Microvolume Quantitation of Nucleic Acids

Philippe R. Desjardins1, Deborah S. Conklin1

1 Thermo Scientific NanoDrop Products, Wilmington, Delaware
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Appendix 3J
DOI:  10.1002/0471142727.mba03js93
Online Posting Date:  January, 2011
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Abstract

Quantitation of DNA and RNA by absorbance and fluorescence spectroscopy has been a powerful tool in life sciences for decades. Classic methods of nucleic acid quantitation require the filling of devices, such as cuvettes and capillaries, with sample (traditional methodologies are described in APPENDIX 3D). Analysis of microvolume samples has become of paramount importance as more molecular biology techniques yield progressively smaller amounts of isolated sample and require accurate quantitation of nucleic acids with minimal consumption of sample. Advances in photonic technologies have resulted in a pioneering microvolume system that combines fiber optic technology with the inherent physical properties of the sample to dramatically reduce measurement volumes, removing the need for cuvettes and capillaries. Since the introduction of the first microvolume instrument, several new designs are now available, providing opportunities to measure nucleic acids using much smaller amounts of material. Altogether, these systems not only reduce measurement volume (as little as 0.5 to 2 µl), but also tend to be more efficient time-wise than traditional methods, making them useful even when sample is plentiful. The protocols in this unit are based on the most widely accepted microvolume systems and are intended as practical alternatives to traditional nucleic acid quantitation methodology. Curr. Protoc. Mol. Biol. 93:A.3J.1-A.3J.16. © 2011 by John Wiley & Sons, Inc.

Keywords: spectroscopy; DNA; RNA; quantitation; microvolume; absorbance; fluorescence

     
 
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Table of Contents

  • Introduction
  • Basic Protocol: Microvolume Nucleic Acid Quantitation Using a Nanodrop Spectrophotometer
  • Alternate Protocol 1: Microvolume Nucleic Acid Quantitation Using a Traditional Spectrophotometer and a Microcell Cuvette
  • Alternate Protocol 2: High-Sensitivity Microvolume Nucleic Acid Quantitation Using a Nanodrop Fluorospectrometer
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol: Microvolume Nucleic Acid Quantitation Using a Nanodrop Spectrophotometer

 Materials
  • Deionized water or appropriate buffer
  • Sample containing nucleic acids
  • NanoDrop 2000 or 2000c Spectrophotometer (Thermo Scientific NanoDrop Products, http://www.thermoscientific.com/nanodrop)
  • Laboratory wipes (e.g., Kimwipes)
  • Pipettor (0 to 2 µl)
  • Nuclease-free, low-retention pipet tips

Alternate Protocol 1: Microvolume Nucleic Acid Quantitation Using a Traditional Spectrophotometer and a Microcell Cuvette

 Materials
  • Sample containing nucleic acids
  • Microcell cuvette: TrayCell (Hellma, http://www.hellmausa.com/) or Optical Ultra LabelGuard Microliter cell (Implen, http://www.implen.de)
  • UV-vis spectrophotometer (any standard cuvette spectrophotometer)
  • Pipettor (0 to 10 µl)
  • Nuclease-free, low-retention pipet tips
  • Laboratory wipes (e.g., Kimwipes)

Alternate Protocol 2: High-Sensitivity Microvolume Nucleic Acid Quantitation Using a Nanodrop Fluorospectrometer

 Materials
  • Sample containing dsDNA
  • PicoGreen dsDNA Quantitation Kit (Invitrogen) including:
    • 20× TE buffer
    • dsDNA standards
    • PicoGreen dsDNA reagent
  • Nuclease-free H2O (e.g., Invitrogen)
  • Nuclease-free, low-retention pipet tips (e.g., Hamilton)
  • 1.5-ml nuclease-free amber microcentrifuge tubes or standard nuclease-free microcentrifuge tubes wrapped in aluminum foil
  • NanoDrop 3300 Fluorospectrometer (Thermo Scientific NanoDrop Products, http://www.thermoscientific.com/nanodrop)
  • Laboratory wipes (e.g., Kimwipes)
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Figures

  •  FigureFigure A.3J.1 The NanoDrop 2000 and 2000c Spectrophotometer microvolume sample retention system. (A) A sample volume of 1 µl is dispensed onto the lower optical surface. (B) Once the instrument lever arm is lowered, the upper optical surface engages with the sample, forming a liquid column with the path length defined by the distance between the two optical surfaces. During each measurement, the sample is assessed at variable path lengths (1-mm, 0.2-mm, 0.1-mm, and 0.05-mm) and an optimal path is automatically determined, providing a wide concentration range for nucleic acid quantification.
  •  FigureFigure A.3J.2 The shorter the path length, the higher the concentration that can be measured.
  •  FigureFigure A.3J.3 To clean the optical pedestals, pipet 2 to 3 µl of clean deionized water onto the lower optical surface. Close the lever arm to ensure the upper pedestal comes in contact with the deionized water. Lift the lever arm and wipe off both optical surfaces with a clean, dry, lint-free laboratory wipe.
  •  FigureFigure A.3J.4 (A) Flattening of the sample droplet is indicative of an unconditioned optical pedestal. (B) Beading-up of the sample droplet is indicative of a properly conditioned optical pedestal.
  •  FigureFigure A.3J.5 A typical nucleic acid absorbance spectrum.
  •  FigureFigure A.3J.6 Microvolume nucleic acid quantitation using the TrayCell microcell cuvette. The sample is pipetted directly onto the center of the optical window. Due to the integrated beam deflection and the use of fiber-optic light conductors, the sample can be measured directly on the optical surface. Using the 1-mm or 0.2-mm reflective cap creates a liquid column of defined path length equal to 1-mm or 0.2 mm, respectively. This generates virtual dilution factors of 1:10 or 1:50, respectively, compared to a standard 1-cm cuvette measurement. The required sample volume is 3 to 5 µl for the 1-mm cap and 0.7 to 4 µl for the 0.2-mm cap.
  •  FigureFigure A.3J.7 Detection limits and respective mass consumptions for a microvolume fluorospectrometer, a traditional cuvette-based fluorometer, and a fluorescence plate reader.
  •  FigureFigure A.3J.8 The Trinean system uses microfluidic channels and chambers to define the 1-mm and 0.2-mm path lengths. Samples are dispensed either manually or by an automatic dispenser into loading wells. Sample fluid then travels by capillary action into a lower chamber where an absorbance measurement is taken. The thickness of this lower measuring chamber represents the shorter 0.2-mm path. The sample fluid then continues to travel by vacuum pressure into a second upper measuring chamber (0.8-mm thick) located directly above the lower measuring chamber and another absorbance measurement is taken. The combined thickness of the first and second chambers is 1-mm and represents the longer path length.
  •  FigureFigure A.3J.9 Spectral interpretation. (A) Typical nucleic acid sample absorbance spectrum. (B) Comparison of nucleic acid sample absorbance spectra with and without two common contaminants.
  •  FigureFigure A.3J.10 Several examples of reagents with absorption in the 220 to 240 nm range that are commonly used with nucleic acids.

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Literature Cited

Literature Cited
    Glasel, J.A. 1995. Validity of nucleic acid purities monitored by A260/A280 absorbance ratios. Biotechniques 18:62-63.
    Ingle, J.D. Jr. and Crouch, S.R. 1988. Spectrochemical Analysis. XV +. Prentice Hall, Englewood Cliffs, N.J.
    Voolstra, C., Jungnickel, A., Borrmann, L., Kirchner, R., and Huber, A. 2006. Spectrophotometric Quantification of Nucleic Acids: LabelGuard Enables Photometric Quantification of Submicroliter Samples Using a Standard Photometer. Implen Applications Note, Munich, Germany.
    Wilfinger, W.W., Mackey, K., and Chomczynski, P. 1997. Effect of pH and Ionic Strength on the Spectrophotometric Assessment of Nucleic Acid Purity: BioTechniques 22:474-481.
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