Oligo Calculator is an oligonucleotide chemical formula and molecular weight calculator and MS peak assignment tool.

Oligonucleotide sequences can be entered using any of the formats shown below, with sulfurizations / phosphorothioate linkages indicated by inserting an asterisk (*) between residues, either:

• Unseparated standard capitalized single-letter codes for 2'-deoxy (DNA) residues, with multiple-letter codes enclosed in round, curly or square brackets

(mG)*(fC)*(mU)GG(mC)*(rA)*(mG)
{mG}*{fC}*{mU}GG{mC}*{rA}*{mG}
[mG]*[fC]*[mU]GG[mC]*[rA]*[mG]

• All residues separated by either a dot, comma or dash (or sulfurization asterisk where required), without brackets

mG*fC*mU.G.G.mC*rA*mG
mG*fC*mU,G,G,mC*rA*mG
mG*fC*mU-G-G-mC*rA*mG

5'- and 3'-termini can be selected from the predefined lists.

MS peaks for assignment can be provided in the form of a comma-separated list and Oligo Calculator will attempt to assign them to deletion sequences, adducts and/or losses.

Click on the mass spectrum to see an example assignment for the sequence above.

A SMILES string can be automatically generated for each oligonucleotide sequence entered, which can be pasted directly as a structure into most chemical drawing software.

Where possible, Oligo Calculator will also provide estimated extinction coefficient values for your sequence.

Predefined termini and residues currently supported are given below (with chemical formulae). Hovering over underlined residue codes will display molecular structures.

Please send comments, questions, residue requests and bug reports to:

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