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- Length
- GC content
- Molecular weight
- Extinction coefficient
- Melting Tmtemperature
- nmole/OD260
- μg/OD260
GC content
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To calculate the molar extinction coefficient, an approach proposed by Richard Owczarzy is used: http://www.owczarzy.net/extinctionDNA.htm. That is for a single-stranded molecule:
Extinction coefficient = sum(extinction coefficients of all dinucleotides) - sum(extinction coefficients of inner mononucleotides) |
TODO: should the table below be simplified?
The table below specified the extinction coefficients for dinucleotides and mononulceotides:
| DNA | RNA | ||
|---|---|---|---|
| Stack or monomer | Extinction coefficient | Stack or monomer | Extinction coefficient |
| pdA | 15400 | pA | 15400 |
| pdC | 7400 | pC | 7200 |
| pdG | 11500 | pG | 11500 |
| pdT | 8700 | pU | 9900 |
| dApdA | 27400 | ApA | 27400 |
| dApdC | 21200 | AdC | 21000 |
| dApdG | 25000 | ApG | 25000 |
| dApdT | 22800 | ApU | 24000 |
| dCpdA | 21200 | CpA | 21000 |
| dCpdC | 14600 | CpC | 14200 |
| dCpdG | 18000 | CpG | 17800 |
| dCpdT | 15200 | CpU | 16200 |
| dGpdA | 25200 | GpA | 25200 |
| dGpdC | 17600 | GpC | 17400 |
| dGpdG | 21600 | GpG | 21600 |
| dGpdT | 20000 | GpU | 21200 |
| dTpdA | 23400 | UpA | 24600 |
| dTpdC | 16200 | UpC | 17200 |
| dTpdG | 19000 | UpG | 20000 |
| dTpdT | 16800 | UpU | 19600 |
For example, let's calculate the molar extinction coefficient ("ε") for "ATGCA":
ε(ATGCA) = ε(AT) + ε(TG) + ε(GC) + ε(CA) - ε(T) - ε(G) - ε(C) = = 22800 + 19000 + 17600 + 21200 - 8700 - 11500 - 7400 = = 53000 |
As for the other statistics, average values are used in case of degenerate base characters.
Extinction coefficient for a double-stranded molecule is calculated as a sum of the extinction coefficients of the two single strands.
Melting
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temperature
The melting temperature is calculated as follows. For sequences of length 15 or longer:
Tm = 64.9 + 41 * (nG + nC - 16.4) / (nA + nT + nG + nC) |
For shorter sequences:
Tm = (nA + nT) * 2 + (nG + nC) * 4 |
Here "nA", "nT", "nC", "nG" denote the number of the corresponding nucleotide.
Context information about a sequence can be found on the All information is contextual, i.e. it shows statistics about the currently selected region (on the selected sequence). The tab includes information about:
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