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The percentage of guanine (G) and cytosine (C) bases in within the sequence or its selected region, for example:
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In this example "1/2" is used for "N" (any nucleotide), "2/3" us used for "B" (that means "C", "G", or "T" according to the IUPAC notation nucleotide code).
Molecular weight
TODO: add description/meaning?
Molecular weight for a single-stranded molecule is calculated as the a 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)*6261.97 RNA molecular weight = nA*267.24 + nU*244.20 + nC*243.22 + nG*283.24 + (n-1)*6261.97 |
Here "nA", "nT", "nC", "nG", "nU" denote the number of the corresponding nucleotide in the molecule, "n" is the number of all bases (62 61.97 is the weight of an internal phosphate).
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TODO: add description/meaning? I think, it's OK for now
To calculate the molar Extinction coefficient (Molar extinction coefficient), an approach proposed by Richard Owczarzy is used: http://www.owczarzy.net/extinctionDNA.htm. That is for a single-stranded molecule:
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TODO: should the table below be simplified? Don't think, if it's necessary
The table below specified the extinction coefficients for dinucleotides and mononulceotides:
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Extinction coefficient for a double-stranded molecule is calculated as a sum of the extinction coefficients of the two single strandsstrands (es1 + es2) multiplied by coefficient of (1 - hypochromicity h260nm). The hypochromicity effect can be taken into account as follows:
h260nm = (0.287fAT + 0.059fGC), where fAT and fGC are fractions of AT and GC base pairs, respectively.
Melting temperature
The melting temperature is calculated as follows. For sequences of length 15 or longer:
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TODO: add description/meaning? DONE
The amount of DNA of RNA represented in nanomoles per 1 unit of absorbance at 260 nm dissolved in 1 ml cuvette with 1 cm pathlength
nmole/OD260 = 1000000 / molarExtCoef
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TODO: add description/meaning? DONE
The amount of DNA of RNA represented in microgrames
μg/OD260 = nmoleOD260 * molarWeight * 0.001;
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