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Molecular weight for a single-stranded molecule is calculated as the sum of the atomic masses of the molecule compounds:
DNA molecular weight = nA*251.24 + nT*242.23 + nC*227.22 + nG*267.24 + (n-1)*62 RNA molecular weight = nA*267.24 + nU*244.20 + nC*243.22 + nG*283.24 + (n-1)*62 |
Here "nA", "nT", "nC", "nG", "nU" denote the number of the corresponding nucleotide in the molecule, "n" is the number of all bases (62 is the weight of an internal phosphate).
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Molecular weight for a double-stranded molecule is calculated as the sum of the single strands molecular weights.
Extinction coefficient
TODO: add description/meaning?
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 Tm
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:
- Common statistics
- Length - number of bases in the analyzed sequence
- GC content - the molar percentage of guanine and cytosine bases in an oligonucleotide sequence
- Molar weight - is the sum of the atomic masses of the constituent atoms for 1 mole of oligonucleotide
- Molar ext. coefficient - the molar extinction coefficient is a physical constant that is unique for each sequence and describes the amount of absorbance at 260nm (A260) of 1 mole/L DNA solution measured in 1 cm path-length cuvette
- Melting TM - melting temperature is the temperature at which an oligonucleotide duplex is 50% in single-stranded form and 50% in double-stranded form
- nmole/OD260 - the amount of oligonucleotide in nanomoles that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm path-length cuvette
- μg/OD260 - the amount of oligonucleotide in micrograms that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm path-length cuvette
- Characters occurrence
- Dinucleotides occurrence (for sequences with the standard DNA and RNA alphabets
Amino acid sequence common statistics
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