Thermo Fisher Scientific NanoDrop One User Manual

NanoDrop Micro-UV/Vis Spectrophotometer

NanoDrop One

User Guide

269-309102 NanoDrop One UG Revision C March 2021

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For U.S. Technical Support, please contact:

Thermo Fisher Scientific 3411 Silverside Road Tatnall Building, Suite 100 Wilmington, DE 19810 U.S.A.

Telephone: 302 479 7707 Toll Free: 1 877 724 7690 (U.S. & Canada only)

For International Support, please contact:

http://www.thermofisher.com/ NanoDropSupport

Contact your local distributor. For contact information go to:

http://www.thermofisher.com/ NanoDropDistributors

E-mail: nanodrop@thermofisher.com

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents.

For Research Use Only. This instrument or accessory is not a medical device and is not intended to be used for the prevention, diagnosis, treatment or cure of disease.

WARNING Avoid an explosion or fire hazard. This instrument or accessory is not designed for use in an explosive atmosphere.

Chapter 1 About the Spectrophotometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

Cuvette Holder. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

USB-A port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

DYMO™ LabelWriter™ 450 USB Label Printer . . . . . . . . . . . . . . . . .12

PR-1 Pedestal Reconditioning Kit . . . . . . . . . . . . . . . . . . . . . . . . . . .12

PV-1 Performance Verification Solution . . . . . . . . . . . . . . . . . . . . . . . 12

Instrument Detection Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Chapter 2 Instrument Set up. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Update Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Setting Up User Account Control (Optional). . . . . . . . . . . . . . . . . . . . . .16

User Account Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16

Security Administration Policies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

For U.S./Canada Support, please contact: . . . . . . . . . . . . . . . . . . . .19

For International Support, please contact: . . . . . . . . . . . . . . . . . . . . .19

Chapter 3 Application Measurement Ranges . . . . . . . . . . . . . . . . . . . . . . . . . .21

Detection Limits for All Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Detection limits for standard applications . . . . . . . . . . . . . . . . . . . . . .21

Detection limits for pre-defined dyes . . . . . . . . . . . . . . . . . . . . . . . . .23

Chapter 4 Nucleic Acid Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Measure dsDNA, ssDNA or RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Measure dsDNA, ssDNA or RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Best practices for nucleic acid measurements . . . . . . . . . . . . . . . . . .27

Nucleic Acid Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29

Settings for Nucleic Acid Measurements . . . . . . . . . . . . . . . . . . . . . . 32

Calculations for Nucleic Acid Measurements . . . . . . . . . . . . . . . . . . .32

Thermo Scientific NanoDrop One User Guide iii

Contents

Measure Microarray. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Measure Microarray Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Microarray Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Settings for Microarray Measurements. . . . . . . . . . . . . . . . . . . . . . . .41

Calculations for Microarray Measurements. . . . . . . . . . . . . . . . . . . . . 45

Measure using a Custom Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49

Measure Nucleic Acid using a Custom Factor . . . . . . . . . . . . . . . . . . 49

Custom Factor Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . .51

Settings for Nucleic Acid Measurements using a Custom Factor . . . .52

Detection Limits for Nucleic Acid Measurements using a Custom

Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53

Measure Oligo DNA or Oligo RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55

Measure Oligo DNA or Oligo RNA . . . . . . . . . . . . . . . . . . . . . . . . . . .55

Oligo Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Settings for Oligo DNA and Oligo RNA Measurements. . . . . . . . . . . .60

Detection Limits for Oligo DNA and Oligo RNA Measurements. . . . . . 62

Calculations for Oligo DNA and Oligo RNA Measurements. . . . . . . . . 63

Chapter 5 Protein Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Measure Protein A280. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67

Measure Protein Concentration at A280 . . . . . . . . . . . . . . . . . . . . . .67

Best practices for protein measurements. . . . . . . . . . . . . . . . . . . . . .69

Protein A280 Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .71

Settings for Protein A280 Measurements . . . . . . . . . . . . . . . . . . . . . . 72

Protein editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75

Detection Limits for Protein A280 Measurements. . . . . . . . . . . . . . . .78

Calculations for Protein A280 Measurements. . . . . . . . . . . . . . . . . . .79

Measure Protein A205. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84

Measure Protein Concentration at A205 . . . . . . . . . . . . . . . . . . . . . .84

Protein A205 Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86

Settings for Protein A205 Measurements . . . . . . . . . . . . . . . . . . . . . . 89

Calculations for Protein A205 Measurements. . . . . . . . . . . . . . . . . . .91

Measure Proteins and Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93

Measure Labeled Protein Samples. . . . . . . . . . . . . . . . . . . . . . . . . . .93

Proteins & Labels Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Settings for Proteins and Labels Measurements. . . . . . . . . . . . . . . . .98

Detection Limits for Proteins and Labels Measurements . . . . . . . . .100

Calculations for Proteins and Labels Measurements . . . . . . . . . . . .100

Measure Protein BCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103

Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .103

Protein BCA Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . .111

Settings for Protein BCA Measurements . . . . . . . . . . . . . . . . . . . . .115

iv NanoDrop One User Guide Thermo Scientific

Contents

Measure Protein Bradford . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117

Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .117

Protein Bradford Reported Results . . . . . . . . . . . . . . . . . . . . . . . . .121

Settings for Protein Bradford Measurements . . . . . . . . . . . . . . . . . . 124

Measure Protein Lowry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .127

To measure Protein Lowry standards and samples . . . . . . . . . . . . .128

Protein Lowry Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

Settings for Protein Lowry Measurements . . . . . . . . . . . . . . . . . . . .132

Measure Protein Pierce 660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135

Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .135

To measure Protein Pierce 660 standards and samples. . . . . . . . . . 136

Protein Pierce 660 Reported Results . . . . . . . . . . . . . . . . . . . . . . . .138

Settings for Protein Pierce 660 Measurements. . . . . . . . . . . . . . . . . 141

Chapter 6 Measure OD600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Measure OD600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .143

To measure OD600 samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .145

OD600 Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147

Settings for OD600 Measurements . . . . . . . . . . . . . . . . . . . . . . . . .148

Calculations for OD600 Measurements . . . . . . . . . . . . . . . . . . . . . .151

Chapter 7 Custom Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Measure UV-Vis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .154

Measure UV-Vis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

Best practices for UV-Vis measurements . . . . . . . . . . . . . . . . . . . . .155

UV-Vis Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .156

Settings for UV-Vis Measurements. . . . . . . . . . . . . . . . . . . . . . . . . .159

Measure Custom. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .161

Measure using a Custom Method . . . . . . . . . . . . . . . . . . . . . . . . . .161

Delete Custom Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .164

Custom Method Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . .165

Manage Custom Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .167

Chapter 8 Measure Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .177

Measure Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .177

Create Kinetics Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .181

Edit Kinetics Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .182

Kinetics Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183

Settings for Kinetic Measurements. . . . . . . . . . . . . . . . . . . . . . . . . .188

Chapter 9 Learning Center . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191

Micro-Volume Sampling—How it Works . . . . . . . . . . . . . . . . . . . . . . .192

Thermo Scientific NanoDrop One User Guide v

Contents

Set Up the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .194

Connect Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .194

Connect an Accessory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .194

Set Up Bluetooth Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Set Up Ethernet Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .199

Set up Wireless Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200

Assess Instrument Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . .202

Operating Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203

Measure a Micro-Volume Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . .204

Best practices for micro-volume measurements. . . . . . . . . . . . . . . .205

Recommended sample volumes . . . . . . . . . . . . . . . . . . . . . . . . . . .206

Measure a Sample Using a Cuvette. . . . . . . . . . . . . . . . . . . . . . . . . . .209

Best practices for cuvette measurements . . . . . . . . . . . . . . . . . . . .210

Prepare Samples and Blanks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .212

Preparing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .212

Run a Blanking Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .215

Basic Instrument Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217

NanoDrop One Home Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217

NanoDrop One Measurement Screens . . . . . . . . . . . . . . . . . . . . . .220

NanoDrop One General Operations . . . . . . . . . . . . . . . . . . . . . . . . .235

Acclaro Sample Intelligence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245

Activate Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245

View Acclaro Sample Intelligence Information. . . . . . . . . . . . . . . . . . 246

Contaminant Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .247

On-Demand Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . .251

Invalid-Results Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .252

Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253

System Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253

Network Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .255

Export Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .256

General Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

Data Deletion Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .259

PC Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .261

PC Control Home Screen overview . . . . . . . . . . . . . . . . . . . . . . . . .261

Control options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .262

Instrument Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .265

Measurement Screen Display Options . . . . . . . . . . . . . . . . . . . . . . .266

Chapter 10 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .267

Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268

Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268

Every 6 Months . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268

Cleaning the Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269

vi NanoDrop One User Guide Thermo Scientific

Contents

Maintaining the Pedestals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .269

Cleaning the Pedestals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .269

Reconditioning the Pedestals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .272

Decontaminating the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . .274

Maintaining the Cuvette Sampling System. . . . . . . . . . . . . . . . . . . . . .276

Instrument Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276

Intensity Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .277

Performance Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .279

Pedestal Image Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284

Chapter 11 Safety and Operating Precautions . . . . . . . . . . . . . . . . . . . . . . . . .285

Operating Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .286

Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287

Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .287

When the System Arrives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Lifting or Moving the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Electrical Requirements and Safety . . . . . . . . . . . . . . . . . . . . . . . . . 290

Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .290

Fire Safety and Burn Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . .291

Optical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .292

Hazardous Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .292

Thermo Scientific NanoDrop One User Guide vii

Contents

viii NanoDrop One User Guide Thermo Scientific

About the Spectrophotometer

NanoDrop OneC Spectrophotometer

Arm

Pedestal

Cuvette holder

Note Locate the instrument away from air vents and exhaust fans to minimize

evaporation

The Thermo Scientific™ NanoDrop™ OneC is a compact, stand-alone UV-Visible spectrophotometer developed for micro-volume analysis of a wide variety of analytes. The patented sample retention system enables the measurement of highly concentrated samples without the need for dilutions.

The NanoDrop One system comes with preloaded software and a touchscreen display. NanoDrop One PC Control software can be installed on a local PC and used to control the instrument and view data. The instrument can be connected to an optional printer with a USB cable or to a remote printer through an Ethernet connection or wireless network.

Note Before operating a NanoDrop One instrument, please read the safety and

operating precautions and then follow their recommendations when using the

instrument.

Thermo Scientific NanoDrop One User Guide 9

1 About the Spectrophotometer

Features

Touchscreen

TheNanoDrop OneC spectrophotometer features the patented micro-volume sample

retention system. The NanoDrop One

dilute samples using standard UV-Visible cuvettes.

TheNanoDrop OneC comes with a built-in, 7-inch high-resolution touchscreen preloaded with easy-to-use instrument control software. The touchscreen can slide left or right to accommodate personal preference, and tilt forward or back for optimal viewing

also features a cuvette holder for analyzing

10 NanoDrop One User Guide Thermo Scientific

Cuvette Holder

Instrument light path

About the Spectrophotometer

Cuvette holder

Features

USB-A port

The NanoDrop OneC includes a cuvette holder for measuring dilute samples, colorimetric assays, cell cultures and kinetic studies. The cuvette system has these features:

• extended lower detection limits

• 37 °C heater option for temperature-sensitive samples and analyses

• micro-stirring option to ensure sample homogeneity and support kinetic studies

For details, see Measure a Sample using a Cuvette.

One USB-A port is located on the front of the instrument and two more USB-A ports are located on instrument back panel.

Thermo Scientific NanoDrop One User Guide 11

1 About the Spectrophotometer

Accessories

This section lists the accessories included for use with the NanoDrop OneC.

DYMO™ LabelWriter™ 450 USB Label Printer

Prints two 5/16-in x 4-in self-adhesive labels for transferring sample data directly into laboratory notebooks or posting on bulletin boards. The software allows printing of

data from each sample measurement or from a group of samples logged and

measured together.

The printer connects to the instrument (front or back) via a USB cable (included).

PR-1 Pedestal Reconditioning Kit

Specially formulated conditioning compound that can be applied to the pedestals to restore them to a hydrophobic state (required to achieve adequate surface tension for accurate sample measurements). The kit includes conditioning compound and applicators. For more information, see Reconditioning the

Pedestals.

PV-1 Performance Verification Solution

Liquid photometric standard used to check instrument performance. For more information, see Performance Verification.

12 NanoDrop One User Guide Thermo Scientific

Instrument Detection Limits

About the Spectrophotometer

Instrument Detection Limits

Measurement Location Pathlength (mm)

Upper Detection Limit (10 mm Equivalent Absorbance)

Pedestal 1.0 12.5

0.2 62.5

0.1 150

0.05 300

0.03 550

Cuvette 10 1.5

2 7.5

115

Thermo Scientific NanoDrop One User Guide 13

1 About the Spectrophotometer

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14 NanoDrop One User Guide Thermo Scientific

Instrument Set up

Register Your Instrument

Register your instrument to receive e-mail updates on software and accessories for the NanoDrop One instrument. An Internet connection is required for registration.

To register your instrument

1. Do one of the following:

– From any PC that is connected to the Internet, use any web browser to

navigate to our website.

On the website, locate NanoDrop One Registration and follow the instructions to register the instrument.

Update Software

Quickly and easily download and install the latest NanoDrop One software and release notes from our website. Follow the steps to update or upgrade the software on your local instrument and/or install or update the NanoDrop One software on a personal computer (PC). An Internet connection is required to download software.

To install or update NanoDrop One software on a PC

1. Insert the USB flash drive containing the installer software into an available USB port on your PC, or open the installation folder downloaded from the internet.

2. Launch Start.exe and click Install. The software installer will run.

To install or update NanoDrop One software on the instrument

1. Copy the .zip file with the new software from your computer to a USB storage device. Do not attempt to unzip the folder.

2. Insert the USB device into any USB port on the NanoDrop One instrument.

3. From the instrument Home screen, tap Settings > System > Update Software and choose the latest version of software.

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2 Instrument Set up

Setting Up User Account Control (Optional)

User account control is managed using the Security Administration application. The Thermo Scientific Security Administration software for NanoDrop One may be purchased for instruments used in labs requiring 21 CFR Part 11 compliance. When you launch Security Administration, you will need to enter your Windows log-in information.

User Account Control

Launch the Security Administration application and select NanoDrop One from the directory on the left to reveal Access Control and System Policies.

Access control

Access control is used to grant or deny individual users or groups access to protected features in the instrument application. Add and remove users and groups to the access list and set access rights using the drop-down for each entity.

16 NanoDrop One User Guide Thermo Scientific

System policies

System Policies is used to set options that define the behavior of the client application. See “Security Administration Policies.”

Security Administration Policies

System policies allow you to assign data and method creation and deletion and editing privileges for users and groups.

Launch the Security Administration application and select NanoDrop One->

System Policies

Setting Up User Account Control (Optional)

Instrument Set up

Thermo Scientific NanoDrop One User Guide 17

2 Instrument Set up

Setting Up User Account Control (Optional)

You can add, delete, or edit policy groups and enable or disable the group’s users permission to delete data. Select NanoDrop One-> Access Control.

When you are finished, select Save. Changes will take effect the next time NanoDrop One is launched.

18 NanoDrop One User Guide Thermo Scientific

Technical Support

For U.S./Canada Support, please contact:

Thermo Fisher Scientific 3411 Silverside Road Tatnall Building, Suite 100 Wilmington, DE 19810 U.S.A.

Telephone: 302 479 7707 Toll Free: 1 877 724 7690 (U.S. & Canada only) Fax: 302 792 7155 E-mail: nanodrop@thermofisher.com Website: www.thermofisher.com/nanodrop

Instrument Set up

Technical Support

For International Support, please contact:

Contact your local distributor. For contact information go to:

http://www.thermofisher.com/NanoDropDistributors

If you are experiencing an issue with your system, refer to the troubleshooting information. If the issue persists, contact us. If you are outside the U.S.A. and Canada, please contact your local distributor.

If your instrument requires maintenance or repair, contact us or your local distributor.

Thermo Scientific NanoDrop One User Guide 19

Instrument Set up

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20 NanoDrop One User Guide Thermo Scientific

Application Measurement Ranges

Detection Limits for All Applications

Note Detection limits provided in the tables below are approximate and apply to

micro-volume measurements only; they are based on the instrument’s photometric absorbance range (10 mm equivalent) of 0–550 A. For measurements with 10 mm pathlength cuvettes, the photometric absorbance range is 0–1.5 A.

Detection limits for standard applications

Sample Type

dsDNA 2.0 ng/µL (pedestal)

ssDNA 1.3 ng/µL (pedestal)

Lower Detection Limit

0.20 ng/µL (cuvette)

0.13 ng/µL (cuvette)

Upper Detection Limit

27,500 ng/µL (pedestal)

75 ng/µL (cuvette)

18,150 ng/µL (pedestal)

49.5 ng/µL (cuvette)

Typical Reproducibility

±2.0 ng/µL for sample concentrations between 2.0 and 100 ng/µL samples; ±2% for samples >100 ng/µL

Thermo Scientific NanoDrop One User Guide 21

3 Application Measurement Ranges

Detection Limits for All Applications

Sample Type

Lower Detection Limit

RNA 1.6 ng/µL (pedestal)

0.16 ng/µL (cuvette)

DNA Microarray

1.3 ng/µL (pedestal)

(ssDNA)

0.13 ng/µL (cuvette)

Purified BSA by Protein A280

IgG by Protein A280

Purified BSA by

0.06 mg/mL (pedestal)

0.006 mg/mL (cuvette)

0.03 mg/mL (pedestal)

0.003 mg/mL (cuvette)

0.06 mg/mL (pedestal) Proteins & Labels

0.006 mg/mL (cuvette)

Protein BCA 0.2 mg/mL (20:1

reagent/sample volume)

Upper Detection Limit

22,000 ng/µL (pedestal)

Typical Reproducibility

±2.0 ng/µL for sample concentrations between 2.0 and

100 ng/µL samples;

60 ng/µL (cuvette)

495 ng/µL (pedestal)

±2% for samples >100 ng/µL

±2.0 ng/µL for sample concentrations between 2.0 and

49.5 ng/µL (cuvette)

100 ng/µL samples; ±2% for samples >100 ng/µL

825 mg/mL (pedestal)

±0.10 mg/mL (for 0.10–10 mg/mL samples); ±2% for samples >10 mg/mL

402 mg/mL (pedestal)

19 mg/mL (pedestal) ±0.10 mg/mL for 0.10–10 mg/mL

samples

8.0 mg/mL (pedestal)

0.20 mg/mL (cuvette)

2% over entire range

0.01 mg/mL over entire range

0.01 mg/mL (1:1

reagent/sample volume)

Protein Lowry 0.2 mg/mL (pedestal) 4.0 mg/mL (pedestal) 2% over entire range

Protein Bradford 100 µg/mL (50:1

reagent/sample volume)

15 µg/mL (1:1 reagent/sample

8000 µg/mL

100 µg/µL

±25 µg/mL for 100–500 µg/mL samples ±5% for 500–8000 µg/mL samples

±4 µg/mL for 15–50 µg/mL samples ±5% for 50–125 µg/mL samples

volume)

Protein Pierce 660

50 µg/mL (15:1 reagent/sample

2000 µg/mL

±3 µg/mL for 50–125 µg/mL samples ±2% for samples > 125 µg/mL

volume)

±3 µg/mL for 25–125 µg/mL samples

25 µg/mL (7.5:1

1000 µg/mL

±2% for samples >125 µg/mL reagent/sample volume)

Based on five replicates (SD=ng/µL; CV=%)

22 NanoDrop One User Guide Thermo Scientific

Note To minimize instrument error with highly concentrated samples, make

dilutions to ensure that measurements are made within these absorbance limits:

• For micro-volume measurements, maximum absorbance at 260 nm (for nucleic acids) or 280 nm (for proteins) should be less than 62.5 A.

• For measurements with 10 mm pathlength cuvettes, maximum absorbance at 260 nm (or 280 nm for proteins) should be less than 1.5 A, which is approximately 75 ng/µL dsDNA.

Detection limits for pre-defined dyes

Application Measurement Ranges

Detection Limits for All Applications

Sample Type

Cy3, Cy3.5, Alexa Fluor 555, Alexa Fluor

Lower Detection Limit

0.2 pmol/µL

(pedestal)

660

Cy5, Cy5.5, Alexa Fluor 647

Alexa Fluor 488, Alexa Fluor 594

0.12 pmol/µL

(pedestal)

0.4 pmol/µL

(pedestal)

Alexa Fluor 546 0.3 pmol/µL

(pedestal)

Values are approximate

Based on five replicates (SD=ng/µL; CV=%)

Upper Detection

Limit

100 pmol/µL (pedestal)

60 pmol/µL (pedestal)

215 pmol/µL (pedestal)

145 pmol/µL (pedestal)

Typical Reproducibility

±0.20 pmol/µL for sample concentrations between 0.20 and

4.0 pmol/µL; ±2% for samples >4.0 pmol/µL

±0.12 pmol/µL for sample concentrations between 0.12 and

2.4 pmol/µL; ±2% for samples >2.4 pmol/µL

±0.40 pmol/µL for sample concentrations between 0.40 and

8.0 pmol/µL; ±2% for samples >8.0 pmol/µL

±0.30 pmol/µL for sample concentrations between 0.30 and

6.0 pmol/µL; ±2% for samples >6.0 pmol/µL

Thermo Scientific NanoDrop One User Guide 23

Application Measurement Ranges

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24 NanoDrop One User Guide Thermo Scientific

Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

Measures the concentration of purified dsDNA, ssDNA or RNA samples that absorb at 260 nm.

Measure dsDNA, ssDNA or RNA

Reported Results

Settings

Detection Limits

Calculations

Measure dsDNA, ssDNA or RNA

Use the dsDNA, ssDNA and RNA applications to quantify purified double-stranded (ds) or single-stranded (ss) DNA or RNA samples. These applications report nucleic acid concentration and two absorbance ratios (A260/A280 and A260/A230). A single-point baseline correction can also be used.

To measure dsDNA, ssDNA or RNA samples

NOTICE

• Do not use a squirt or spray bottle on or near the instrument as liquids will flow into the instrument and may cause permanent damage.

• Do not use hydrofluoric acid (HF) on the pedestals. Fluoride ions will permanently damage the quartz fiber optic cables.

Thermo Scientific NanoDrop One User Guide 25

4 Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

Before you begin...

Before taking pedestal measurements with the NanoDrop One instrument, lift the instrument arm and clean the upper and lower pedestals. At a minimum, wipe the pedestals with a new laboratory wipe. For more information, see Cleaning the

Pedestals.

To measure nucleic acid

1. From the Home screen, select the Nucleic Acids tab and select dsDNA,

2. Specify a baseline correction if desired.

3. Pipette 1–2 µL blanking solution onto the lower pedestal and lower the arm, or

ssDNA or RNA, depending on the samples to be measured.

insert the blanking cuvette into the cuvette holder.

Tip: If using a cuvette, make sure to align the cuvette light path with the instrument light path.

4. Tap Blank and wait for the measurement to complete.

Tip: If Auto-Blank is On, the blank measurement starts automatically after you lower the arm. (This option is not available for cuvette measurements.)

5. Lift the arm and clean both pedestals with a new laboratory wipe, or remove the blanking cuvette.

6. Pipette 1-2 µL sample solution onto the pedestal and lower the arm, or insert the sample cuvette into the cuvette holder.

7. Start the sample measurement:

– Pedestal: If Auto-Measure is On, lower arm; if Auto-Measure is off, lower arm

and tap Measure.

– Cuvette: Tap Measure.

When the sample measurement is completed, the spectrum and reported values are displayed (see the next section).

8. When you are finished measuring samples, tap End Experiment.

9. Lift the arm and clean both pedestals with a new wipe, or remove the sample cuvette.

26 NanoDrop One User Guide Thermo Scientific

Typical nucleic acid spectrum

Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

Comparison of nucleic acid spectra with and without two common contaminants

Best practices for nucleic acid measurements

• Isolate and purify nucleic acid samples before measurement to remove impurities. Depending on the sample, impurities could include DNA, RNA, free nucleotides, proteins, some buffer components and dyes. See Preparing

Samples for more information.

Note Extraction reagents such as guanidine, phenol, and EDTA contribute absorbance between 230 nm and 280 nm and will affect measurement results if present in samples (even residual amounts).

Thermo Scientific NanoDrop One User Guide 27

4 Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

• Ensure the sample absorbance is within the instrument’s absorbance detection

• Blank with the same buffer solution used to resuspend the analyte of interest.

• Run a blanking cycle to assess the absorbance contribution of your buffer

• For micro-volume measurements:

limits.

The blanking solution should be a similar pH and ionic strength as the analyte solution.

solution. If the buffer exhibits strong absorbance at or near the analysis wavelength (typically 260 nm), you may need to choose a different buffer or application. See Choosing and Measuring a Blank for more information.

– Ensure pedestal surfaces are properly cleaned and conditioned.

– If possible, heat highly concentrated or large molecule samples, such as

genomic or lambda DNA, to 63 °C (145 °F) and gently (but thoroughly) vortex before taking a measurement. Avoid introducing bubbles when mixing and pipetting.

– Follow best practices for micro-volume measurements.

– Use a 1-2 µL sample volume. See Recommended Sample Volumes for more

information.

• For cuvette measurements (NanoDrop One

instruments only), use compatible

cuvettes and follow best practices for cuvette measurements.

Nucleic Acid Reported Results

dsDNA measurement screen

For each measured sample, the dsDNA, ssDNA and RNA applications show the UV absorbance spectrum and a summary of the results. Below is an example of the measurement screen of the PC control software:

Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

Application

Sampling method

Sample name of next measurement; select to edit

Measure sample

Run Blank

UV spectrum

End experiment

Menu of options; click to open

Right click graph area to view

options

Mammalian

display

Contaminant Detection

mouse icon to toggle on and off

Menu of table options; click to choose which columns to report

; select

Sample name; select to edit

Nucleic acid concentration

Purity ratios

Click row to select sample and update spectrum.

Measurement screen of PC Control software

Note Micro-volume absorbance measurements and measurements taken with

nonstandard cuvettes are normalized to a 10.0 mm pathlength equivalent.

Thermo Scientific NanoDrop One User Guide 29

4 Nucleic Acid Applications

Measure dsDNA, ssDNA or RNA

The following is an example of the measurement screen of the local control:

Menu of options; tap to open

Pinch and zoom to adjust axes; double-tap to reset

Sample name; tap to edit

Nucleic acid concentration

UV spectrum

Swipe screen left to view table with more measurement results

Tap to select unit

Tap to end experiment and export data

Purity ratios

Tap r ow to select sample and update spectrum; tap more rows to overlay up to five spectra. Press and hold sample row to view measurement details.

Drag tab down/up to see more/less sample data

Measurement screen of NanoDrop One local control software

30 NanoDrop One User Guide Thermo Scientific

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