TECHVAULT > READING ROOM > QUICK REFERENCE

Molecular Weight (Anhydrous)

Molecular weight (MW) is the sum of the atomic masses of the constituent atoms for 1 mole of oligonucleotide. The anhydrous molecular weight represents the pure oligo free of any of the counter ions or water molecules that are normally weakly bound to an oligo after synthesis. This calculation gives with the molecular weight measured by mass spectroscopy.

Molecular weight of an oligomer is a sum of the weights of individual bases and chemical modifications. Oligos are typically synthesized without a 5'-phosphate group, which must be subtracted.

Anhydrous MW = ΣIndividual Base MW + ΣIndividual Mod MW - PO2H + H2 

DNA bases: The molecular weight of DNA nucleotides is as follows:

dA 313.2
dC 289.2
dG 329.2
dT 304.2
dU 290.2
DI 314.2

RNA bases: The molecular weight of an RNA nucleotide is the weight of a DNA nucleotide + 15.999, accounting for the additional oxygen atom present (Example: rA is dA (313.209) + 15.999 = 329.208). When determining the weight of uracil (rU), start with dU and not thymine (dT).

2'-O-Methyl bases: The molecular weight of an 2'-O-Methyl RNA nucleotide is the weight of a DNA nucleotide + 30.026, accounting for the the addditional methoxy group (-OCH3) present (For example: mA is dA (313.209( + 30.026 = 343.235). When determining the weight of uracil (mU), start with dU and not thymine (dT).

LNA bases: The molecular weight of an LNA nucleotide is the weight of a DNA nucleotide + 28.011, accounting for the bridging oxygen and carbon from the 2' carbon to the 4' carbon (-OCH2-) present (For example: +A is dA (313.209) + 28.011 = 341.220). The exception is LNA C, which contains an additional methyl group off of the 5-carbon (14.026)

Phosphorothioated bases: The molecular weight of a phosphorothioate nucleotide is the weight of a nucleotide (DNA, RNA, 2'-O-Methyl, LNA) + 16.061, accounting for the substitution of one sulfur atom for a non-bridging oxygen atom in the phosphodiester backbone (For example: A* is A (313.209) + 16.061 = 329.270). Phosphorothioate modification refers to substitutions affecting the internucleoside linkages and does not involve the free 3'- or 5'- ends. Thus a 20-mer phosphorothioate oligonucleotide has 19 phosphorothioate linkages.