Thermo Scientific NanoDrop One, User Manual

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6
Measure Oligo DNA or Oligo RNA
Thermo Scientific NanoDrop One User Guide 49
Related Topics
• Detection Limits for All Applications
Calculations for Oligo DNA and Oligo RNA Measurements
As with the other nucleic acid applications, the Oligo
applications use the
Beer-Lambert equation to correlate
absorbance with concentration based on the sample’s
extinction coefficient and pathlength. Because
oligonucleotides are short, single-stranded molecules (or
longer molecules of repeating sequences), their
spectrum and extinction coefficient (

) are closely
dependent on base composition and sequence.
(The generally accepted extinction coefficients and
factors for single-stranded DNA and RNA provide a
reasonable estimate for natural, essentially randomized,
sequences but not for short, synthetic oligo sequences.)
To ensure the most accurate results, we use the exact
value of

260
to calculate oligonucleotide concentration.
The NanoDrop software allows you to specify the base
sequence of an oligonucleotide before it is measured.
For any entered base sequence, the software uses the
equation at the right to calculate the extinction
coefficient.
Extinction Coefficients for Oligonucleotides
The software uses the nearest neighbor method and the following formula
to calculate molar extinction coefficients for specific oligonucleotide base
sequences:
where:

= molar extinction coefficient in L/mole-cm

1 =

nearest neighbor

2 =

individual bases

3 =

modifications, such as fluorescent dyes
Tip : The extinction coefficient is wavelength specific for
each oligonucleotide and can be affected by buffer type,
ionic strength and pH.

260

1

2

3
1
N

+
2
N 1 –

–
1
N 1 –

=