Technical Note 166

DS-11 Series Comparison to NanoDrop™ One

Introduction

The DeNovix DS-11 Series instruments and the NanoDrop One are used for rapid quantification of nucleic acids and proteins. The DeNovix DS-11 Series Spectrophotometer / Fluorometer offer best-in-class limits of detection, the broadest dynamic range, intuitive ease of use and powerful networking features that are superior to the NanoDrop One. This note presents a comparison of features (Table 1) and side-by-side instrument performance (Tables 2 and 3).

Developed by the Originators of Microvolume UV-Vis

The DeNovix team includes one of the founders of NanoDrop Technologies Inc. as well as core team members that were involved with the company. The DeNovix DS-11, introduced to the market in 2013, was the first standalone, touchscreen-controlled, and network-connected UV-Vis spectrophotometer in the world. In collaboration with the Life Science community, DeNovix has expanded the instrument’s features and functionality. In 2015, a highly sensitive fluorometer was integrated into the system, creating the DS-11 Series Spectrophotometer / Fluorometer. The patented (US9442009) DS-11 FX+ features best-in-class limits of detection for microvolume absorbance (0.75 – 37500 ng/µL dsDNA) and fluorescence quantification (0.5 pg/µL dsDNA). Labs may select the integrated model, which fits all current and future research needs by combining microvolume UV-Vis, cuvette UV-Vis and fluorescence detection into one unit.

Table 1: DS-11 Series Comparison to NanoDrop™ One
 DeNovix DS-11 SeriesNanoDrop™ Onec
Fluorescence OptionYes - DS-11 FX and DS-11 FX+ (UV,Blue,Red,Green)None
Dynamic Range (dsDNA)0.5 pg/μL* - 37500 ng/μL0.2 ng/μL - 27500 ng/μL
Protein PerformanceOutstandingOnly if sample column is properly formed
Microvolume Lower Detection LimitdsDNA: 0.75 ng/μL, BSA: 0.04 mg/mLdsDNA: 2.0 ng/μL, BSA: 0.06 mg/mL
Cuvette Lower Detection LimitdsDNA: 0.04 ng/μL, BSA: 0.002 mg/mLdsDNA: 0.2 ng/μL, BSA: 0.006 mg/mL
Max ConcentrationdsDNA: 37500 ng/μL, BSA: 1125 mg/mLdsDNA: 27500 ng/μL, BSA: 820 mg/mL
Wavelength Range190-840 nm190-850 nm
Absorbance Range0.015 - 750 A0.04 - 550 A
Wavelength Accuracy (Absorbance)0.5 nm1 nm
Absorbance Accuracy1.5% at 0.75 AU at 260nm3% at 0.97 AU at 302nm
Microvolume Pathlength0.5 to 0.02 mm1.0 to 0.03 mm
Pathlength VerificationSmartPath® Technology with BridgeTesting®Auto adjusting
Pathlength ControlPrecision screw driven by high resolution servo motorAdjustment screw driven by stepper motor
Contamination Alert SoftwareSmartQC™ Sample GuidanceYes
Data ExportNetwork Drives and Printers, Email, USB, Label PrintersUSB, Label Printer, Networks
NetworkingWi-Fi and EthernetWi-Fi not available in all areas, Ethernet
Color ChoicesArctic White, Brazilian Blue, Tungsten Silver, Fire RedNo
ErgonomicsOptimized screen and sample pedestal locationExtended reach required

SmartPath Technology with Bridge Testing

DeNovix Spectrophotometers employ proprietary algorithms and hardware that overcome previous limitations of microvolume instruments. Analysis begins at a pathlength of 0.5 mm and compresses the sample during the measurement until the optimum pathlength is reached. DS-11 Series instruments do not stretch the droplet. Compressing prevents an unbridged condition (broken column) that can lead to inaccurate results (Figure 1).

On systems that rely on stretching samples, a broken column may occur if insufficient sample volume is pipetted for a microvolume measurement, if samples have low surface tension (common for protein solutions) or if the measurement surface loses its hydrophobic property. With Bridge Testing, DeNovix instruments detect if a sample is not bridging the optical surfaces and automatically compensates to provide a correct measurement in real time. Conversely, the NanoDrop One stretches the sample column to 1.0 mm and only alerts the user to a sample column anomaly without reporting a measurement result.

Figure 1: Top – DS-11 Series showing compression of sample droplet. Bottom – Competitor instrument showing sample stretching and breaking of the sample column.

DeNovix dsDNA Fluorescence Assays

DeNovix manufactures three ranges of highly sensitive and selective dsDNA assays. These assays, when combined with the DS-11 Series Fluorometer, enable quantification of dsDNA to 0.5 pg/µL, which is 1000x greater sensitivity than microvolume spectrophotometers. Each assay is a simple two-point standard, mix-and-measure kit. The assays allow for accurate quantification of dsDNA in the presence of RNA, degraded DNA and other contaminants.

Microvolume Performance Evaluation Methods

A 40 mg/mL solution of dsDNA was gravimetrically prepared using biotechnology grade fish sperm DNA sodium salt (Amresco cat #1B1509-256) and HPLC grade water (Ricca cat #9153-1). A series of dilutions from 12500 to 0.75 ng/µL was then prepared in HPLC grade water.

Reference concentrations for the dilutions were determined using an Agilent 8453 (Agilent, Santa Clara CA) in a 1 mm quartz cuvette (Starna, cat #1-Q-1). The reference value for DNA solutions with absorbance values outside of the Agilent’s upper range of 2.0 A (equivalent to 1000 ng/μL dsDNA) were determined by gravimetrically diluting these samples to fall within the linear range of the reference spectrophotometer. Measurements were made using the dsDNA app for each instrument.

Due to the challenges of creating high concentration dsDNA samples (600-750 A), performance was evaluated using nicotinic acid and the Custom Formula Methods app on the DS-11. An 18.5 mg/mL solution of nicotinic acid was prepared gravimetrically using 99.5% Nicotinic Acid (Sigma cat #72309-100) and 0.1 N HCl (Fisher cat #SA50-1) (Ricca cat #9153-1). A series of dilutions was prepared from 18.5 to 13.5 mg/mL.

The applicable measurement app was launched on each instrument, and a microvolume mode Blank measurement was made using 1 μL of HPLC grade water. Five sample measurements were then made for each concentration. Fresh 1 μL aliquots were used for each replicate measurement. The sample solution was removed after each measurement by wiping the upper and lower sample surfaces with a clean, dry laboratory wipe. The results of this evaluation are shown in Tables 2 and 4.

Fluorescence Performance Evaluation Methods

The DS-11 FX+ Fluoro dsDNA app and DeNovix dsDNA Quantification Assays were used in the quantification of dsDNA for this evaluation. Each assay was prepared as described in the manufacturer’s protocol. Samples were mixed and incubated at room temperature for five minutes. Three replicate measurements were taken for each sample. DeNovix Assays were measured on the DeNovix Fluorometer (Table 3).

DeNovix Broad Range and High Sensitivity Assays: A series of dilutions of calf thymus DNA was prepared in TE buffer. Working solution (190 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube (DeNovix cat #TUBE-PCR-0.5-500). dsDNA (10 µL) was added to each tube in the standard range, and volume was adjusted for total mass in the extended range.

Ultra High Sensitivity Assay: Working solution (200 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube. dsDNA (10 µL) was added to each tube.

Table 2: Microvolume Performance Data
ExpectedDeNovix DS-11 NanoDrop™ One 
ng/µLng/µL% error%CVng/µL% error%CV
0.970.7027.542.23Below Specification Limits
2.002.8040.08.293.0854.013.26
4.054.8820.58.824.8419.510.33
6.055.646.789.647.5224.3054.12
7.386.837.456.656.788.133.69
13.4914.215.344.1813.261.700.85
26.7427.663.444.2826.720.070.78
50.2353.316.131.3553.566.630.54
108.26113.04.380.35112.84.190.53
255.23259.91.830.60263.43.200.15
513.26509.20.790.35521.61.620.09
1036.81020.71.550.141070.23.220.22
2082.82102.10.930.172113.71.480.13
4720.84628.41.960.374524.34.160.11
10390101182.620.6799973.780.12
12616124441.360.49120424.550.26
26269242957.510.79237739.500.14

Table 3: Fluorescence Performance Data

ExpectedDeNovix DS-11 FX+ NanoDrop™ One
ng/µLng/µL%CVAssay*
0.00050.000366.89UHSFluorescence quantitation not possible.
0.00100.001098.75UHSRequires purchase of additional instrument.
0.00200.00182.23UHS
0.01000.00851.06UHS
0.05000.04520.40UHS
0.100.070.00HS
0.300.250.16HS
1.000.790.10HS
3.003.040.20HS
10.010.60.36HS
25.026.80.11BR
50.053.80.10BR
1001060.09BR
2001960.14BR
100010500.01BR
.

Table 4: High Absorbance Sample Performance
ExpecteddsDNA EquivalentDeNovix DS-11NanoDrop™ One
Absng/µLAbs% error%CVAbs
60030000588.81.870.35Above Specification Limits
65032500628.93.240.41
70035000676.73.360.66
75037500732.72.441.32

Summary

The DeNovix DS-11 Series Spectrophotometer / Fluorometer delivers greater accuracy and sensitivity than the Thermo Fisher Scientific NanoDrop One. The DS-11 also offers a broader dynamic range, greater ease of use and provides researchers with superior flexibility and functionality. The DS-11 Series Spectrophotometer / Fluorometer combines microvolume absorbance and fluorescence measurements on one instrument, supplying the user with tools to measure both routine and difficult samples. With the DS-11 Series, labs are equipped for today’s complex workflow as well as for the challenges of future assays. The DS-11 Series and DeNovix Assays combined provide superior sensitivity and a much broader dynamic range for dsDNA quantification (0.5 pg/µL – 37500 ng/µL) than the NanoDrop One.

NanoDropTM and NanoDropTM One are registered trademarks of Thermo Fisher Scientific. 

Revised 19 Oct 2020