chem_correction {TmCalculator} | R Documentation |
Corrections of melting temperature with chemical substances
Description
Corrections coefficient of melting temperature with DMSO and formamide and these corrections are rough approximations.
Usage
chem_correction(
DMSO = 0,
fmd = 0,
DMSOfactor = 0.75,
fmdmethod = c("concentration", "molar"),
fmdfactor = 0.65,
ptGC
)
Arguments
DMSO |
Percent DMSO |
fmd |
Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar"). |
DMSOfactor |
Coefficient of Tm decreases per percent DMSO. Default=0.75 von Ahsen N (2001) <PMID:11673362>. Other published values are 0.5, 0.6 and 0.675. |
fmdmethod |
"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar |
fmdfactor |
Coefficient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72. |
ptGC |
Percentage of GC(%). |
Details
fmdmethod = "concentration"
Correction = - factor*percentage_of_formamide
fmdmethod = "molar"
Correction = (0.453*GC/100 - 2.88) x formamide
Author(s)
Junhui Li
References
von Ahsen N, Wittwer CT, Schutz E , et al. Oligonucleotide melting temperatures under PCR conditions: deoxynucleotide Triphosphate and Dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin Chem 2001, 47:1956-C1961.
Examples
chem_correction(DMSO=3)
chem_correction(fmd=1.25, fmdmethod="molar", ptGC=50)