The numbers used to calculate the molecular weight of the sequences are from the page maintained by ThermoFisher Scientific.
| Base | DNA | RNA |
| A | 313.2 | 329.2 |
| T | 304.2 | n/a |
| U | n/a | 306.2 |
| C | 289.2 | 305.2 |
| G | 329.2 | 345.2 |
The equations used are:
dsDNA (linear, PCR)
(An × 313.2) + (Tn × 304.2) + (Cn × 289.2) + (Gn × 329.2) + (Tn × 313.2) + (An × 304.2) + (Gn × 289.2) + (Cn × 329.2)
dsDNA (linear, Restriction cut)
(An × 313.2) + (Tn × 304.2) + (Cn × 289.2) + (Gn × 329.2) + (Tn × 313.2) + (An × 304.2) + (Gn × 289.2) + (Cn × 329.2) + (79 × 2)
dsDNA (circular)
(An × 313.2) + (Tn × 304.2) + (Cn × 289.2) + (Gn × 329.2) + (Tn × 313.2) + (An × 304.2) + (Gn × 289.2) + (Cn × 329.2)
ssDNA (PCR)
(An × 313.2) + (Tn × 304.2) + (Cn × 289.2) + (Gn × 329.2)
ssDNA (Restriction cut)
(An × 313.2) + (Tn × 304.2) + (Cn × 289.2) + (Gn × 329.2) + 79
ssRNA
(An × 329.2) + (Un × 306.2) + (Cn × 305.2) + (Gn × 345.2) + 159
[source]
Ambiguous base codes are permitted:
R: A or G
Y: C or T/U
K: G or T/U
M: A or C
S: C or G
W: A or T/U
B: C, G or T/U
D: A, G or T/U
H: A, C or T/U
V: A, C or G
N: A, C, G or T/U
Calculator behavior:
- When ambiguous bases are found, the average value of all possible bases is used to estimate the molecular weight.
- The range gives an estimate of the maximum and minimum values possible given the presence of ambiguous bases. The molecular weight, max and min estimates will be equal for sequence that contains no ambiguous bases.
- The radio boxes below the entry area drive the analysis. If ssRNA is selected, all T’s are converted to U’s. For all DNA options, U’s are converted to T’s.
- Fasta format is supported, but if more than one sequence is entered only the first sequence is analyzed.
- Beware of garbage in/garbage out. This calculator will estimate the molecular weight of any string entered into the text box after removing all characters that do not correspond to the list of standard bases. The string “Zip. Zap! Zoo?” will have everything but the “A” removed and be given the molecular weight of 313.2.
