RNA and DNA quantification instruments offered by Thermo Fisher Scientific: Qubit, NanoDrop and plate reader platforms

Detection technologies used for RNA/DNA quantification

DNA quantification and RNA quantification, generally referred to as nucleic acid quantification, is commonly performed to determine the average concentration of DNA or RNA in a sample prior to proceeding with downstream experiments. Sample purity is also an important consideration to accurately calculate the amount of DNA or RNA in a sample. There are two optical technologies commonly used quantify nucleic acids: UV-Vis measurement and fluorescence measurement. Choosing the right technology for your samples, workflow and throughput results in accurate RNA or DNA quantification and can save significant time and money by helping to prevent downstream experimental failures.

  Photometry (UV-Vis) Fluorescence
How is the optical signal generated? The photometric measurement of nucleic acids is based on the intrinsic absorptivity properties of nucleic acids (DNA and RNA). When an absorption spectrum is measured, nucleic acids absorb light with a characteristic peak at 260 nm. The fluorometric measurement of nucleic acids is based upon the use of fluorogenic dyes that bind selectively to DNA or RNA.
  Graph of absorbance spectrum used for RNA/DNA quantification, with peak at 260nm
Typical RNA/DNA absorbance spectrum.
Cartoon of assay tube illustrating fluorescent dyes selectively bound to DNA, RNA or protein for protein/RNA/DNA quantification
Fluorescent dyes selectively bind to DNA, RNA or protein. Dyes only emit signal when bound to the target.
How is the optical signal measured?
  • The signal is measured by spectrophotometers or spectrometers. The attenuation in the light that reaches the detector after passing through the sample is measured in relation to the incident light and expressed as absorbance values of the sample in the solution.
  • The signal is measured by fluorometers. Sample is excited with filtered light (at the excitation wavelength, and the emitted light (at the emission wavelength) is recorded by a detector.
  Simple graphic showing how a spectrophotometer works: light source, sample and detector Simple graphic showing how a fluorometer works: light source, excitation filter, sample, emission filter, and detector
 
  • Wavelength separation can take place before or after the light has passed the sample, and the optical light path can be horizontal or vertical.
  • Wavelength separation can take place in various ways (for example with filters or with monochromators)
How is the concentration of nucleic acids calculated?
  • Concentrations of nucleic acids can be directly calculated from their measured absorbance values at 260 nm, using the Beer-Lambert's equation:

    where:
    • C= nucleic acid concentration in molar (M)
    • A=UV absorbance in absorbance units (AU)
    • ε=wavelength-dependent molar absorptivity coefficient (or extinction coefficient) in M-1cm-1
    • L= light path in cm (cm)
  • This concentration calculation is automated in many instruments.
  • Concentrations of nucleic acids are measured using the fluorescence signal of the sample and a calibration curve is generated from standard samples of known concentration and fit to appropriate regression models.
    Graph of typical fluorescence standard curve for RNA/DNA quantification
    Typical Fluorescence Standard Curve.
  • The limit of detection and linear response of the measurements are specific to each assay.
What are the advantages?
  • It is simple—no sample preparation, dyes, or standards are required
  • Can provide direct measurements of purity ratios—A260/280 and A260/230
  • Can provide information on contaminants—can identify non-nucleic acid contamination in samples (proteins, phenol, guanidine salts) and provide corrected concentrations (applicable to NanoDrop One/OneC instruments)
  • It is specific—performed measurement is selective for DNA, ds DNA, ssDNA, and RNA
  • It is sensitive—can measure pg/mL; it is the recommended method for very diluted nucleic acid samples
  • It is accurate despite contamination being present in the sample, including nucleic acid contaminants
What are the disadvantages?
  • It is not selective—does not distinguish between DNA or RNA
  • It has limited sensitivity—detection limits are higher than fluorescence-based methods
  • It takes longer—reagent and sample preparation are required
  • No purity information is provided

We offer a range of instruments to perform nucleic acid quantification using either photometry of fluorescence measurements.

TOP

Choice instruments for photometric UV-Vis RNA/DNA quantification

Well-known Thermo Scientific instruments for UV-Vis RNA/DNA quantification include the NanoDrop One/OneC Spectrophotometer for convenient, single-sample microvolume analysis, the NanoDrop 8000 Spectrophotometer for 8-sample microvolume analysis, and choice of the Multiskan Sky Microplate Spectrophotometer or the Varioskan LUX Multimode Reader for up to 16 microvolume samples as well as 96-384-well plates. The table below provides additional detail on instrument performance.

  NanoDrop One spectrophotometer instrument photo NanoDrop 8000 spectrophotometer instrument photo Multiskan Sky Microplate spectrophotometer instrument photo Varioskan LUX Multimode Microplate Reader instrument photo
  NanoDrop One/Onec Nanodrop 8000 Multiskan Sky Varioskan LUX
What is the lower detection limit (dsDNA)?
  • Pedestal: 2.0 ng/µL
  • Cuvette: 0.2 ng/µL
2.5 ng/µL Depends on sample format and volume used (in the case of microplates)*
See details
  • Cuvette: 0.45 ng/µL
  • µDrop Plate: 9 ng/µL
Microplates:
96 well plates (normal)
  • 70 µL (minimum) 2.1 ng/µL
  • 140 µL (good) 1.1 ng/µL
  • 370 µL (maximal) 0.4 ng/µL
96 well plates (half-area)
  • 35 µL (minimum) 2.1 ng/µL
  • 60 µL (good) 1.2 ng/µL
  • 180 µL (maximal) 0.5 ng/µL
384 well plates
  • 20 µL (minimum) 2.5 ng/µL
  • 40 µL (good) 1.3 ng/µL
  • 120 µL (maximal) 0.5 ng/µL
Depends on sample format and volume used (in the case of microplates)*
See details
  • Cuvette: 0.15 ng/µL
  • µDrop Plate: 3 ng/µL
Microplates:
96 well plates (normal)
  • 70 µL (minimum) 0.7 ng/µL
  • 140 µL (good) 0.4 ng/µL
  • 370 µL (maximal) 0.5 ng/µL
96 well plates (half-area)
  • 35 µL (minimum) 0.7 ng/µL
  • 60 µL (good) 0.4 ng/µL
  • 180 µL (maximal) 0.1 ng/µL
384 well plates
  • 20 µL (minimum) 0.8 ng/µL
  • 40 µL (good) 0.4 ng/µL
  • 120 µL (maximal) 0.2 ng/µL
What is the upper detection limit (dsDNA)?
  • Pedestal: 27 500 ng/µL
  • Cuvette: 75 ng/µL
3700 ng/µL Depends on sample format and volume used (in the case of microplates)
See details
  • Cuvette: 125 ng/µL
  • µDrop Plate: 2500 ng/µL
Microplates:
96 well plates (normal)
  • 70 µL (minimum) 590 ng/µL
  • 140 µL (good) 310 ng/µL
  • 370 µL (maximal) 120 ng/µL
96 well plates (half-area)
  • 35 µL (minimum) 560 ng/µL
  • 60 µL (good) 320 ng/µL
  • 180 µL (maximal) 110 ng/µL
384 well plates
  • 20 µL (minimum) 690 ng/µL
  • 40 µL (good) 350 ng/µL
  • 120 µL (maximal) 120 ng/µL
Depends on sample format and volume used (in the case of microplates)
See details
  • Cuvette: 200 ng/µL
  • µDrop Plate: 4000 ng/µL
Microplates:
96 well plates (normal)
  • 70 µL (minimum) 950 ng/µL
  • 140 µL (good) 500 ng/µL
  • 370 µL (maximal) 190 ng/µL
96 well plates (half-area)
  • 35 µL (minimum) 900 ng/µL
  • 60 µL (good) 520 ng/µL
  • 180 µL (maximal) 190 g/µL
384 well plates
  • 20 µL (minimum) 1100 ng/µL
  • 40 µL (good) 570 ng/µL
  • 120 µL (maximal) 200 ng/µL
What are the available sample formats?
  • Drop (1 µL)
  • cuvettes
Drop (1 µL)
  • 96-384 well plates
  • µDrop Plate (2-10 µL)
  • cuvettes (not all models)
  • 6-384 well plates
  • µDrop Plate (2-10 µL)
  • cuvettes (not all models)
How many samples can be measured at a time? (throughput) One sample at a time Up to 8 Dependent on assay format
See details
  • one sample at a time with cuvettes
  • up to 16 with µDrop plate
  • up to 96 with 96-well plates
  • up to 384 with 384 well plates
Dependent on assay format
See details
  • one sample at a time with cuvettes
  • up to 16 with µDrop plate
  • up to 96 with 96-well plates
  • up to 384 with 384 well plates
What volume of sample is required to measure? 1 µL 1 µL As little as 2 µL depending on assay format
See details
  • 2-10 µL with µDrop Plate (smallest volume required)
  • 70-300 µL with 96 well plates (normal)
  • 20-100 µL with 384 well plates
  • 1 mL with 10x10 mm cuvettes (70 µL for microcuvettes)
As little as 2 µL depending on assay format
See details
  • 2-10 µL with µDrop Plate (smallest volume required)
  • 70-300 µL with 96 well plates (normal)
  • 20-100 µL with 384 well plates
  • 1 mL with 10x10 mm cuvettes (70 µL for microcuvettes)
How much time it takes to measure one sample? 8 seconds < 20 seconds Around 1 minute for 16 microvolume samples in the µDrop Plate
See details When performed with the user interface touch screen or SkanIt software (fast mode)
Around 1.3 minutes for 16 microvolume samples in the µDrop Plate
See details When performed with the user interface touch screen or SkanIt software (fast mode)
Does it provide spectral data of the sample? Yes Yes Yes Yes
Does it give information on sample purity? Yes
See details It provides full spectral data (A260/A280 and A260/A230 ratios) as well as Acclaro Contaminant Analysis
Yes
See details It provides full spectral data (A260/A280 and A260/A230 ratios)
Yes
See details It provides full spectral data (A260/A280 and A260/A230 ratios)
Yes
See details It provides full spectral data (A260/A280 and A260/A230 ratios)
Does it detect specific contaminants in the sample? Yes
See details Acclaro Sample Intelligence technology detects protein, phenol and guanidine salts and it gives true concentration of the nucleic acids
No
See details Some information is available, based on the purity ratios
No
See details Some information is available, based on the purity ratios
No
See details Some information is available, based on the purity ratios
Does it distinguish between DNA and RNA in the sample? No No No No
Does it support oligonucleotide quantification? Yes
See details With embedded applications and custom methods
Yes
See details With embedded applications and custom methods
Yes Yes
Does it provide pre-configured protocols? Yes
See details There are user interface touch screen and custom-protocols
Yes Yes
See details There are pre-configured protocols in the interface touch screen and SkanIt software Cloud Library, free with SkanIt Software
Yes
See details There are pre-configured protocols in the SkanIt software Cloud Library, free with SkanIt Software
Does it connect to the Thermo Fisher Connect? Yes No Yes No
Does it provide 21CFR Part 11 compliance? No No Yes
See details with SkanIt software Drug Discovery Edition
Yes
See details with SkanIt software Drug Discovery Edition
Does it offer robotic automation compatibility? No No Yes Yes
How is the instrument operated? Via a touch screen user interface With a PC software (Nanodrop 8000 Operating software) Via a touch screen user interface or the PC software (SkanIt software) Via a PC software (SkanIt software)
What is the overall ease of use? ++++ +++ ++++ +++
What is the basic protocol? See details
  1. Pipette buffer on pedestal and blank instrument
  2. Pipette sample directly on pedestal
  3. Follow instructions on touchscreen to run protocol
  4. Results are available within seconds
See details
  1. Pipette buffer on all 8 pedestals and blank instrument
  2. Pipette samples directly on 8 pedestals
  3. Run protocol using PC software
  4. Results are available within seconds
See details
  1. Pipette blank(s) and samples in microplates or µDrop plate
  2. Choose how you want to run your assay:
    • Choose the pre-configured assay using the touch screen
    • Choose the pre-built assay in the SkanIt Cloud Library within SkanIt Software
    • Set up the assay using SkanIt Software
  3. Results are available quickly
See details
  1. Pipette blank(s) and samples into microplates or µDrop plate
  2. Either choose the pre-built protocol in the SkanIt Cloud Library or set-up the assay with SkanIt Software
  3. Results are available quickly
What is the instrument price category? Medium Medium Medium High
What are the ownership costs? No recurring costs No recurring costs If using µDrop Plate, no recurring costs; otherwise UV-compatible clear plates If using µDrop Plate, no recurring costs; otherwise UV-compatible clear plates
* Theoretical limit of detection (LOD), estimated according to IUPAC, based on the precision of the blanks (3*SD), from the precision specifications of Multiskan Sky and Varioskan LUX microplate readers.

TOP

Choice instruments for fluorescence RNA/DNA quantification

High-performing and popular instruments for performing fluorescence RNA or DNA quantification include the Invitrogen Qubit 4 Fluorometer for single-sample microvolume fluorescence measurements, the Invitrogen Qubit Flex Fluorometer for 8-sample microvolume fluorescence measurements, the Thermo Scientific Fluoroskan Microplate Fluorometer for 96-384-well microplate filter-based fluorescence measurements, and the Thermo Scientific Varioskan LUX Multimode Microplate Reader for 96-1536-well microplate monochromator-based fluorescence measurements. The table below provides additional detail on instrument performance.

  Qubit 4 Fluorometer instrument photo Qubit Flex Fluorometer instrument photo Fluoroskan Microplate Fluorometer instrument photo Multimode Microplate Reader instrument photo
  Qubit 4 Qubit Flex Fluoroskan Family Varioskan LUX
What is the lower concentration limit (dsDNA)? 0.005 ng/µL* 0.005 ng/µL* Depends on the Quant-iT assay kit, standard concentrations and curve fittings used**
See details 0.006 ng/µL
Depends on the Quant-iT assay kit, standard concentrations and curve fittings used**
See details 0.003 ng/µL
What is the upper detection limit (dsDNA)? 2000 ng/µL* 2000 ng/µL* Depends on the Quant-iT assay kit and assay conditions Depends on the Quant-iT assay kit and assay conditions
What are the available sample formats? Qubit assay tubes
See details Low-fluorescence, thin-walled polypropylene tubes
Qubit Flex tube strips
See details Low-fluorescence, thin-walled PCR tube strips
96-384 well plates 96-1536 well plates
How many samples can be measured at a time? (throughput) 1 Up to 8 Dependent on assay format
See details
  • up to 96 with 96-well plates
  • up to 384 with 384 well plates
Dependent on assay format
See details
  • up to 96 with 96-well plates
  • up to 384 with 384 well plates
  • up to 1536 with 1536 well plates
What volume of sample is required to measure? 1-20 µL 1-20 µL Dependent on assay format, fluorophore that is measured, among others Dependent on assay format, fluorophore that is measured, among others
Does it give information on sample purity? No No No No
Does it detect contaminants in the sample? No No No No
Does it distinguish between DNA and RNA in the sample? Yes
See details Using fluorescent dyes that are specific for DNA or RNA
Yes
See details Using fluorescent dyes that are specific for DNA or RNA
Yes
See details Using fluorescent dyes that are specific for DNA or RNA
Yes
See details Using fluorescent dyes that are specific for DNA or RNA
Does it support oligonucleotide quantification? Yes
See details With ssDNA assay kit
Yes
See details With ssDNA assay kit
Yes
See details With Quant-iT OliGreen assay kit
Yes
See details With Quant-iT OliGreen assay kit
Does it provide pre-configured protocols? Yes
See details There are pre-configured protocols in the user interface touch screen
Yes
See details There are pre-configured protocols in the user interface touch screen
Yes
See details There are pre-configured protocols in the SkanIt Cloud Library, free with SkanIt Software
Yes
See details There are pre-configured protocols in the SkanIt Cloud Library, free with SkanIt Software
Does it connect to the Thermo Fisher Connect? Yes Yes Yes No
Does it provide 21CFR Part 11 compliance? No No Yes
See details with SkanIt software Drug Discovery Edition
Yes
See details with SkanIt software Drug Discovery Edition
Does it offer robotic automation compatibility? No No Yes Yes
What is the overall ease of use? ++++ ++++ ++ ++
What is the basic protocol? See details
  1. Prepare working solutions of reagent using on-board Reagent Calculator
  2. Pipette samples and standards according to instructions shown on touch screen
  3. Results are available within seconds
See details
  1. Prepare working solutions of reagent using on-board Reagent Calculator
  2. Pipette samples and standards according to instructions shown on touch screen
  3. Results are available within seconds
See details
  1. Prepare reagents, sample(s) and standards according to specific Quant-iT kit instructions
  2. Pipette them in microplates
  3. Either select pre-built protocol from SkanIt Cloud Library or set-up assay using SkanIt Software
  4. Measure the plates with the instrument
See details
  1. Prepare reagents, sample(s) and standards according to specific Quant-iT kit instructions
  2. Pipette them in microplates
  3. Either select pre-built protocol from SkanIt Cloud Library or set-up assay using SkanIt Software
  4. Measure the plates with the instrument
What is the instrument price category? Low Low-Medium Medium High
What are the ownership costs?
  • Requires Qubit Assays
  • Requires thin-walled polypropylene tubes
See details Recommended:
Qubit tubes
See details Recommended:
Qubit Flex tube strips
See details Recommended:
non-treated Nunc plates
See details Recommended:
non-treated Nunc plates
* Reported here are the lower and upper quantitation ranges measured with Qubit dsDNA High sensitivity (HS) kit (Q32851) Qubit dsDNA Broad Range (BR) kit (Cat. No. Q32850) respectively and using variable sample volume (1-20 µL).

** Limit of Detection (LOD) using the Quant-iT dsDNA Assay HS Kit (Cat. No. Q33120) as instructed. LOD estimated according to IUPAC, based on the precision of the blanks (3*SD). Results will vary depending on the curve fittings, standard concentrations and used kits.

UV-Vis and Vis Spectrophotometry

Meet your analytical challenges with our complete line of ultraviolet-visible (UV-Vis) spectrophotometers. Our award-winning designs and user-friendly software help you quantify, assess purity, and more.

Learn more

Fluorometers and Fluorescence

Use fluorometers to quantify, detect and monitor analytes and their reactions by measuring the intensity of the fluorescent signal from dyes attached to biological molecules as well as naturally fluorescent molecules based on signature excitation (Ex) and emission (Em) wavelengths.

Learn more

TOP

Ordering information

Q: What is the difference between UV and Fluorescence DNA quantification? Which DNA quantification technology should I choose?
A: UV and Fluorescence technologies work differently to quantify DNA. UV quantification relies on the intrinsic absorptivity of DNA and RNA molecules, while fluorescence quantification uses dyes that specifically bind to your molecule of choice. With UV technology, quantification isn't as sensitive, but it has the broadest dynamic range and also gives data about sample purity--plus it is the fastest because there is no reagent prep. With fluorescence technology you get higher sensitivity and molecule-specific data, but it has lower dynamic range and reagent prep is required, so it takes a little longer. The technology you need depends on what you need for your experiment.
Learn more

Q: Which is the best DNA quantification instrument? Which is the best RNA quantification instrument?
A: All of the DNA instruments offered by Thermo Fisher Scientific are of excellent quality. To find the right instrument to quantify DNA or RNA in your lab, explore the detailed comparison of UV-Vis spectrophotometers (link to #spectrophotometers) and fluorometers (link to #fluorometers). Things like sensitivity, throughput and budget may be initial considerations when selecting a DNA quantification instrument. You may also consider whether you need target specificity, sample purity information, or broad dynamic range.
See UV-Vis spectrophotometers
See fluorometers

TOP