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Why do your molecular weight calculations seem higher than normal?

Molecular weight is the sum of the atomic masses of the constituent atoms for one mole of a compound (6 x 1023 molecules). IDT reports the anhydrous molecular weight. For oligonucleotides, a simple algorithm can be written to calculate molecular weight based on shorthand sequence notation. Component pieces include bases (deoxyribonucleosides), internucleoside phosphate linkages, and any modifying pendant groups.

Note that mass spectrometry does not directly measure mass but rather measures the mass/charge ratio; the X-axis of the spectrum is mass/charge, not simply mass. Ideally, a single ionized species is present (molecules that gain a single proton, measured as M-H+). Some molecules gain 2 protons in the desorption process and represent M-2H+; such multiple-ionized species are rare and can be distinguished from the single-ionized species due to their altered mass/charge ratio.

To calculate the molecular weight value of an unmodified oligonucleotide, simply sum the values of molecular weight (MW) for the individual bases (provided below in the monophosphate form) in the sequence. (Note that oligos have 5'- and 3'-terminal hydroxyls unless specifically modified to end in a phosphate group.)

For DNA bases
dA - 313.209; dG - 329.208;
dT - 304.196; dU - 290.169;
dI - 314.194.

Free Acid
This represents the anhydrous molecular weight of the pure oligo free of any complexed salts (counter ions) that can associate with an oligo after synthesis. This calculation corresponds to the molecular weight measured by mass spectrometry.

Calculation
Sum the weights of individual bases (as described above), subtracting the weight of H2PO4: Anhydrous MW = S ( Individual Base MW ) - 63. 980 + 2.016

Simple summation of individual bases calculates the molecular weight of an oligo with 5'-phosphate. The above equation corrects for this and converts to the 5'-OH form.

Sample Calculation
Example sequence: 5'- ATG TAA TGT TTG GTC CGC -3' nA=3, nG=5, nC=3, nT=7; Using the formula above, the molecular weight of this oligo is (313.209 W nA) + (329.208 W nG) + (289.184 W nC) + (304.196 W nT) - 63. 980 + 2.016 = 5440.6 g/mole.