Thermo Scientific NanoDrop One User manual

NanoDrop Micro-UV/Vis Spectrophotometer
NanoDrop One
User Guide
269-309102 NanoDrop One UG Revision B July 2020

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The contents of this document are subject to change without notice. All technical information in this
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supersede all previous information received by the purchaser.
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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.

Thermo Scientific NanoDrop One User Guide iii
C
Chapter 1 About the Spectrophotometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Cuvette Holder. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
USB-A port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
DYMO™ LabelWriter™ 450 USB Label Printer . . . . . . . . . . . . . . . . .10
PR-1 Pedestal Reconditioning Kit . . . . . . . . . . . . . . . . . . . . . . . . . . .10
PV-1 Performance Verification Solution . . . . . . . . . . . . . . . . . . . . . . .10
Instrument Detection Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chapter 2 Instrument Set up. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Register Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Update Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Setting Up User Account Control (Optional). . . . . . . . . . . . . . . . . . . . . .14
User Account Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Security Administration Policies . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
For U.S./Canada Support, please contact: . . . . . . . . . . . . . . . . . . . .17
For International Support, please contact: . . . . . . . . . . . . . . . . . . . . .17
Chapter 3 Application Measurement Ranges . . . . . . . . . . . . . . . . . . . . . . . . . .19
Detection Limits for All Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Detection limits for standard applications . . . . . . . . . . . . . . . . . . . . . .19
Detection limits for pre-defined dyes . . . . . . . . . . . . . . . . . . . . . . . . .21
Chapter 4 Nucleic Acid Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Measure dsDNA, ssDNA or RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Measure dsDNA, ssDNA or RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Best practices for nucleic acid measurements . . . . . . . . . . . . . . . . . .25
Nucleic Acid Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Settings for Nucleic Acid Measurements . . . . . . . . . . . . . . . . . . . . . .30
Calculations for Nucleic Acid Measurements . . . . . . . . . . . . . . . . . . .30
Contents

Contents
iv NanoDrop One User Guide Thermo Scientific
Measure Microarray. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Measure Microarray Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Microarray Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Settings for Microarray Measurements. . . . . . . . . . . . . . . . . . . . . . . .37
Calculations for Microarray Measurements. . . . . . . . . . . . . . . . . . . . .41
Measure using a Custom Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Measure Nucleic Acid using a Custom Factor . . . . . . . . . . . . . . . . . .45
Custom Factor Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Settings for Nucleic Acid Measurements using a Custom Factor . . . .48
Detection Limits for Nucleic Acid Measurements using a Custom
Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Measure Oligo DNA or Oligo RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Measure Oligo DNA or Oligo RNA . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Oligo Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Settings for Oligo DNA and Oligo RNA Measurements. . . . . . . . . . . .56
Detection Limits for Oligo DNA and Oligo RNA Measurements. . . . . .57
Calculations for Oligo DNA and Oligo RNA Measurements. . . . . . . . .58
Chapter 5 Protein Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Measure Protein A280. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Measure Protein Concentration at A280 . . . . . . . . . . . . . . . . . . . . . .61
Best practices for protein measurements. . . . . . . . . . . . . . . . . . . . . .63
Protein A280 Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Settings for Protein A280 Measurements . . . . . . . . . . . . . . . . . . . . . .66
Protein editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Detection Limits for Protein A280 Measurements. . . . . . . . . . . . . . . .72
Calculations for Protein A280 Measurements. . . . . . . . . . . . . . . . . . .73
Measure Protein A205. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Measure Protein Concentration at A205 . . . . . . . . . . . . . . . . . . . . . .78
Protein A205 Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80
Settings for Protein A205 Measurements . . . . . . . . . . . . . . . . . . . . . .81
Calculations for Protein A205 Measurements. . . . . . . . . . . . . . . . . . .83
Measure Proteins and Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Measure Labeled Protein Samples. . . . . . . . . . . . . . . . . . . . . . . . . . .85
Proteins & Labels Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . .87
Settings for Proteins and Labels Measurements. . . . . . . . . . . . . . . . .89
Detection Limits for Proteins and Labels Measurements . . . . . . . . . .91
Calculations for Proteins and Labels Measurements . . . . . . . . . . . . .92
Measure Protein BCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . . .95
Protein BCA Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Settings for Protein BCA Measurements . . . . . . . . . . . . . . . . . . . . .106

Contents
Thermo Scientific NanoDrop One User Guide v
Measure Protein Bradford . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109
Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .109
Protein Bradford Reported Results . . . . . . . . . . . . . . . . . . . . . . . . .113
Settings for Protein Bradford Measurements . . . . . . . . . . . . . . . . . .116
Measure Protein Lowry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .119
To measure Protein Lowry standards and samples . . . . . . . . . . . . .120
Protein Lowry Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . .122
Settings for Protein Lowry Measurements . . . . . . . . . . . . . . . . . . . .124
Measure Protein Pierce 660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Measure Total Protein Concentration . . . . . . . . . . . . . . . . . . . . . . . .127
To measure Protein Pierce 660 standards and samples. . . . . . . . . .128
Protein Pierce 660 Reported Results . . . . . . . . . . . . . . . . . . . . . . . .130
Settings for Protein Pierce 660 Measurements. . . . . . . . . . . . . . . . .133
Chapter 6 Measure OD600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135
Measure OD600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135
To measure OD600 samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .137
OD600 Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
Settings for OD600 Measurements . . . . . . . . . . . . . . . . . . . . . . . . .140
Calculations for OD600 Measurements . . . . . . . . . . . . . . . . . . . . . .143
Chapter 7 Custom Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .145
Measure UV-Vis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .146
Measure UV-Vis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .146
Best practices for UV-Vis measurements . . . . . . . . . . . . . . . . . . . . .147
UV-Vis Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .148
Settings for UV-Vis Measurements. . . . . . . . . . . . . . . . . . . . . . . . . .151
Measure Custom. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .153
Measure using a Custom Method . . . . . . . . . . . . . . . . . . . . . . . . . .153
Delete Custom Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .156
Custom Method Reported Results. . . . . . . . . . . . . . . . . . . . . . . . . .157
Manage Custom Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .159
Chapter 8 Measure Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169
Measure Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169
Create Kinetics Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .173
Edit Kinetics Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .174
Kinetics Reported Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .175
Settings for Kinetic Measurements. . . . . . . . . . . . . . . . . . . . . . . . . .180
Chapter 9 Learning Center . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .183
Micro-Volume Sampling—How it Works . . . . . . . . . . . . . . . . . . . . . . .184

Contents
vi NanoDrop One User Guide Thermo Scientific
Set Up the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .186
Connect Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .186
Connect an Accessory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .186
Set Up Bluetooth Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . .186
Set Up Ethernet Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
Set up Wireless Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .192
Assess Instrument Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . .194
Operating Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .195
Measure a Micro-Volume Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . .196
Best practices for micro-volume measurements. . . . . . . . . . . . . . . .197
Recommended sample volumes . . . . . . . . . . . . . . . . . . . . . . . . . . .198
Measure a Sample Using a Cuvette. . . . . . . . . . . . . . . . . . . . . . . . . . .201
Best practices for cuvette measurements . . . . . . . . . . . . . . . . . . . .202
Prepare Samples and Blanks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .204
Preparing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .204
Run a Blanking Cycle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .207
Basic Instrument Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .209
NanoDrop One Home Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . .209
NanoDrop One Measurement Screens . . . . . . . . . . . . . . . . . . . . . .212
NanoDrop One General Operations . . . . . . . . . . . . . . . . . . . . . . . . .227
Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .237
System Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .237
Network Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .239
Export Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .240
General Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .242
Data Deletion Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .243
PC Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245
PC Control Home Screen overview . . . . . . . . . . . . . . . . . . . . . . . . .245
Control options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .246
Instrument Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .249
Measurement Screen Display Options . . . . . . . . . . . . . . . . . . . . . . .250
Chapter 10 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .251
Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .252
Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .252
Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .252
Every 6 Months . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .252
Cleaning the Touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253
Maintaining the Pedestals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253
Cleaning the Pedestals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .253
Reconditioning the Pedestals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .256
Decontaminating the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . .258
Maintaining the Cuvette Sampling System. . . . . . . . . . . . . . . . . . . . . .260

Contents
Thermo Scientific NanoDrop One User Guide vii
Instrument Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .260
Intensity Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .261
Performance Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .263
Pedestal Image Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .268
Chapter 11 Safety and Operating Precautions . . . . . . . . . . . . . . . . . . . . . . . . .269
Operating Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .270
Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .271
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .271
When the System Arrives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .273
Lifting or Moving the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . .273
Electrical Requirements and Safety . . . . . . . . . . . . . . . . . . . . . . . . .274
Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .274
Fire Safety and Burn Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . .275
Optical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .276
Hazardous Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .276

Contents
viii NanoDrop One User Guide Thermo Scientific

Thermo Scientific NanoDrop One User Guide 7
1
About the Spectrophotometer
The Thermo Scientific™ NanoDrop™ OneCis 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 Locate the instrument away from air vents and exhaust fans to minimize
evaporation
Note Before operating a NanoDrop One instrument, please read the safety and
operating precautions and then follow their recommendations when using the
instrument.
NanoDrop OneCSpectrophotometer
Arm
Pedestal
Cuvette holder

1About the Spectrophotometer
Features
8 NanoDrop One User Guide Thermo Scientific
Features
TheNanoDrop OneCspectrophotometer features the patented micro-volume sample
retention system. The NanoDrop OneCalso features a cuvette holder for analyzing
dilute samples using standard UV-Visible cuvettes.
Touchscreen
TheNanoDrop OneCcomes 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