ThermoFisher Scientific NanoDrop Eight, User Manual

Page: 37 / 152

4
Nucleic Acid Applications
Measure Oligo DNA or Oligo RNA
Thermo Scientific NanoDrop Eight User Guide 37
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 –

=