Molecular weight and mass

Calculating the chemical formula

If the chemical formula is first calculated, various properties can then be derived from it. The simplest way of calculating the chemical formula is to add the unit formulae of each base, listed in Table 1, then substract PO3H (because there is no phosphate linkage at the 3′-end), and add H2 (because both 3′-end and the 5′-end are protonated) to give the formula of the oligonucleotide (Table 2).

Table 1Chemical formulae of the standard bases in DNA and RNA oligonucleotides

BaseFormula (DNA)Formula (RNA)
AC10H12O5N5PC10H12O6N5P
GC10H12O6N5PC10H12O7N5P
CC9H12O6N3PC9H12O7N3P
TC10H13O7N2P(C10H13O8N2P)
U(C9H11O7N2P)C9H11O8N2P

Table 2Chemical formulae of the DNA oligonucleotide dAGCT and the RNA oligonucleotide AGCU

Oligonucleotide sequenceFormula
dAGCTC39H50O22N15P3
AGCUC38H48O26N15P3

Under physiological conditions, the phosphate oxygen atoms are deprotonated (Table 3).

Table 3Chemical formulae of the DNA oligonucleotide dAGCT and the RNA oligonucleotide AGCU under physiological conditions

Oligonucleotide sequenceFormula
dAGCTC39H47O22N15P3-
AGCUC38H45O26N15P3- Figure 1 | Chemical structure of the DNA oligonucleotide dAGCT (left) and the RNA oligonucleotide AGCU (right)

Molecular weight

Calculating the molecular weight

The molecular weight can be calculated from the chemical formula by using standard values of the molecular weight of each atom. For example, each chlorine atom contributes approximately 35.5 to the molecular weight. These values are typically not whole numbers, partly because of isotopes (chlorine occurs naturally as roughly 75% 35Cl and 25% 37Cl).

Uses of molecular weight

Molecular weight is used to calculate concentration and yield.

Molecular mass

Monoisotopic mass

When calculating the molecular mass, individual isotopes are considered separately. The monoisotopic mass is calculated using tne mass of the most common isotop of each element. This is often also the lighest isotope.

Mass spectrometry

Mass spectrometry is the only experimental technique that can distinguish between isotopes, and therefore the only technique with which the mass is more important than the molecular weight.

Comparing molecular weight and molecular mass

For small molecules, the molecular weight is often the same as the monoisotopic mass (when rounded to the nearest integer). As the molecule gets larger, the two properties diverge.