacity
observed; with 8 M, ~70% reduced
control MBP binding capacity and
reduced purity observed

Other Additives CaCl

2

Essential component for £5 mM; use with buffer such as
purification of Ca

2+

-binding MES, MOPS, or PIPES buffer to

proteins eliminate precipitation of Ca

2+

with

either fluoride- or phosphate-

Cl

–

triggers cleavage during containing Profinity eXact buffers
load and wash steps

MgCl

2

Essential metal cofactor for £5 mM; if higher Mg

2+

nucleases concentrations are desired, use

magnesium acetate instead

Cl

–

triggers cleavage during
load and wash steps Do not add to Profinity eXact elution

buffer—Mg

2+

precipitates with F–;
instead, use an elution buffer with an
alternative trigger, such as 10 mM
NaN

3

, with 100 mM sodium

phosphate, pH 7.2

9

Section 3
Profinity eXact

™

System Strategies

1. Basic purification strategy—create and purify an imprecise fusion
that ensures initial purification success with minimal optimization by
incorporating a Thr-Ser spacer.

a. Determine cloning method and construct fusion protein

RIC-ready pPAL7 (Section 4.6)

Supercoiled pPAL7 (Section 4.7)

b. Express Profinity eXact™affinity-tagged fusion protein

E. coli

culturing and expression (Section 5.1)

Solubility check of expressed fusion protein (Section 5.2)

c. Lyse cells and store lysate at 4°C

Bacterial lysis and extraction reagent
(provided with mini spin volumn purification kit)

Cell resuspension buffer (100 mM sodium
phosphate, pH 7.2) and lyse using desired
lysis method

d. Purify protein with chloride-free wash (100 mM sodium phosphate,

pH 7.2; 4°C) and elution (100 mM sodium fluoride, 100 mM sodium
phosphate, pH 7.2; room temperature) buffers using appropriate
purification protocol

Spin column (Section 6.2)

Bio-Scale™Mini cartridge with LC instrument (Section 6.3)

Bio-Scale Mini cartridge with syringe (Section 6.4)

Gravity column (Section 6.5)

2. Precise purification strategy—create a precise fusion to obtain a
completely tag-free, purified protein

a. Consider, if known, the P1' and P2' (first two N-terminal amino

acids of target protein) residues’ effect on cleavage kinetics

10

Appendix A: N-terminal Target Protein Structure and
Cleavage Kinetics

Appendix B: Intrinsic Cleavage Rates

Appendix C: Triggered Cleavage Rates

b. Determine cloning method and construct fusion protein

RIC-ready pPAL7 (Section 4.6)

Supercoiled pPAL7 (Section 4.7)

c. Express Profinity eXact™affinity-tagged fusion protein

E. coli

culturing and expression (Section 5.1)

Solubility check of expressed fusion protein (Section 5.2)

d. Lyse cells and store lysate at 4°C

Select appropriate chloride-free lysis buffer (Section 5.3.1)

Lyse using desired lysis method (Section 5.3.6)

e. Identify appropriate buffers and conditions

Select appropriate chloride-free wash buffer (Section 6.1.1)

f. Purify protein using appropriate purification protocol

Spin column (Section 6.2)

Bio-Scale Mini cartridge with LC instrument (Section 6.3)

Bio-Scale Mini cartridge with syringe (Section 6.4)

Gravity column (Section 6.5)

11

Section 4
Cloning and Expression Process

4.1 pPAL7 Expression Vector

The pPAL7 expression vector utilizes the T7lac promoter to strongly
express a Profinity eXact fusion protein in

E. coli

cells producing T7 RNA
polymerase. The pPAL7 plasmid constitutively expresses the lacI repressor
and confers ampicillin resistance to the host cell (Figure 3). The Profinity
eXact™tag is an 8.2 kD affinity tag that functions as an N-terminal fusion
tag (Figure 3).

4.2

E. coli

C-Max5aaCloning Host Cell

The

E. coli

C-Max5a cells [F–j80 dlacZDM15 D(

lac

ZYA-

arg

F)U169

rec

A1

endA1

hsd

R17(r

k

–

, m

k

+

)

phoA sup

E44 l

–

thi

-1

gyr

A96 relA1] are chemical
competent transformation cells that are specifically designed to maximize
cloning success. This

E. coli

K12 derivative facilitates isolation of
high-quality plasmid DNA and is an ideal host strain for transformation of
ligation cloning reactions.

4.3

E. coli

BL21(DE3) Expression Host Cell

E. coli

BL21(DE3) cells [

E. coli

B F

-

dcm ompT hsd

S(r

B

–

, m

B

–

)

gal l(DE3)

]
are used for high-level protein expression with T7 RNA polymerase-based
expression systems. The strain is a derivative of

E. coli

B, which is deficient

in the

lon

protease as well as the

ompT

outer membrane protease,

facilitating the isolation of intact recombinant proteins. The host is a lysogen
of lDE3 and contains the T7 RNA polymerase gene—integrated into the
chromosome—under control of the lacUV5 promoter. 1–2 mM
isopropyl-b-D-thiogalactopyranoside (IPTG) is used to induce the expression
of recombinant proteins cloned into vectors downstream of a T7lac promoter
and transformed into the

E. coli

BL21(DE3) cells.

12

Fig. 3. pPAL7 vector map.

Table 5. Features of the pPAL7 Expression Vector.

Vector Feature Vector Position

T7

lac

promoter 1–17
Profinity eXact tag 92–316
MCS

SpeI 318
NcoI 325
BamHI 333
EcoRI 345
XhoI 351
NotI 358

T7 terminator 413–460

bla

(AmpR) 1,079–1,936

Ori

2,499

lacI

4,634–5,713

13

4.4 Cloning Region Sequence

Fig. 4. Sequence of Profinity eXact tag and cloning region.

4.5 General Cloning Guidelines

The pPAL7 vector is provided in both linearized and supercoiled form in
the Profinity eXact cloning and expression starter kit. The linearized
plasmid (Profinity eXact RIC-ready pPAL7 vector) may be ligated with
PCR products possessing compatible overhangs generated by either the
restriction-independent cloning (RIC) or traditional restriction enzyme
digestion method. Both the RIC-ready and the supercoiled pPAL7 vector
may be used to generate either precise- or imprecise-fusion proteins:

Precise fusions

—purifications result in a tag-free target protein
without extra amino acids after cleavage of the Profinity eXact
tag.

Imprecise fusions

—purifications result in the retention of a spacer
(e.g., Thr-Ser) at the N-terminus of the target protein. Presence
of the Thr-Ser spacer ensures successful purifications with
minimal optimization.

14

T7 Promoter lac Operator -

1 TAATACGACT CACTATAGGG GAATTGTGAG CGGATAACAA TTCCCCTCTA GAAATAATTT TGTTTAACTT TAAGAAGGAG
ATTATGCTGA GTGATATCCC CTTAACACTC GCCTATTGTT AAGGGGAGAT CTTTATTAAA ACAAATTGAA ATTCTTCCTC

Profinity eXact Tag (92-316) -

NdeI

GlyGlyLys SerAsnGlyGlu LysLysTyr IleValGly PheLysGlnGly PheLysSer CysAlaLys

81 ATATACATAT GGGAGGGAAA TCAAACGGGG AAAAGAAATA TATTGTCGGG TTCAAACAGG GCTTTAAGAG CTGCGCTAAG
TATATGTATA CCCTCCCTTT AGTTTGCCCC TTTTCTTTAT ATAACAGCCC AAGTTTGTCC CGAAATTCTC GACGCGATTC

Profinity eXact Tag (92-316) -

LysGluAspVal IleSerGlu LysGlyGly LysLeuGlnLys CysPheLys TyrValAsp AlaAlaSerAla ThrLeuAsn·

161 AAGGAGGATG TCATTTCTGA AAAAGGCGGG AAACTCCAAA AGTGCTTCAA ATATGTAGAC GCAGCTAGCG CTACATTAAA
TTCCTCCTAC AGTAAAGACT TTTTCCGCCC TTTGAGGTTT TCACGAAGTT TATACATCTG CGTCGATCGC GATGTAATTT

Profinity eXact Tag (92-316) -

SapI

Cleavage Recognition Sequences -

·GluLysAla ValGluGluLeu LysLysAsp ProSerVal AlaTyrValGlu GluAspLys LeuPheLys AlaLeuThrSer·

241 CGAAAAAGCT GTAGAAGAAT TGAAAAAAGA TCCGAGCGTC GCGTACGTAG AAGAAGACAA GCTCTTCAAA GCTTTGACTA
GCTTTTTCGA CATCTTCTTA ACTTTTTTCT AGGCTCGCAG CGCATGCATC TTCTTCTGTT CGAGAAGTTT CGAAACTGAT

Profinity eXact Cleavage Site

NcoI

SpeI

·SThrMetAla GlySerGly CysGluPheLeu GluAlaAla Ala***

321 GTACCATGGC GGGATCCGGC TGCGAATTCC TCGAGGCGGC CGCATAAGCC CGAAAGGAAG CTGAGTTGGC TGCTGCCACC
CATGGTACCG CCCTAGGCCG ACGCTTAAGG AGCTCCGCCG GCGTATTCGG GCTTTCCTTC GACTCAACCG ACGACGGTGG

T7 Terminator

401 GCTGAGCAAT AACTAGCATA ACCCCTTGGG GCCTCTAAAC GGGTCTTGAG GGGTTTTTTG CTGAAAGGAG GAACTATATC
CGACTCGTTA TTGATCGTAT TGGGGAACCC CGGAGATTTG CCCAGAACTC CCCAAAAAAC GACTTTCCTC CTTGATATAG

-

XhoI -

BamHI EcoRI NotI STOP

HindIII SpeI

-

Optimal room-temperature purification of the target protein with the
Profinity eXact resin is dependent upon the amino acid residues in the first
two positions of the target protein. (Residues 1 and 2 are referred to as
positions P1' and P2', respectively.) Target proteins with a P1' proline are
not subject to resin cleavage and elution; on the other hand, proteins with
a P1' cysteine have a particularly high intrinsic cleavage and elution rate
with the Profinity eXact resin, even in the absence of a fluoride-containing
elution buffer. Refer to Appendices A-C for more details. Target proteins
with these challenging P1'-P2' amino acid residues should be cloned with
a threonine-serine spacer. This spacer maximizes successful purification
results, regardless of the target protein’s P1'-P2' residues or any effect its
N-terminal structure may have on the Profinity eXact tag’s resin-binding
properties.

If the presence of an additional Thr-Ser dipeptide (208 Da) at the
N-terminus of the target protein is not an issue, cloning of a target gene
and the spacer into the vector is the recommended strategy—requiring the
least amount of purification optimization (either using the SpeI cloning site
or obtaining a PCR target gene product with the Thr-Ser spacer at the
N-terminus).

4.6 Cloning With the Linearized, RIC-Ready pPAL7 Vector

4.6.1 RIC Cloning

Because this cloning method is completely free of any use of restriction
enzymes, it is independent of restriction enzyme sites within the target
protein and is thus ideal for high-throughput cloning. The RIC-ready
vector has been prepared to generate the

dephosphorylated

overhangs

depicted in Figure 5.

Fig. 5. RIC-ready pPAL7 vector.

15

AAGCTCTTCA HO-AATTCCTCGAGG
TTCGAGAAGTTTC-OH GGAGCTCC

ready pPAL7

-

Forward and reverse PCR primers starting with the predefined eight bases
illustrated in Step 1 are used to PCR the target gene. Using the 3'Æ5'
exonuclease activity of T4 DNA polymerase, the PCR product is treated
with T4 DNA polymerase in the presence of dGTP to create overhangs
compatible with the RIC-ready pPAL7 vector. The prepared insert and
RIC-ready vector are then ligated using standard ligation techniques and
finally transformed into an appropriate

Escherichia coli

cloning host such

as the

E. coli

C-Max5a competent cells provided with the Profinity eXact

system.

Method

1. PCR-amplify target gene using iProof™high-fidelity DNA
polymerase.

Both forward and reverse primers must be 5'-phosphorylated to
clone into the dephosphorylated vector, and they must contain the
following DNA sequences (Nindicates target DNA sequence):

Thr-Ser

Forward primer: 5' – P-AAGCTTTG(ACTTCT)NNNNNNNNN… – 3'

Optional

stop

Reverse primer: 5' – P-AATTCTTANNNNNNNNN… – 3'

The optional ACTTCT (Thr-Ser) spacer of the forward primer can be
included to minimize all target protein effects on cleavage of the
Profinity eXact tag. If the template is an ampicillin-resistant plasmid, it
may be DpnI-treated post PCR amplification to ensure background-free
transformants.

2. Purify, if desired, PCR product by either excising and purifying
band following agarose gel electrophoresis, or using PCR
Kleen™spin column kit (catalog #732-6000).

3. Generate RIC-ready pPAL7 vector-compatible overhangs by T4
DNA polymerase treatment of purified PCR product.

16

Amount of purified PCR product used in reaction mix: 0.2–1 pmol

T4 DNA polymerase: 5 U/pmol DNA fragment (Novagen; add DTT

to 5 mM in reaction mix) or
5 U/µg DNA fragment (Promega) or
1 U/µg DNA fragment (NEB)

ddH2Ox µl
PCR fragment y µl
10 × T4 DNA polymerase buffer 2 µl
100 mM dGTP 0.5 µl
T4 DNA polymerase z µl

Total 20 µl

Incubate reaction 20 min at 12°C; then inactivate the polymerase by
incubating 20 min at 75°C; store on ice until ready to use. Further
purification of the reacted product is unnecessary.

Note: Shorter or longer incubations or use of higher temperatures
during the T4 DNA polymerase treatment may result in reduced
cloning efficiency.

4. Ligate 2 µl (20 ng) RIC-ready pPAL7 vector and RIC-prepared PCR
product insert using T4 DNA ligase and standard ligation protocol.

If using a quick ligase, incubate ligation mix for 20 min at room
temperature. The slightly longer incubation time is recommended
because of the short three-base overhang.

Ligations with molar ratios of (1–10)/1 (insert/vector) are typical.

5. Transform

E. coli

C-Max5aachemical competent cells within 30 min

of completion of the ligation reaction.

17

Add 1–5 µl ligation mix to each 50 µl aliquot of competent cells.
Incubate on ice, 30 min. Heat shock at 42°C, exactly 30 sec. Quickly
return to ice and incubate 2 min. Add 250 µl SOC recovery medium to
transformation mix. Shake tubes at 37°C, 1 hr; best results are
obtained when recovery cultures are shaken horizontally, to maximize
oxygen transfer rate. Dilute cells (e.g., 1/20¥) with SOC medium. Plate
undiluted and diluted cells on relatively dry, LB+100 µg/ml ampicillin
agar plates and incubate 37°C, 16–18 hr.

As an example, when a 10/1 molar ratio of a 1.1 kb MBP RIC-prepared
insert to RIC-ready pPAL7 vector (37 ng insert/20 ng vector) is used
with the described ligation and transformation protocols, transformation
efficiencies of >1×107CFU/µg DNA are typically achieved with >95%
correct clone yield.

4.6.2 Restriction Enzyme Digestion Cloning

Using appropriate PCR primers, the target gene may also be amplified
and digested with a suitable Type IIS restriction enzyme and EcoRI to
obtain a PCR product with overhangs compatible with the RIC-ready
pPAL7 vector.

Method

1. PCR-amplify target gene using iProof high-fidelity DNA poly­merase.

The forward primer must contain a recognition sequence for a suitable
Type IIS restriction enzyme that generates a three-base, 5'-overhang
(e.g., BspQI or EarI). The reverse primer must contain an EcoRI
recognition sequence and an in-frame stop codon. Note that the uncut
vector contains a stop codon after the NotI site, in frame with the
Profinity eXact tag.

18

If the template is an ampicillin-resistant plasmid, it may be DpnI-treated
post PCR amplification to ensure background-free transformants.

2. Digest PCR product with EcoRI and Type IIS restriction enzymes
corresponding to forward primer.

3. Purify, if desired, PCR product by either excising and purifying
band following agarose gel electrophoresis, or using PCR
Kleen™spin column kit (catalog #732-6000).

4. Ligate 2 µl (20 ng) RIC-ready pPAL7 vector and restriction
enzyme-digested PCR product insert using T4 DNA ligase and
standard ligation protocol.

Ligations with molar ratios of (1–10)/1 (insert/vector) are typical.

5. Transform

E. coli

C-Max5aachemical competent cells within

30 min of completion of ligation reaction.

19

Restriction

Enzyme (and

Isoschizimers)

BspQI (SapI/

LguI/PciSI)

EarI (Bst6I/

Eam1104I/Ksp632I)

Bolded sequences must be present in primer.

ACTTC

AAG represents 5’-three-base overhang generated upon BspQI or EarI digestion

X represents additional bases to improve restriction enzyme digestion efficiency.

N represents target protein gene sequence.

Restriction

Enzyme

EcoRI G/AATTC 5’ – XXGAATTCTTANNNNNNNNNNNNNN… – 3’

T sequence is optional; include to create a fusion protein with a Thr-Ser spacer for ideal

binding and cleaving kindetics.

Enzyme

Cleavage

GCTCTTC (1/4) 5’ – XXGCTCTTCAAAGCTTTG(ACTTCT)NNN… – 3’

CTCTTC (1/4) 5’ – XXCTCTTCAAAGCTTTG( ACTTCT)NNNN… – 3’

Enzyme

Cleavage

stop

Forward Primer

Reverse Primer

.

Add 1–5 µl ligation mix to each 50 µl singles aliquot of competent
cells. Incubate on ice, 30 min. Heat shock at 42°C, exactly 30 sec.
Quickly return to ice and incubate 2 min. Add 250 µl SOC recovery
medium to transformation mix. Shake tubes at 37°C, 1 hr; best results
are obtained when recovery cultures are shaken horizontally, to
maximize oxygen transfer rate. Dilute cells (e.g., 1/20¥) with SOC
medium. Plate undiluted and diluted cells on relatively dry,
LB+100 µg/ml ampicillin agar plates and incubate 37°C, 16–18 hr.

4.7 Cloning with the Supercoiled pPAL7 Vector

When using the supercoiled pPAL7 vector, a conventional cloning strategy
is employed—using a PCR-amplified gene and standard restriction
enzymes to create vector-compatible overhangs for ligation. Both the
supercoiled pPAL7 vector and the PCR product are digested with HindIII
(to create a precise fusion) or SpeI (for an imprecise fusion). A second
restriction enzyme that digests the vector and the PCR product at one of
the available downstream restriction sites (i.e., NcoI, BamHI, EcoRI, XhoI,
or NotI) in the vector’s MCS enables directional cloning. The plasmid and
insert are then ligated and transformed into an appropriate host using
standard techniques.

Method

1. PCR-amplify target gene using iProof high-fidelity DNA poly­merase.

The forward primer must contain the bolded sequence below. The
reverse primer must contain an appropriate enzyme recognition
sequence and a stop codon. The following choices of primer
sequences and enzymes may be used:

20

If an imprecise fusion is desired, but the spacer length is not critical,
the forward PCR primer may be designed for cloning into NcoI,
BamHI, EcoRI, or XhoI.

Should a target gene contain an internal HindIII site that would preclude
cloning into the vector’s HindIII site, a forward primer may be designed
that utilizes a Type IIS restriction enzyme to generate a four-base,
HindIII-compatible, 5’-overhang (e.g., BsaI, BsmAI, or BsmBI). The
design of this forward primer is similar to the Type IIS restriction
enzyme method described on page 18.

If the template is an ampicillin-resistant plasmid, it may be DpnI-treated
post PCR amplification to ensure background-free transformants.

2. Digest PCR product and supercoiled pPAL7 vector with appropriate
upstream and downstream restriction enzymes.

3. Purify, if desired, PCR product by either excising and purifying
band following agarose gel electrophoresis, or using PCR
Kleen™spin column kit (catalog #732-6000).

4. Ligate supercoiled pPAL7 vector and restriction enzyme-digested
PCR product insert using T4 DNA ligase and standard ligation
protocol.

Ligations with molar ratios of (1–10)/1 (insert/vector) are typical.

5. Transform

E. coli

C-Max5aachemical competent cells within 30 min

of completion of ligation reaction.

Forward Primer with HindIII

p

21

sequence

Forward Primer with SapI

sequence

Forward Primer with SpeI

sequence

Reverse Primer with/NotI sequence (BamHI,

EcoRI, XhoI, or NcoI sequence may also be
used)

Bolded sequences must be present in primer.

ACTTCT sequence is optional; include to create a fusion protein with a Thr-Ser spacer for ideal binding
and cleaving kinetics.

X represents additional bases to improve restriction enzyme digestion efficiency.

N re

resents target protein gene sequence.

Precise Fusion 5’–XXAAGCTTTG(ACTTC T)NNN…–3’

Precise Fusion 5’–XXGCTCTTCAAAGCTTTG(ACTTC T)NNN…–3’

Imprecise Fusion 5’ – XXACTAGTNNNNNNN… – 3’

5’ – XXGCGGCCGCTTA

Stop

NNNN… –

3’

Add 1–5 µl ligation mix to each 50 µl aliquot of competent cells.
Incubate on ice, 30 min. Heat shock at 42°C, exactly 30 sec. Quickly
return to ice and incubate 2 min. Add 250 µl SOC recovery medium to
transformation mix. Shake tubes at 37°C, 1 hr; best results are
obtained when recovery cultures are shaken horizontally, to maximize
oxygen transfer rate. Dilute cells (e.g., 1/20¥) with SOC medium. Plate
undiluted and diluted cells on relatively dry, LB+100 µg/ml ampicillin
agar plates and incubate 37°C, 16–18 hr.

Section 5
Protein Expression and Lysate Preparation

5.1 Protein Expression

Glucose is a catabolite repressor of the lac operon (19) and, in conjunction with
the lacI repressor and T7lac promoter from pPAL7, affords tighter
background control of target gene expression prior to induction. Maximum
plasmid stability of pPAL7 constructs within

E. coli

BL21(DE3) bacteria is
achieved by cultivating the cells and inoculum cultures on LB plates and in
liquid medium—both supplemented with 0.5–1.0% glucose (13, 17).

1. Purify cloned expression vector from cloning strain by DNA

miniprep.

The Aurum™plasmid mini kit (catalog #732-6400) may be used to
quickly obtain high purity plasmid DNA.

2. Transform

E. coli

BL21(DE3) chemical competent cells with the

purified plasmid DNA.

Add 0.5 µl purified DNA to a 50 µl aliquot of competent cells. Incubate
on ice, 30 min. Heat shock at 42°C, exactly 30 sec. Quickly return to
ice and incubate 2 min. Add 250 µl SOC recovery medium to
transformation mix. Shake tubes at 37°C, 1 hr; best results are
obtained when recovery cultures are shaken horizontally, to maximize
oxygen transfer rate. Dilute cells (e.g., 1/20¥) with SOC medium. Plate
undiluted and diluted cells on relatively dry, LB+100 µg/ml ampicillin+0.5%
glucose agar plates and incubate 37°C, 16–18 hr.

22

3. Prepare overnight seed culture by inoculating 2 ml LB+100 µg/ml

ampicillin + 0.5% glucose.

Shake culture at 37°C, 16–18 hours.

4. Inoculate expression culture with overnight seed culture.

After inoculation of suitable expression medium supplemented with
100 µg/ml ampicillin, shake expression culture at desired temperature
until cell density (OD

600

) reaches 0.5–0.7. Induce expression of target

protein by addition of 1–2 mM isopropyl-b-D-thiogalactopyranoside
(IPTG); for cultures expressed at 37°C continue shaking for 3–4 hr.
Collect culture sample for analysis in Step 5. Harvest cells by
centrifugation. Lyse cells immediately or freeze cell paste.

5. Analyze whole cell culture by Experion™or SDS-PAGE to verify

target protein expression.

The Quick Solubility Screening Protocol, below, may be followed to
determine whether the expressed protein is in the soluble or insoluble
lysate fraction.

5.2 Quick Solubility Screening Protocol

Before choosing a purification strategy, it is useful to determine the
approximate expression level of a protein and to determine if the
overexpressed target protein partitions into the soluble or insoluble lysate
fraction. Soluble proteins are typically purified with the native purification
procedure, while insoluble proteins may be solubilized with detergents or
urea.

23

The following procedure provides a quick screen for solubility and
expression level:

1. Pellet ~2 ml

E. coli

culture by centrifuging at 16,000 × g for 1 min

at 4°C.

Decant supernatant.

2. Resuspend pellet in 500 µl of bind/wash buffer and sonicate for

60 sec, on ice, in 10 sec pulses.

Transfer 50 µl of the sonicate to a tube, and label as the

Total

sample.

3. Centrifuge lysate at 16,000 × g for 5 min at 4°C; transfer supernatant

to a clean tube.

Transfer 50 µl of the supernatant to a tube, and label

Soluble

.

4. Resuspend insoluble pellet in 500 µl of bind/wash buffer containing

4 M urea.

5. Centrifuge lysate at 16,000 × g for 5 min at 4°C.

Transfer 50 µl of the supernatant to a tube, and label

Insoluble

6. To each 50 µl Total, Soluble, and Insoluble samples, add 150 µl

Laemmli sample buffer, and heat for 5 min at 95°C.

7. Load 10 µl of each sample on SDS-PAGE gel.

8. Examine soluble and insoluble fractions for target protein.

Approximate the expression level, and determine partitioning of the
target protein. A partitioning profile of a soluble target protein, with
approximate expression level, can be seen in Figure 6.

24

Fig. 6. Partioning profile. Precision Plus Protein™molecular weight markers were loaded in

lane 1, followed by the total, soluble, and insoluble fractions in lanes 2–4 respectively. The
gel depicts Profinity eXact™affinity-tagged maltose binding protein (MBP), which partitions
into the soluble fraction and can be purified using the native purification protocol.

5.3 Lysate Preparation

5.3.1 Lysis/Cell Resuspension Buffer Selection (NaCl, Tris-HCl, and pH)

The Profinity eXact bind/wash buffer (100 mM sodium phosphate,
pH 7.2; provided in the mini purification starter kit (catalog #156-3006) may
be used to resuspend cells for lysis. To prevent target protein cleavage and
elution during the lysate loading step, resuspension and lysis buffers
should not contain any chloride ions (e.g., NaCl). If a higher ionic
concentration is desired to reduce possible electrostatic interactions
between contaminant proteins and the resin, sodium acetate or a higher
sodium phosphate concentration may be used (e.g., 300 mM).

Similarly, Tris-HCl buffers should be avoided because of the chloride
present in the acid conjugate. Tris buffers still may be used by utilizing Tris
base and acetic acid to produce a CI–-free, Tris-acetate buffer with the
proper pH. A Tris-phosphate buffer may likewise be made with Tris base
and phosphoric acid.

25

!

The Profinity eXact purification resin is fully functional at pH 6–8. Intrinsic
cleavage of some proteins due to high OH–concentrations during the
lysate loading and wash steps may be observed if the lysis and wash
buffer pH are greater than 7.5. Lysis buffers close to pH 7.0 are therefore
preferred. On the other hand, using a lysis buffer at a pH below 7.0 may
help minimize intrinsic cleavage for those proteins with non-ideal P1'–P2'
amino acids. When adjusting the buffer pH with an acid, avoid any use of
HCl; instead, use a Cl–-free acid such as H3PO4or HOAc.

5.3.2 Nucleases and MgCl

2

Nucleases may be added to the lysate to reduce the viscosity caused by
DNA. In most situations, Mg2+ions will not need to be added to the lysate
for effective nuclease activity. However, if the addition of magnesium is
desired, add magnesium acetate or magnesium sulfate, instead of
magnesium chloride. Elimination of chloride ions will maximize final product
yield.

5.3.3 Protease Inhibitors

The Profinity eXact purification resin is unaffected by most protease
inhibitors and protease inhibitor cocktails (see Table 4). The fully compatible
protease cocktails tested include combinations of the following inhibitors:
AEBSF, aprotinin, benzamidine, E-64, EDTA, leupeptin, pepstatin A,
phenanthroline, and PMSF. Please refer to the manufacturer’s literature
for specific inhibitor combinations and concentrations. Exposure of the
resin to 0.5 mM PMSF for greater than 3 hours is not recommended.

5.3.4 Urea and Guanidine-HCl

Urea and guanidine-HCl are often used to solubilize proteins expressed in
inclusion bodies or otherwise insoluble. Purifications with the Profinity
eXact resin can be run with up to 2 M urea without affecting binding capacity
or column performance. Proteins solubilized in 4 M urea can also be
purified, although lower yields may be observed. Concentrations of urea
above 4 M are not recommended, as both yield and target protein purity
suffer. The chloride ions present in guanidine-HCl preclude the use of this
denaturant.

26

5.3.5 Profinity eXact MBP Control Lysate

The Profinity eXact MBP control lysate is a lyophilized

E. coli

lysate that
contains recombinant Profinity eXact affinity-tagged maltose binding protein
(Met-Lys P1'–P2'). Upon purification, the 40 kD tag-free MBP protein is
recovered.

For use with the Profinity eXact mini purification spin kit, add 10 mL
Profinity eXact bind/wash buffer to the lyophilized control lysates, and gently
swirl or mix the buffer until the lyophilized cake is completely
resuspended. Store the vial on ice, and use within 30 min of preparation for
best results. Load 0.5 ml of resuspended lysate into a Profinity eXact mini
spin column or 5 ml lysate onto a 1 ml cartridge.

5.3.6 Lysis Protocol

1. Lyse cells using either method a or b:

a. For cell lysis by sonication, or other mechanical method,

resuspend cells in lysis buffer at buffer/wet cell paste ratio of
5–10 ml buffer/g wet cell paste.

b. Lyse cells using sodium phosphate-based bacterial lysis and

extraction reagent (pH 7.5).

The bacterial lysis and extraction reagent was developed for quick
lysis and extraction of recombinant proteins expressed in

E. coli

for
purification with the Profinity eXact system. This lysis solution has the
same formulation as the Profinia™bacterial lysis/extraction reagent
(250 ml, catalog #620-0220).

Using the volume of lysis and extraction reagent suggested in Table 6,
completely resuspend the cell pellet with the lysis solution by
vortexing or vigorously pipetting the lysate. Vortex for an additional
minute. For lysis of cell pellets from larger bacterial cultures, a 10 ml/1 g
ratio of lysis and extraction reagent solution to wet cell paste is
recommended.

27

Table 6. Recommended Lysis Volumes.

CCuullttuurree CCeellll LLyyssiiss aanndd EExxttrraaccttiioonn

VVoolluummee DDeennssiittyy RReeaaggeenntt RReeccoommmmeennddeedd LLyyssiiss MMeetthhoodd

((mmLL)) ((OODD

660000

)) VVoolluummee

1.5 1.5–3.0 300 µL Vortex 1 min

40 1.5–3.0 5 mL Incubate 10 min

2. Centrifuge lysate at ≥≥10,000 × g, 30 min. Transfer supernatant to
separate container until ready to purify.

3. Filter lysate with 0.45-µm (or 1.0-µm) filter.

To preserve the flow characteristics of the Bio-Scale™Mini Profinity
eXact cartridges or any prepared gravity flow columns, it is recommended
that the whole cell lysate be centrifuged at high speed and filtered
(e.g., 0.45 µm membrane) prior to application.

4. Chill lysate to 4°C prior to loading on resin.

Maintaining the lysate on ice reduces target protein degradation and
minimizes potential cleavage and elution during the lysate loading
step. Using lysate and wash buffers at 4°C is the easiest and most
effective method of addressing proteins sensitive to intrinsic cleavage.

Section 6
Purification Procedures

6.1 General Guidelines

6.1.1 Wash Buffer Selection

For maximum yield, prevent target protein cleavage and elution during
the wash step by ensuring wash buffers do not contain any chloride
ions (e.g., NaCl). If a higher ionic concentration is desired to reduce possible

electrostatic interactions between contaminant proteins and the resin, sodium
acetate or a higher sodium phosphate concentration may be used
(e.g., 300 mM).

Similarly, Tris-HCl buffers should be avoided because of the chloride present
in the acid conjugate. Tris buffers may still be used by utilizing Tris base and

28

!

!

acetic acid to produce a chloride-free, Tris-acetate buffer with the proper pH.
A Tris-phosphate buffer may likewise be made with Tris base and phosphoric
acid.

The Profinity eXact™purification resin is fully functional at pH 6–8. Some intrinsic
cleavage due to high OH– concentrations during the wash steps may be
observed if the wash buffer pH is greater than 7.5. Wash buffers close to
pH 7.0 are therefore preferred. On the other hand, using a wash buffer at a
pH below 7.0 may help to minimize intrinsic cleavage for those proteins with
non-ideal P1'–P2' amino acids. When adjusting the buffer pH with an acid,
avoid any use of HCl; instead, use a Cl–-free acid such as phosphoric acid or
acetic acid.

Wash buffers should be prechilled to 4°C to minimize target elution during the
wash step. The Profinity eXact bind/wash buffer may be stored at 4°C for
ease of use.

6.1.2 Lysate Loading

As mentioned previously, lysates should be maintained at 4°C to ensure
maximum purified protein yields. Improved purification results of multimeric
proteins are typically observed by loading a diluted lysate preparation and
using substoichiometric amounts of the fusion protein, compared to the available
number of Profinity eXact tag binding sites.

6.1.3 Profinity eXact MBP Control Lysate

The Profinity eXact MBP control lysate is a lyophilized

E. coli

lysate that
contains recombinant Profinity eXact affinity-tagged maltose binding protein
(Met-Lys P1'–P2'). Upon purification, the 40 kD tag-free MBP protein is
recovered.

For use with the Profinity eXact mini purification spin kit, add 10 ml Profinity
eXact bind/wash buffer to the lyophilized control lysates, and gently swirl or
mix the buffer until the lyophilized cake is completely resuspended. Store the
vial on ice, and use within 30 min of preparation for best results. Load 0.5 ml
of resuspended lysate into a Profinity eXact mini spin column or 5 ml lysate
onto a 1 ml cartridge.

29

!

6.1.4 Cleavage and Elution

Elution of target proteins is typically conducted by incubating the resin in
100 mM sodium fluoride, 100 mM sodium phosphate buffer, pH 7.2, at room
temperature, for 30 min. However, if elution at 4°C is desired, the resin should
be incubated for at least 16 hr to ensure complete cleavage.

Elution of some slow-cleaving proteins may be accelerated by replacing the
sodium fluoride with 10 mM sodium azide in 100 mM sodium phosphate,
pH 7.2 buffer, or using prolonged elution incubation. The azide-containing
buffer is also an excellent alternative for eluting proteins that would otherwise
require a subsequent buffer-exchange step.

Finally, if purified

uncleaved

fusion protein is desired, the Profinity eXact
affinity-tagged target protein may be eluted by applying 0.1 M H3PO4resin
regeneration solution instead of fluoride-containing elution buffer.

6.1.5 Cleaning and Regeneration

The Profinity eXact resin can be regenerated with 0.1 M H3PO4by stripping
off the cleaved Profinity eXact tag from the S189 ligand. Use of the acid
cleaning solution also effectively removes contaminants from the resin.
Immediately after the cleaning step, the resin should be re-equilibrated with
bind/wash buffer or storage buffer (100 mM sodium phosphate, 0.02% sodium
azide, pH 7.2) to prevent loss of activity. Because the resin is base stable,
residual contaminants may also be removed by washing the resin with 0.1 M
NaOH. However, after cleaning with NaOH, the resin should be equilibrated
with bind/wash buffer. The Profinity eXact tag must then be removed using
the aforementioned H3PO4regimen.

6.2 Profinity eXact Mini Spin Column Kit Purifications

Each prepacked spin column contains 100 µl settled resin. One column
volume (CV) is equivalent to one volume of settled resin (i.e., 1 CV = 100 µl,
for a spin column).

Prepare the Profinity eXact MBP control lysate as described on page 29.

Reserve a small amount of lysate prior to loading the sample onto the column.
This will serve as a sample for the

lysate

lane for later analysis (e.g., SDS-PAGE).
All centrifugation steps are carried out at room temperature at 1,000 × g for
30 sec. If a centrifuge is unavailable, the spin columns may be drained by
gravity flow.

30

1. Prechill bind/wash buffer on ice or at 4°C.

2. Remove storage buffer from packed spin column.

Snap off end cap of spin column, and retain the cap for later use to plug
the spin column. Place spin column in a 2 ml collection tube and
centrifuge 1,000 × g, 30 sec. Decant filtrate and replace spin column in
collection tube.

3. Preequilibrate spin column with 2 × 500 µl wash buffer.

Because the storage buffer contains 0.02% sodium azide as a bactericide,
this pre-equilibration step must be performed to remove the azide
triggering ion. Add the first 500 µl aliquot of wash buffer; centrifuge;
decant filtrate. Repeat. Plug the spin column by inverting the snap-off
cap and inserting it into the bottom of the spin column.

4. Add up to 600 µl chilled, clarified

E. coli

lysate—depending on

expression level—to each spin column.

Use a pipet to gently mix lysate with the resin. Cap the column.

Use 500 µl of the resuspended Profinity eXact MBP control lysate as a
purification positive control.

5. Gently mix 5–20 min at 4°C on rocking platform or rotator.

For quick screening, incubate the lysate and resin at room temperature
for 1–5 min.

When using the spin column format, purification of larger proteins (>75 kD)
may benefit from longer incubations at 4°C.

6. Collect unbound, flow-through material.

Carefully twist and remove end cap. Retain end cap, place the spin column
in a clean collection tube. Centrifuge and collect the flowthrough; label
the fraction

Flowthrough

.

When purifying proteins of low expression, higher volumes of lysate may
be applied to the resin by repeating Steps 4–6.

7. Insert spin column into new 2 ml collection tube.

8. Wash the resin with 500 µl wash buffer.

Mix contents using a pipet or by inverting the capped spin column.

31

!

9. Centrifuge, repeat wash step.

Remove remaining unbound proteins by centrifuging. Save the flow
through from both wash steps and label fractions

Wash 1

and

Wash 2

.
Additional washes with more stringent wash buffers may be performed at
this stage if required for the target protein being purified.

10. Plug spin column with inverted, snap-off end cap.

11. Elute tag-free protein by adding 500 µl elution buffer.

Mix contents with a pipet or by inverting the capped spin column.
Incubate samples at room temperature for at least 30 min. with occasional
mixing throughout. For maximum yield, the capped column should be
placed on a rocking platform or rotary mixer. For cleavage incubations
performed at 4°C, incubate at least 12 hr.

Carefully twist and remove end cap. At the end of the incubation, place
column in a new collection tube, and centrifuge to obtain released,
tag-free target protein. Save the eluates for further analysis.

12. Analyze collected fractions from above steps by A

280

, Experion,

SDS-PAGE, ELISA, western blot, etc.

6.3 Bio-Scale™Mini Cartridge Purifications with LC
Instrumentation

Profinity eXact resin-packed 1 ml Bio-Scale Mini cartridges are typically run at
up to 3 ml/min (720 cm/hr), but may be run at flow rates up to 4 ml/min
(1,000 cm/hr). The 5 ml cartridges should be run at flow rates up to
10 ml/min (480 cm/hr). The back pressure at these flow rates should be less
than 10 psi. To avoid over pressurization of the cartridges during 4°C
chromatography purifications, linear velocities £ 480 cm/hr (240 cm/hr, for a
5 ml cartridge) are recommended if the lysate or wash buffer contains 20%
glycerol or other viscous additives.

One column volume (CV) is equivalent to one volume of settled resin (i.e.,
1 CV = 1 ml, for a 1 ml cartridge).

Reserve a small amount of lysate prior to loading sample onto the column.
This will serve as sample for the lysate lane for later analysis (e.g., SDS-PAGE).
Note: Flow rates are given for a 1 ml cartridge. (Flow rates for a 5 ml
cartridge are provided in parenthesis.)

£

32

Part 1: Buffer Preparation

1. Prepare wash buffer (0.1 M sodium phosphate, pH 7.2).

Avoid NaCl in the wash buffer. See Wash Buffer Selection section, page

28. Store wash buffer at 4°C.

2. Prepare elution buffer (0.1 M sodium phosphate, 0.1 M sodium
fluoride, pH 7.2).

3. Prepare cleaning solution (0.1 M H3PO4)

Be sure to prepare a 0.1 M phosphoric acid (cf. 0.1 N).

4. Prepare storage buffer (0.02% sodium azide, 0.1 M sodium phosphate,
pH 7.2).

Part 2: Sample Loading and Washing

5. Equilibrate cartridge with 10 CV wash buffer at 3 ml/min (10 ml/min).

Because the storage buffer contains 0.02% sodium azide as a bactericide,
this equilibration step must be performed to remove the azide triggering
ion.

6. Load cell extract/lysate at 1 ml/min (5 ml/min).

For a 1 ml cartridge, a 5 ml lysate load is typical.

7. Wash cartridge with at least 10 CV wash buffer at 3 ml/min
(10 ml/min), or until UV trace has achieved baseline.

Applying wash buffer at a higher flow rate (compared to lysate loading)
shortens the process and will reduce potential intrinsic cleavage.
Additional washes with more stringent wash buffers may be performed at
this stage if required for the target protein being purified.

Part 3: Elution

8. Equilibrate cartridge with 2 CV Elution Buffer at 3 ml/min (10 ml/min) or
until cartridge effluent conductivity indicates that cartridge is
saturated with elution buffer; stop pump.

9. Incubate cartridge in elution buffer for at least 30 min, room
temperature.

For 4°C cleavage, incubate the cartridge for at least 12 hr.

33

!

!

10. Restart pumping at 3 ml/min (10 ml/min) of elution buffer and
collect eluate containing purified target protein.

The OD

280

may be used to monitor the elution of the purified protein and

determine when to stop the elution process.

Alternatively, protein may be eluted by pumping elution buffer at 0.1 ml/min
(0.5 ml/min). In this case, the slow flow rate is maintained until 5 CV
elution buffer is applied.

Part 4: Cleaning

11. Wash cartridge with at least 5 CV equilibration buffer at 3 ml/min
(10 ml/min).

12. Clean cartridge with 3 CV cleaning solution at 3 ml/min (10 ml/min).

13. Neutralize cartridge with 5 CV wash buffer at 3 ml/min (10 ml/min).

14. Apply at least 2 CV storage buffer by pump or syringe to the cartridge;
cap cartridge and store at 4°C.

6.4 Bio-Scale Mini Cartridge Purifications With Syringe

If a liquid chromatography system is unavailable, a syringe may be used to
apply lysate and buffers to a cartridge. A 20+ ml, luer-fitting syringe is
suggested. One column volume (CV) is equivalent to one volume of settled
resin (i.e., 1 CV = 1 ml, for a 1 ml cartridge).

Reserve a small amount of lysate prior to loading sample onto the column.
This will serve as sample for the

lysate

lane for later analysis (e.g., SDS-PAGE).

Part 1: Buffer Preparation

1. Prepare wash buffer (0.1 M sodium phosphate, pH 7.2).

Avoid NaCl in the wash buffer. See Wash Buffer Selection section,

page 28. Store wash buffer at 4°C.

2. Prepare elution buffer (0.1 M sodium phosphate, 0.1 M sodium
fluoride, pH 7.2).

When using a syringe, the elution buffer should be kept at 4°C.

3. Prepare cleaning solution (0.1 M H3PO4).

34

!

Be sure to prepare a 0.1 M phosphoric acid (cf. 0.1 N).

4. Prepare storage buffer (0.02% sodium azide, 0.1 M sodium phosphate,
pH 7.2).

Part 2: Sample Loading and Washing

5. Remove plugs from each end of cartridge and

retain plugs

for later

use (Steps 9 and 15).

6. Equilibrate cartridge with at least 10 CV wash buffer.

Because the storage buffer contains 0.02% sodium azide as a bactericide,
this equilibration step must be performed to remove the azide triggering
ion. Fill syringe with Wash buffer, attach to cartridge and push full volume
through the cartridge.

7. Load chilled (4°C) cell extract/lysate.

Fill syringe with desired volume of lysate, attach to cartridge and push full
volume through the cartridge. For a 1 ml cartridge, a 5 ml lysate load is
typical.

8. Wash cartridge with at least 15 CV wash buffer.

Fill syringe with wash buffer, attach to cartridge and push full volume
through the cartridge. Additional washes with more stringent wash
buffers may be performed at this stage if required for the target protein
being purified.

Part 3: Elution

9. Fill syringe with 6 CV elution buffer and apply 1.5 CV to cartridge.

Collect the 1.5 CV filtrate in 0.5 CV fractions and analyze fractions for
target protein. Some purified protein is often collected in the second
fraction.

The syringe may be left attached to the cartridge inlet end; plug the outlet
using the retained luer plug from Step 5.

35

!

10. Incubate cartridge in elution buffer for at least 30 min, room
temperature.

If performing the incubation at 4°C, incubate the cartridge for at least 12 hr.

11. Apply remaining 5 CV elution buffer.

The bulk of the target protein is typically collected in the first five elution
fractions.

Part 4: Cleaning

12. Wash cartridge with at least 5 CV wash buffer.

13. Clean cartridge with 3 CV cleaning solution.

14. Neutralize cartridge with 5 CV wash buffer.

15. Equilibrate the cartridge with 2 CV storage buffer; cap cartridge and
store at 4°C.

6.5 Gravity Column Purifications

The Profinity eXact affinity resin may be packed in a Bio-Rad Econo-Pac

®

column for use in a gravity purification format. Columns packed with 1–4 ml
resin exhibit the most practical flow characteristics. One column volume (CV)
is equivalent to one volume of settled resin (i.e., 1 CV = 1 ml, for a column
packed with 1 ml settled resin).

Reserve a small amount of lysate prior to loading sample onto the column.
This will serve as sample for the lysate lane for later analysis (e.g., SDS-PAGE).

Part 1: Buffer and Column Preparation

1. Prepare wash buffer (0.1 M sodium phosphate, pH 7.2).

Avoid NaCl in the wash buffer. See Wash Buffer Selection section,

page 28. Store wash buffer at 4°C.

2. Prepare elution buffer (0.1 M sodium phosphate, 0.1 M sodium
fluoride, pH 7.2).

3. Prepare cleaning solution (0.1 M H

3PO4

).

Be sure that 0.1 M phosphoric acid is used (cf. 0.1 N).

36

!

4. Prepare storage buffer (0.02% sodium azide, 0.1 M sodium
phosphate, pH 7.2).

Part 2: Column Preparation

5. Mix resin gently to completely resuspend 50% (v/v) resin slurry.

6. Transfer 2–8 ml 50% resin slurry to Econo-Pac column; allow
storage buffer to completely drain.

Part 3: Sample Loading and Washing

7. Equilibrate column with 10 CV Wash buffer.

Because the storage buffer contains 0.02% sodium azide as a bactericide,
this equilibration step must be performed to remove the azide triggering
ion. Apply wash buffer to resin and allow buffer to gravity drain.

8. Load chilled (4°C) cell extract/lysate.

Apply lysate to resin and allow buffer to gravity drain.

9. Wash cartridge with at least 15 CV cold wash buffer.

Upon complete draining of the wash buffer, plug the Econo-Pac column.
Additional washes with more stringent wash buffers may be performed at
this stage if required for the target protein being purified.

Part 4: Elution

10. Apply 5 CV elution buffer to plugged column.

Mix the resin with the elution buffer by using a pipet.

11. Incubate column in elution buffer for at least 30 min, room
temperature.

If performing the incubation at 4°C, incubate the column for at least 12 hr.

12. Collect purified protein.

Remove the column’s plug and allow eluate containing the purified target
protein to gravity drain into collection tube.

37

!

Part 5: Cleaning

13. Wash column with at least 5 CV wash buffer.

14. Clean column with 3 CV eleaning solution.

15. Neutralize resin with 5 CV wash buffer.

16. Equilibrate resin with 2 CV storage buffer; cap cartridge and store
at 4°C.

Appendix A
N-terminal Target Protein Structure and
Cleavage Kinetics

The N-terminal structure of a target protein may affect the binding of
N-terminal affinity tags to their ligands. Protein GB(6 kD) is one example of
a protein with high N-terminal structure. To assess the effect of N-terminal
structure on the cleavage properties of the Profinity eXact™tag, a fusion
protein was constructed to deliberately place the last two amino acids of
the Profinity eXact tag (P1 = Leu, P2 = Ala) within the b1-strand of the
four-stranded GBb-sheet fold (Figure 7), thus obscuring the cleavage site
in a construct termed -2. Binding of the eXact-GBfusion protein to S189
remains strong, even though it requires local unfolding of GB.

38

Fig. 7. N-terminal interactions of Profinity eXact affinity-tagged GB. The cognate

sequence of the Profinity eXact tag is partially shown in yellow (KLFKAL); the P1' amino acid
(Ala) and the P2' amino acid (Tyr) GBare shown in cyan. Notice that the P2, P1, P1' and P2'
amino acids are all part of the b-strand. The hydrogen bonds that would likely be broken for
the fusion protein to bind to the affinity resin are shown by the dashed lines. The tyrosine side
chain of the P2' amino acid is buried in the hydrophobic core of GB.

The relative rates of cleavage of a series of -2 GBmutants as a function of
P1' and P2' amino acids are similar to the GFP series (Figure 9 and Figure 10,
see pages 42–43), but the absolute rates are about 10-fold slower than
GFP. Even with the GB-occluded processing site, all P1' amino acids—
except E, I, D, and P—are >90% processed in 30 minutes (with P2' = Y).
Apparently, the strong binding of the Profinity eXact tag to the S189
subtilisin ligand is able to disrupt the N-terminal structure of GBenough to
permit productive substrate binding interactions and processing at
reasonable rates for almost all P1', P2' combinations. The processing of
P1' = E (P2' = Y) is about 70% complete in 30 minutes with 0.1 M KF and
P1' = I or D (P2' = Y) is 50% processed in 30 minutes. As mentioned
previously, a fusion containing a proline residue in the P1' position is not
processed.

39

Although practical elution times are generally achieved with no spacer
amino acids (+0 constructs), the use of a two amino acid spacer between
the Profinity eXact tag and the target protein can minimize any negative
impact of N-terminal target protein structure on cleavage kinetics. This
effect is demonstrated by a series of Profinity eXact tag-GBmutants in
which length of the connection between the Profinity eXact tag and G

B

was varied (Table 7).

Table 7. Profinity eXact Tag: GBFusion Constructs.

Spacer Length Fusion Construct

(# Amino Acids)

+0 Profinity eXact tag - M A

Y G

B

+1 Profinity eXact tag - M A T Y G

B

+2 Profinity eXact tag - M A T T Y G

B

+3 Profinity eXact tag - M A T T T Y G

B

+4 Profinity eXact tag - M A T G T T Y G

B

Amino acids that are structured in GBare underlined and in red.

The kinetics of these constructs as a function of fluoride concentration are
shown in Figure 8.

Fig. 8. Cleavage rates vs. [fluoride] for Profinity eXact tag-GBfusions.

40

The results show that while N-terminal structure can slow cleavage kinetics,
the cleavage rate of the +2 construct is about five-times faster than the +1
construct. The effect of lengthening the insertion beyond +2 diminishes for
a purification application.

Because the average rate of triggered cleavage using the EEDKLFKAL
cognate sequence is quite fast relative to the requirements for convenient
purification (cleavage rate > 0.1 min–1), almost any target protein, except
those with proline at the P1' positions, should work in the Profinity eXact
system. A slow P1' amino acid (E, V, I, or D) in combination with extensive
N-terminal structure may require some increase of the standard incubation
time in fluoride for good recovery of the target protein.

Appendix B
Intrinsic Cleavage Rates

Intrinsic cleavage rates are dependent not only upon P1'–P2' residues.
High N-terminal target protein structure and lower purification temperatures
(relative to 25°C) will minimize intrinsic cleavage. Therefore, Figure 9 is
presented as a relative guide to assist in determining cloning and purification
strategies.

Intrinsic rates <0.03 min–1are desired for minimum product loss during
lysate loading and resin washing. Except for targets with a P1'-cysteine,

use of 4°C lysate and wash buffers will alleviate most intrinsic
cleavage issues. Intrinsic cleavage may also be reduced by addition of a

Thr-Ser spacer during cloning.

41

Fig. 9. Effect of P1'–P2' amino acids on intrinsic cleavage rate (rates derived from a
green fluorescent protein (GFP) fusion in presence of 100 mM sodium phosphate
buffer, pH 7.2; room temperature).

Appendix C
Triggered Cleavage Rates

For elution of target protein, fluoride ion-triggered cleavage rates >0.1 min

–1

will yield rates conducive to successful purification. Proteins with a
P1'-proline will not be cleaved and must be cloned with a spacer
(e.g., Thr-Ser) for proper purification. A spacer should also be considered
for proteins with a P2'-Pro (with P1'- Asp, Ile, Val, or Glu) or a P1'-Asp.

Purification of fusion proteins with slower anticipated triggered cleavage
rates should be incubated with elution buffer for at least 1 hour.

42

Fig. 10. Effect of P1'–P2' amino acids on triggered cleavage rate (rates derived from a
GFP fusion in presence of 100 mM sodium fluoride, 100 mM sodium phosphate buffer,
pH 7.2; room temperature).

43

Appendix D
Comprehensive Chemical Compatibility
List

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Triggering Ions F–, Cl–, N

3

–

, NO

2

–

, HCO

2

–

Triggers cleavage of fusion Remove from all

llyyssiiss aanndd

and elution of target protein

wwaasshh

buffers for highest

yields

See Table 3 for ionic
concentrations to use as
trigger in elution buffer

Salts Sodium acetate Reduces nonspecific protein £3 M (an excellent substitute

binding due to ionic for NaCl in lysis and wash
interactions buffers)

NNaaCCll

or

KKCCll

Triggers cleavage of fusion Remove from all

llyyssiiss aanndd

and elution of target protein

wwaasshh

buffers—use sodium
acetate or sodium phosphate
instead to reduce electrostatic
interactions

Buffers Tris-HCl Cl–in lysis and wash buffers Substitute with Tris-acetate or

triggers cleavage and elution Tris-phosphate and adjust pH
of target protein with acetic or phosphoric acid

Tris-acetate 50 mM tested

Tris-phosphate 50 mM tested

HEPES 50 mM tested

PIPES 50 mM tested

MOPS 50 mM tested

MES 50 mM tested

Sodium acetate 200 mM tested

Sodium bicarbonate 200 mM tested

Sodium borate 100 mM tested

Acids HCl Cl–in lysis and wash buffers Avoid use of HCl for highest

triggers cleavage of fusion yields; instead, use acids such
and elution of target protein as phosphoric or acetic acid

44

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Detergents Non-ionic (NP-40, Solubilizes proteins £5% (v/v)

Triton®X-100,
Tween®-20)

Zwitterionic (CHAPS, Solubilizes proteins £5% (v/v or w/v)

CHAPSO,
Dodecyl-b,
D-maltoside,
Octylthioglucoside)

Ionic (CTAB, Sarkosyl, Significantly lowers yields Remove from all buffers

SDS)

Protease PMSF F–may lower yield slightly by 0.5 mM; no adverse effects
Inhibitors triggering cleavage of fusion when incubated with resin for up

and elution of target protein to 3 hr

TLCK 100 µM

TPCK 100 µM

Pharmingen

™

F–may lower yield slightly 2×
Protease Inhibitor
Cocktail

Calbiochem®Protease 1×

Inhibitor Cocktail
Set I

Roche cOmplete F–may lower yield slightly 1×

Protease Inhibitor
Tablet

Lysis Solutions Bacterial Lysis and 1×

Extraction Reagent
(Bio-Rad)

B-PER®in phosphate 1×

buffer (Pierce)

B-PER Cl–from Tris-HCl results in 1×

slightly lower yield

ReadyPreps™Lysis

solutions (Epicentre) Do not use

BugBuster®(EMD) 1×

FastBreak™Cell Lysis 1×

(Promega)

CelLytic™Express Do not use

(Sigma)

45

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Sulfhydrl b-mercaptoethanol 20 mM
(Reducing) Dithiothreitol (DTT) 10 mM
Agents Tris-(2-carboxyethyl) 5 mM

phosphine (TCEP)

Denaturants Guanidine•HCl Solubilizes proteins Remove from all

llyyssiiss aanndd

wwaasshh

buffers

Urea Cl–triggers cleavage of fusion

during load and wash steps £2 M; with 4 M, ~30%

reduced control MBP binding
capacity observed; with 8 M,
~70% reduced control MBP
binding capacity, and lower
purity observed

Metal Chelators EDTA Metalloprotease inhibitor 20 mM

EGTA Metalloprotease inhibitor 20 mM

Other Additives CaCl

2

Essential component for £5 mM; use with buffer such

purification of Ca2+-binding as MES, MOPS, or PIPES buffer

proteins to eliminate precipitation of

Ca2+with either fluoride- or
phosphate-containing Profinity
eXact buffers

Cl–triggers cleavage of fusion

during load and wash steps

MgCl

2

Essential metal cofactor for £5 mM; if higher Mg

2+

nucleases concentrations are desired,

Cl–triggers cleavage of fusion use magnesium acetate

during load and wash steps instead

Do not add to Profinity eXact
elution buffer—Mg

2+

precipitates with F–; instead,
use elution buffer with
alternative trigger, such as
10 mM NaN3, 100 mM sodium
phosphate, pH 7.2

Glycerol Stabilizer 20%; higher concentrations

do not affect resin, but do
increase viscosity

Ethylene glycol Stabilizer 20% (v/v)

Ethanol Stabilizer 20% (v/v)

Sorbitol Stabilizer 20% (w/v)

Sucrose 20% (w/v)

46

RReeaaggeenntt GGrroouupp RReeaaggeenntt CCoommmmeennttss AAcccceeppttaabbllee CCoonncceennttrraattiioonn

Imidazole 200 mM

Ammonium sulfate 15%; use of higher

concentrations is dependent
upon target’s solubility

Sodium sulfate 100 mM

DMSO Stabilizer 5%

DNase/RNase Reduce lysate viscosity 200 U nuclease, 10 U Rnase I

Appendix E
Troubleshooting Guide

Premature elution of cleaved, target protein is observed:

Fusion protein • Insert Thr-Ser spacer between Profinity eXact™tag

and target protein by cloning into pPAL7’s SpeI site

Lysis • For maximum yields, do not use lysis buffers and

reagents that contain triggering ions, specifically
Cl–or F

–

• Maintain lysate at 4°C prior to loading

• Shorten incubation time

• Utilize lysis buffer with pH <7.0

Wash • Pre-chill wash buffer to 4°C prior to use

• Do not use lysis buffers and reagents that contain
triggering ions, specifically Cl–or F–. When preparing
wash buffer, substitute sodium acetate (NaOAc) for
NaCl; do not use HCl to adjust pH—phosphoric or
acetic acid should be used

• Utilize wash buffer with pH <7.0

Target protein remains uncleaved and/or does not elute completely:

Fusion protein • Verify that first amino acid (P1') downstream of the

Profinity eXact cleavage site is not proline

• If first amino acid of target protein is undesirable for
cleavage, insert amino acid spacer (e.g., Thr-Ser)
immediately downstream of cleavage site by
site-directed mutagenesis or clone into SpeI site of
pPAL7

47

!

!

Elution • Incubate resin with elution buffer for longer time (try

up to 1 hour at room temperature or overnight at
4°C)

• If performing elution at 4°C, incubate overnight

• Increase fluoride concentration in elution buffer
(see Figure 8)

• Substitute 10 mM sodium azide for fluoride in
elution buffer

• Elute with application of second volume of elution
buffer to spin column resin

Eluate contains significant contaminants:

Load • Dilute lysate for multimeric proteins

• Reduce fusion protein load amount to achieve
subsaturating level bound to resin

• Incubate lysate with resin for up to an hour at 4°C
to increase binding capacity of target fusion protein

Wash • Perform additional wash step

• Reduce nonspecific, electrostatic binding by
increasing ionic concentration of wash buffer; use
up to 0.3 M Sodium phosphate, NaOAc, or
(NH4)2SO4(pH 7.2), or amend wash buffer with any
of the aforementioned salts. Do not use NaCl

• Reduce hydrophobic interactions by decreasing
salt concentration of wash buffer

• Supplement wash buffer with suitable detergent
(see Appendix D: Comprehensive Chemical
Compatibility List)

48

Fusion protein binds poorly to the resin:

Fusion Protein • Proteins with high N-terminal structure may interfere

with binding; adding amino acid spacer (i.e., Thr­Ser) between Profinity eXact tag and target protein
will improve tag’s accessibility

Lysis • If using urea to help solubilize proteins, use [urea]

<4 M; higher urea concentrations reduce binding
capacity

Load • Allow lysate to incubate with resin for up to an hour

at 4°C or for 30 minutes at room temperature;
lysates with fusion proteins >75 kD often benefit
from a longer incubation period

• When purifying multimeric proteins, avoid saturating
resin; diluting lysate may also improve yields

Resin • Resin previously used must be regenerated to

remove cleaved Profinity eXact tag; apply three
column volumes of 0.1M H3PO4to resin

Appendix F
References

1. Amor-Mahjoub M et al., The effect of the hexahistidine-tag in the
oligomerization of HSC70 constructs, J Chromatogr B 844, 328–334 (2006)

2. Araujo APU et al., Influence of the Histidine Tail on the Structure and Activity
of Recombinant Chlorocatechol 1,2-Dioxygenase, Biochem Biophys Res
Commun 272, 480–484 (2000)

3. Bryan PN, Protein engineering of subtilisin, Biochim Biophys Acta 1543,
203–222 (2000)

4. Cadel S et al., Expression and purification of rat recombinant aminopeptidase
B secreted from baculovirus-infected insect cells, Protein Expr Purif 36, 19–30
(2004)

5. Chant A et al., Attachment of a histidine tag to the minimal zinc finger protein
of the Aspergillus nidulans gene regulatory protein AreA causes a
conformational change at the DNA-binding site, Protein Expr Purif 39,
152–159 (2005)

6. Dubendorff JW and Studier FW, Controlling basal expression in an inducible
T7 expression system by blocking the target T7 promoter with lac repressor,
J Mol Biol 219, 45–59 (1991)

49

7. Fang J and Ewald D, Expression cloned cDNA for 10-deacetylbaccatin
III-10-O-acetyltransferase in

Escherichia coli

: a comparative study of three

fusion systems, Protein Expr Purif 35, 17-24 (2004)

8. Fonda I et al., Attachment of histidine tags to recombinant tumor necrosis
factor-alpha drastically changes its properties, Scientific World Journal 2,
1312–1325 (2002)

9. Goel A et al., Relative position of the hexahistidine tag effects binding properties
of a tumor-associated single-chain Fv construct, Biochim Biophys Acta 1523,
13–20 (2000)

10. Kenig M et al., Influence of the protein oligomericity on final yield after affinity
tag removal in purification of recombinant proteins, J Chromatogr A 1101,
293–306 (2006)

11. Kim KM et al., Post-translational modification of the N-terminal His tag interferes
with the crystallization of the wild-type and mutant SH3 domains from chicken
src tyrosine kinase, Acta Crystallogr D 57, 759–762 (2001)

12. Kurz M et al., Incorporating a TEV cleavage site reduces the solubility of nine
recombinant mouse proteins, Protein Expr Purif 50, 68–73 (2006)

13. Pan S and Malcolm BA, Reduced background expression and improved plas­mid stability with pET vectors in BL21 (DE3), Biotechniques 29, 1234–8 (2000)

14. Ruan B et al., Engineering subtilisin into a fluoride-triggered processing
protease useful for one-step protein purification, Biochemistry 43, 14539–46
(2004)

15. Schmeisser H et al., Binding characteristics of IFN-alpha subvariants to
IFNAR2-EC and influence of the 6-Histidine tag, J Interferon Cytokine Res 26,
866–876 (2006)

16. Smyth DR et al., Crystal structures of fusion proteins with large affinity tags,
Protein Sci 12, 1313–1322 (2003)

17. Studier FW, Protein production by auto-induction in high density shaking
cultures, Protein Expr Purif 41, 207–34 (2005)

18. Wu J and Filutowicz M, Hexahistidine (His6)-tag dependent protein dimerization:
a cautionary tale, Acta Biochim Pol 46, 591–599 (1999)

19. Yudkin MD and Moses V, Carabolite repression of the lac operon. Repression
of translation, Biochem J 113, 423–0 (1969)

50

Appendix G
Ordering Information

Catalog # Description

156-3008 Profinity eXact Expression and Purification Starter Kit

156-3000 Profinity eXact Cloning and Expression Starter Kit

156-3006 Profinity eXact Mini Spin Purification Starter Kit, 10 pack

156-3001 Profinity eXact RIC-Ready Expression Vector, 20 reactions

156-3002 Profinity eXact Supercoiled Expression Vector, 20 reactions

156-3003 BL21 (DE3) Chemi-Competent Expression Cells, 10 reactions

156-3004 Profinity eXact Antibody Reagent

156-3005 Profinity eXact Purification Resin, 10 ml

156-3007 Profinity eXact Mini Spin Columns, 10 pack

732-4646 Bio-Scale Mini Profinity eXact Cartridges, 2 × 1 ml

732-4647 Bio-Scale Mini Profinity eXact Cartridges, 4 × 1 ml

732-4648 Bio-Scale Mini Profinity eXact Cartridges, 1 × 5 ml

51

Appendix H
Legal Information

Profinity eXact™vectors, tags and resins are exclusively licensed under
patent rights of Potomac Affinity Proteins. This product is intended for
research purposes only. For commercial applications or manufacturing
using these products, commercial licenses can be obtained by contacting
the Life Science Group Chromatography Marketing Manager, Bio-Rad
Laboratories, Inc., 6000 Alfred Nobel Drive, Hercules, CA 94547, Tel
(800) 4BIORAD.

Academic and Non-Profit Laboratory Assurance Letter

The T7 expression system is based on technology developed at
Brookhaven National Laboratory under contract with the U.S. Department
of Energy and is the subject of patent applications assigned to Brookhaven
Science Associates, LLC. (BSA). BSA will grant a non-exclusive license
for use of this technology, including the enclosed materials, based upon
the following assurances:

1. These materials are to be used for noncommercial research purposes
only. A separate license is required for any commercial use, including
the use of these materials for research purposes or production purposes
by any commercial entity. Information about commercial licenses may
be obtained from the Office of Intellectual Property & Sponsored
Research, Brookhaven National Laboratory, Bldg. 185, P.O. Box
5000, Upton, New York 11973-5000; Tel [phone].

2. No materials that contain the cloned copy of T7 gene 1, the gene for
T7 RNA polymerase, may be distributed further to third parties outside
of your laboratory, unless the recipient receives a copy of this license
and agrees to be bound by its terms. This limitation applies to strains
BL21(DE3), BL21(DE3)pLysS, and BL21(DE3)pLysE, and any
derivatives you may make of them.

You may refuse this license by returning the enclosed materials unused.
By keeping or using the enclosed materials, you agree to be bound by the
terms of this license.

52

Commercial Entities Doing Business in the United States

A separate license is required for any commercial use, including the use of
these materials for research purposes or production purposes by any
commercial entity prior to purchasing any T7 products. Please contact
your licensing department to confirm that your company already holds a
license from BSA or information about commercial licenses may be
obtained from the Office of Intellectual Property & Sponsored Research,
Brookhaven National Laboratory, Bldg. 185, P.O. Box 5000, Upton, New
York 11973-5000; Tel [phone].

BioLogic DuoFlow™, Bio-Scale™Mini, C-Max™, Econo-Pac®, Experion™, iProof™,
PCR Kleen

™

, Precision Plus Protein™, Profinia™, and Profinity eXact™are trade-

marks of Bio-Rad Laboratories, Inc.
BD Pharmigen

™

is a trademark of BD Biosciences.

B-PER

®

is a registered trademark of Pierce Biotechnology, Inc.

BugBuster

®

and Calbiochem®are registered trademarks of EMD Biosciences.

CelLytic

™

is a trademark of Sigma-Aldrich.

FastBreak

™

is a trademark of Promega.

ReadyPreps

™

is a trademark of Epicentre Biotechnologies.

Superflow

™

is a trademark of Sterogene Bioseparations.

Triton

®

is a registered trademark of Union Carbide.

Tween

®

is a registered trademark of ICI Americas Inc.

53

Bio-Rad

10011260 Rev A

Laboratories, Inc.

Life Science
Group

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