TmCalculator (version 1.0.0)

chem_correction: Correct melting temperature with chemical substances

Description

Correct a given melting temperature with DMSO and formamide, and these corrections are rough approximations.

Usage

chem_correction(Tm, DMSO = 0, fmd = 0, DMSOfactor = 0.75, 
fmdfactor = 0.65, fmdmethod = "concentration", ptGC = NULL)

Arguments

Tm

Melting temperature

DMSO

Percent DMSO

fmd

Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar").

DMSOfactor

Coeffecient 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.

fmdfactor

Coeffecient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72.

fmdmethod

"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar.

ptGC

Content of GC

Details

fmdmethod = "concentration" Tm = Tm - factor*percentage_of_formamide

fmdmethod = "molar" Tm = Tm + (0.453(f(GC)) - 2.88) x [formamide]

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

# NOT RUN {
chem_correction(70, DMSO=3) #67.75
chem_correction(70, fmd=5) #66.75
chem_correction(70, fmdmethod="molar", fmd=1.25,ptGC=50) #66.68
# }