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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 1 ⎪ Chemical formulae of the standard bases in DNA and RNA oligonucleotides
| Base | Formula (DNA) | Formula (RNA) |
|---|---|---|
| A | C10H12O5N5P | C10H12O6N5P |
| G | C10H12O6N5P | C10H12O7N5P |
| C | C9H12O6N3P | C9H12O7N3P |
| T | C10H13O7N2P | (C10H13O8N2P) |
| U | (C9H11O7N2P) | C9H11O8N2P |
Table 2 ⎪ Chemical formulae of the DNA oligonucleotide dAGCT and the RNA oligonucleotide AGCU
| Oligonucleotide sequence | Formula |
|---|---|
| dAGCT | C39H50O22N15P3 |
| AGCU | C38H48O26N15P3 |
Under physiological conditions, the phosphate oxygen atoms are deprotonated (Table 3).
Table 3 ⎪ Chemical formulae of the DNA oligonucleotide dAGCT and the RNA oligonucleotide AGCU under physiological conditions
| Oligonucleotide sequence | Formula |
|---|---|
| dAGCT | C39H47O22N15P33- |
| AGCU | C38H45O26N15P33- |
Figure 1 | Chemical structure of the DNA oligonucleotide dAGCT (left) and the RNA oligonucleotide AGCU (right)
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).
Molecular weight is used to calculate concentration and yield.
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 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.
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.
Our free online Nucleic Acids Book contains information on all aspects of nucleic acids chemistry and biology.
