Bio-rad 485 User Manual

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Model 485

Gradient Former

Instruction

Manual

Catalog Number

165-4120

For Technical Service Call Your Local Bio-Rad Office or in the U.S. Call 1-800-4BIORAD (1-800-424-6723)

Table of Contents

Page

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

Section 2 Pouring Multiple Gradient Gels in the Multi-Casting Chamber...........2

2.1 Calculate the Volume of Acrylamide to Prepare.......................................................2

2.2 Calculate the Chamber Volumes ...............................................................................2

2.3 Reassemble the Multi-Casting Chamber...................................................................2

2.4 Pour the Gels ..............................................................................................................2

2.4.1 Pour Linear Gradient Gels ............................................................................2

2.4.2 Pour Convex Exponential Gradient Gels......................................................3

Section 3 Pouring One Large-Format Linear Gradient Gel ...................................4

3.1 Calculate the Volume of Acrylamide to Prepare.......................................................4

3.2 Calculate the Chamber Volumes ...............................................................................4

3.3 Set Up the Glass Plate for Casting.............................................................................4

3.4 Pour the Gel................................................................................................................4

3.4.1 Pour a Linear or Concave Gradient Gel from the Top.................................4

3.4.2 Pour a Linear or Convex Gradient Gel from the Bottom.............................5

Section 4 Gradient Former Car e and Maintenance.................................................6

Section 5 Product Inf ormation....................................................................................6

Appendix A Estimated Volume of Acrylamide for 12 Mini-PROTEAN 3 Gels.........6

Section 1 Introduction

The Model 485 Gradient Former is primarily used to construct reproducible linear and exponential polyacrylamide gradient gels. It has a 175 ml capacity, making it ideal for preparation of up to 12 identical Mini-PROTEAN®3 gradient gels. It can also be used to prepare PROTEAN II gels.

The mixing (labeled "light") and reservoir (labeled "heavy") chambers have identical dimensions. The outlet from the mixing chamber leads into a multi-casting chamber. The exponential piston is available as an accessory; it is used to fix the volume in the mixing chamber to produce concave or convex exponential gradients.

Figure 1.1 Model 485 Gradient Former, major parts

1.1 Specifications

Overall size 10 cm x 10 cm x 16 cm (W x L x H) Weight 500 g Capacity 40–175 ml Materials of construction Body Machined from an acrylic block Valve stem Delrin

Stopcock Plastic Piston Delrin Tubing Tygon

1/8” ID

Exponential piston

Mixing chamber

(light)

Reservoir chamber

(heavy)

Luer taper coupling

Valve stem

Y-connector

Stopcock

Tubing

Multi-casting

Chamber

Section 2 Pouring Multiple Gradient Gels in the Multi-Casting Chamber

Note: This procedure can be used to produce gels with either a linear or a convex exponential gradient. Cast a minimum of 4 Mini-PROTEAN 3 gels using this procedure.

An inexperienced user should practice all steps ahead of time so that the procedure is completed quickly. The best guarantee of reproducibility from gradient to gradient is careful technique on the part of the operator.

Wear rubber gloves to prevent exposure to unpolymerized acrylamide, a neurotoxin.

2.1 Calculate the Volume of Acrylamide to Prepare

The first time gels of a certain thickness are cast, it is necessary to empirically determine the required volume of acrylamide. If you are using the Mini-PROTEAN 3 multi-casting chamber, assemble the stack of Mini-PROTEAN 3 sandwiches (as described in the multi-casting chamber manual) and inject a measured volume of water through the stopcock. You will prepare this volume (+5 ml) of acrylamide. (A minimum working volume of 40 ml is required for the gradient former.) Disassemble the chamber and dry all components.

See Appendix A for additional information.

2.2 Calculate the Chamber Volumes

To create a linear gradient, the volume in each chamber is ½ the total gel volume required (or 20 ml, whichever is greater.)

For a convex exponential gradient, the light solution in the mixing chamber will be ¼ the total gel volume (minimum 10 ml) and the heavy solution in the reservoir chamber will be equal to the total gel volume (minimum 40 ml).

Combine all reagents except the initiators (usually APS and TEMED), and degas each solution under vacuum for at least 15 minutes.

2.3 Reassemble the Multi-Casting Chamber

Refer to the Mini-PROTEAN 3 multi-casting chamber instruction manual. Be certain that all of the parts are clean and dry.

2.4 Pour the Gels

Note: If the flow rate is kept constant, the gradients will be reproducible. Tubing size, the volume of acrylamide in the chambers, and the rate of stirring must be kept constant. If the rate of stirring changes, then the amount of acrylamide pulled into the front chamber from the back chamber when the connection between the two chambers is opened will vary. This will change the gradient.

2.4.1 To Pour Linear Gradient Gels

a. Arrange the tubing so that there is as short a distance as possible between the stopcock

opening and the inlet to the gel casting chamber. Note: The level of the gradient former stopcock must be placed above the top of the gel

sandwich. This creates a hydrostatic head large enough to pour the gels within 10 minutes from the time the initiators are added to the light solution. To create uniform gradients, all of the acrylamide must be in the gel sandwich before polymerization begins.

b. Add a 1" stirbar in the mixing chamber (with the valve stem closed.) The mixing

chamber is labeled "light". Place the gradient former on a magnetic stir plate. c. Add the initiators to the light solution, swirl it 8 to 10 times, and pour the mixture into the

mixing chamber. This is the start of the 10 minutes. d. Add the initiators to the heavy solution, swirl it 8 to 10 times, and pour it into the

reservoir chamber. Start the stir plate and adjust the speed so that you get good mixing;

the bottom level of the vortex should be nearly the same as the acrylamide level in the

reservoir chamber. e. Quickly open the valve stem and stopcock. The acrylamide will flow down the tubing to

the gel sandwich. Do not allow air bubbles to enter the gel. Overlay the acrylamide with

water or water-saturated isobutanol. Note: each gel must have the same volume of

overlay solution. For a continuous buffer system, insert a comb at an angle (this reduces

the chance of bubble formation.) f. Close the stopcock on the multi-casting chamber after the gels are cast. Remove the

tubing. Immediately flush the system with water to prevent polymerization of residual

acrylamide within the gradient former.

2.4.2 To Pour Convex Exponential Gradient Gels

a. Arrange the tubing so that there is as short a distance as possible between the stopcock

opening and the inlet to the gel casting chamber. Note: The level of the gradient former stopcock must be placed above the top of the gel

b. Add a 1" stirbar in the mixing chamber (with the valve stem closed.) The mixing

chamber is labeled "light". Place the gradient former on a magnetic stir plate. c. Add the initiators to the light solution, swirl 8 to 10 times, and pour into the mixing

chamber, leaving the valve stem closed. This is the start of the 10 minutes. d. Immediately fix the volume with the exponential piston by inserting the piston into the

chamber to 1 cm above the level of the acrylamide and tightening the screw-top handle

to hold the piston in place. e. Add the initiators to the heavy solution, swirl it 8 to 10 times, and pour it into the

reservoir chamber. Start the stir plate and adjust the speed so that you get good mixing;

the bottom level of the vortex should be nearly the same as the acrylamide level in the

reservoir chamber. f. Quickly open the valve stem and stopcock. The acrylamide will flow down the tubing to

the gel sandwich. Do not allow air bubbles to enter the gel. Overlay the acrylamide with

water or water-saturated isobutanol. Note: each gel must have the same volume of

overlay solution. For a continuous buffer system, insert a comb at an angle (this reduces

the chance of bubble formation.) g. Close the stopcock on the multi-casting chamber after the gradient is cast. Remove the

tubing. Immediately flush the system with water to prevent polymerization of residual

acrylamide within the gradient former.

Section 3 Pouring One Large-Format Gradient Gel

Pouring a single Mini-PROTEAN 3 gradient gel is not recommended. The minimum volume for the gradient former is 40 ml, and you should use nearly all of the solution in pouring a gradient gel. These instructions are intended for casting large-format polyacrylamide gels.

Wear rubber gloves to prevent exposure to unpolymerized acrylamide, a neurotoxin. Note: If the rate of flow is kept constant, then the gradients will be reproducible. Tubing

size, the needle size and size of the hole in the needle, the volumes in the chambers, and the rate of stirring of the stir plate must be kept constant. If the rate of stirring changes, then the amount of acrylamide pulled into the front chamber from the back chamber when the connection between the two chambers is opened will vary. This will change the gradient.

3.1 Calculate the Volume of Acrylamide to Prepare

The first time gels of a certain thickness are cast, it is necessary to empirically determine the required volume of acrylamide. Inject a measured volume of water into the gel sandwich. You will prepare this volume (+5 ml) of acrylamide. (A minimum working volume of 40 ml is required for the gradient former.) Disassemble the chamber and dry all components.

3.2 Calculate the Chamber Volumes

To create a linear gradient, the volume in each chamber is ½ the total gel volume required (or 20 ml, whichever is greater.)

For a concave exponential gradient, the heavy solution in the mixing chamber will be ¼ the total gel volume (minimum 10 ml) and the light solution in the reservoir chamber will be equal to the total gel volume (minimum 40 ml).

Combine all reagents except the initiators (usually APS and TEMED), and degas each solution under vacuum for at least 15 minutes.

3.3 Assemble the Glass Plate Sandwich

Set up the glass plate for casting (as indicated in the electrophoresis cell instruction manual.)

3.4 Pour the Gel

Note: The level of the gradient former stopcock must be placed above the top of the gel sandwich. This creates a hydrostatic head large enough to pour the gel within 10 minutes from the time the initiators are added to the light solution. To create uniform gradients, all of the acrylamide must be in the gel sandwich before polymerization begins.

3.4.1 Pour a Linear or Concave Gradient Gel from the Top

The heavy solution is poured into the mixing chamber since it enters the sandwich first, flowing to the bottom. The light solution, which flows into the gel last, is poured into the

reservoir chamber. Note: For this application, the heavy solution will be poured in the mixing chamber labeled "light", and the light solution will be poured in the mixing chamber labeled "heavy".

a. Arrange the tubing so that there is as short a distance as possible between the stopcock

opening and the needle at the end of the tubing. (Alternatively, you can cut the end of

the tubing at an angle.) The end of the needle or tubing will lie against the glass plate

while the acrylamide is being poured into the sandwich. b. Place a 1" stirbar in the mixing chamber (with the valve stem closed.) The mixing

chamber is labeled "light". c. Add the initiators to the light solution, swirl it 8 to 10 times, and pour the mixture into the

reservoir chamber (which is labeled "heavy"). This is the start of the 10 minutes. Leave

the valve stem closed. d. Add the initiators to the heavy solution, swirl it 8 to 10 times, and pour it into the mixing

chamber (which is labeled "light"). Start the stir plate and adjust the speed so that you

get good mixing; the bottom level of the vortex should be nearly the same as the

acrylamide level in the reservoir chamber. For a concave gradient, insert the exponential piston into the mixing chamber to 1 cm above

the level of the acrylamide, tighten the screw top handle to hold the piston in place, and then start the stir plate.

e. Quickly open the valve stem and stopcock. The acrylamide will flow through the tubing

and needle to the gel sandwich. Do not allow air bubbles to enter the gel. Overlay the

acrylamide with water or water-saturated isobutanol. For a continuous buffer system,

insert a comb. (The comb should be inserted at an angle to prevent the formation of

bubbles.) f. Remove the tubing and disassemble the gradient former. Immediately flush the system

with water to prevent polymerization of residual acrylamide within the gradient former.

3.4.2 Pour a Linear or Convex Gradient Gel from the Bottom

In this case, the light solution goes into the mixing chamber (labeled "light") and the heavy solution goes into the reservoir (labeled "heavy"). The light solution enters the gel from the bottom and travels to the top, and the heavy solution follows, filling in the bottom of the gel.

Wear rubber gloves to prevent exposure to unpolymerized acrylamide, a neurotoxin. a. Arrange the tubing so that there is as short a distance as possible between the stopcock

opening and the needle at the end of the tubing. Insert the needle into the gel sandwich

through the gasket on the bottom of the casting stand. b. Place a 1" stirbar in the mixing chamber (with the valve stem closed.) The mixing

chamber is labeled "light". c. Add the initiators to the light solution, swirl it 8 to 10 times, and pour the mixture into the

mixing chamber (which is labeled "light"). This is the start of the 10 minutes. Leave the

valve stem closed.

For a convex gradient, insert the exponential piston into the mixing chamber to 1 cm above the level of the acrylamide, tighten the screw top handle to hold the piston in place.

d. Add the initiators to the heavy solution, swirl it 8 to 10 times, and pour it into the

reservoir chamber (which is labeled "heavy"). Start the stir plate and adjust the speed so

that you get good mixing; the bottom level of the vortex should be nearly the same as the

acrylamide level in the resevoir chamber. e. Quickly open the valve stem and stopcock. The acrylamide will flow through the tubing

and needle to the gel sandwich. Do not allow air bubbles to enter the gel. Overlay the

acrylamide with water or water-saturated isobutanol. For a continuous buffer system, insert

a comb. (The comb should be inserted at an angle to prevent the formation of bubbles.) f. Remove the tubing and disassemble the gradient former. Immediately flush the system

with water to prevent polymerization of residual acrylamide within the gradient former.

Section 4 Gradient Former Care and Maintenance

After use, disassemble the gradient former and rinse all parts with distilled water. If the gel polymerizes in the gradient former during casting or before the system can be flushed with water, remove the valve stem and stopcock and rinse thoroughly. The needle can be replaced (catalog number 165-2007). A Tubing Connection Kit (catalog number 165-2008) includes replacement Tygon tubing, a luer fitting, stopcock, and a Y connector. Do not use organic solvents, strong acid solutions or ethanol in the gradient former.

Section 5 Product Information

Catalog Number Description

165-4120 Model 485 Gradient Former 165-2006 Exponential Piston 165-2007 Gradient Pouring Needles, 2 165-2008 Tubing Connection Kit, includes stopcock, tapered luer coupling,

tubing (1/8 inch ID, 3 feet), and Y-connector

Appendix A Estimated V olume of Acrylamide for 12 Mini-PROTEAN 3 Gels

The first time gels of a certain thickness are cast, it is necessary to empirically determine the required volume of acrylamide. Assemble the stack, and inject a measured volume of water through the stopcock. Prepare this volume (+5 ml) of acrylamide.

As a guideline, this is the estimated volume of acrylamide for 12 Mini-PROTEAN 3 gels: Spacer plates Volume for 12 gels Volume to prepare

0.5 mm 70 ml 75–80 ml

0.75 mm 80 ml 85–90 ml

1.0 mm 100 ml 105–110 ml

1.5 mm 140 ml 145–150 ml

Sample calculation: preparing twelve 1.0 mm 4–20% gradient gels:

Casting twelve 1.0 mm gels requires 100 ml; prepare 110 ml. Divide the total volume by 2 to get the volume required for each chamber. (For this example,

make 55 ml for the light chamber and 55 ml for the heavy chamber.) Solution Volume Calculations:

Light Solution (4%)

Acrylamide 30% stock solution (30%) (X ml) = (4%) (55 ml) X = 7.3 ml

Tris-Cl Buffer

1.5M Tris-Cl stock buffer pH 8.8 (1.5M) (X ml) = (.375M) (55 ml) X = 13.8 ml

Water (55 ml)–(7.3 ml + 13.8 ml) = XX= 34 ml

APS 10% Stock solution (500 µl) / (100 ml) = (X µl) / (55 ml) X = 275 µl

TEMED 10% of the APS volume; (275 µl) / 10 = XX= 27.5 µl

Heavy Solution (20%)

Acrylamide 30% Stock solution (30%) (X ml) = (20%) (55 ml) X = 36.7 ml

Tris-Cl Buffer

1.5M Tris-Cl Stock Buffer pH 8.8 (1.5M) (X ml) = (.375M) (55 ml) X = 13.8 ml

Water (55 ml)–(36.7 ml + 13.8 ml) = XX= 4.5 ml

APS (500 µl) / (100 ml) = ( X µl) / (55 ml) X = 275 µl

TEMED 10% the APS volume; (275 µl) / 10 = XX= 27.5 µl

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Bio-rad 485 User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual