Nucleora / Tools / Oligo properties

Oligo molecular weight and extinction coefficient

Molecular weight for the 5′ end your oligo actually has, the nearest-neighbour extinction coefficient at 260 nm, and conversions between nmol, µg and A₂₆₀ units.

OLoligo propertiescomputed in this page

Input

Oligonucleotide · 5′→3′, plain or FASTA

Strand

5′ end

Measured A₂₆₀ · optional

Path length, cm

Amount to convert · optional

Unit

Result

Method: molecular weight from exact nucleotide formulae; ε₂₆₀ by the nearest-neighbour model for an unpaired strand. Limit: modified bases, dyes and linkers are not modelled, and nearest-neighbour ε₂₆₀ is an estimate (see Method).

METHOD

How it is calculated

Molecular weight. The mass of a single strand is the sum of its nucleoside monophosphates minus one water per phosphodiester bond, computed from elemental formulae and IUPAC atomic weights. That gives the 5′-phosphate form. A synthetic oligo normally carries a 5′-OH, which is one HPO₃ lighter, and an in-vitro transcript carries a 5′-triphosphate, two HPO₃ heavier.

M(5′-p) = Σ M(NMP_i) − (N − 1)·M(H₂O) M(5′-OH) = M(5′-p) − M(HPO₃)

Extinction coefficient. The nearest-neighbour model adds the published dinucleotide values along the strand and subtracts the mononucleotide value of every internal base:

ε₂₆₀ = Σ_i=1^N−1 ε(N_iN_i+1) − Σ_i=2^N−1 ε(N_i)

DNA values are those of Cantor, Warshaw and Shapiro (1970); RNA values as tabulated by Puglisi and Tinoco (1989). Concentration then follows from Beer-Lambert: c = A₂₆₀ / (ε₂₆₀ · l).

How far to trust ε₂₆₀. Cavaluzzi and Borer (2004) report that predictions accounting for nearest-neighbour frequency or base composition give concentrations 10 to 30 % too low for typical single-stranded DNA used as PCR primers. Treat the concentration as an estimate, not a measurement.

Which calculation this page matches

Molecular weight agrees with Biopython's Bio.SeqUtils.molecular_weight to within 0.004 g/mol on 45 test sequences, and ε₂₆₀ reproduces the published dinucleotide table exactly.

References

Cantor CR, Warshaw MM, Shapiro H (1970) Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9:1059-1077. doi:10.1002/bip.1970.360090909
Puglisi JD, Tinoco I Jr (1989) Absorbance melting curves of RNA. Methods Enzymol 180:304-325. doi:10.1016/0076-6879(89)80108-9
Cavaluzzi MJ, Borer PN (2004) Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res 32:e13. doi:10.1093/nar/gnh015

WORKED EXAMPLE

A worked example, computed by this page

The M13/pUC forward (−20) sequencing primer, GTAAAACGACGGCCAGT (positions 379 to 395 of pUC19, GenBank L09137.2), as a synthetic DNA oligo with a 5′-OH:

Molecular weight	5,228.42 g/mol
ε₂₆₀	172,500 M⁻¹cm⁻¹
nmol per A₂₆₀ unit	5.797
µg per A₂₆₀ unit	30.310
GC	52.9 %

So one A₂₆₀ unit of this primer in 1 mL is about 5.80 nmol, and dissolving it to 100 µM takes 58.0 µL of buffer per A₂₆₀ unit, within the 10 to 30 % uncertainty described above.

WHERE THIS RUNS

The calculation runs in your browser

The arithmetic on this page is JavaScript executing in your browser. The sequence you enter is not sent anywhere: the calculator makes no network request with it, and there is no account, upload or server-side step. You can disconnect from the network after the page has loaded and the calculator keeps working.