chem_correction: Corrections of melting temperature with chemical substances

In TmCalculator: Melting Temperature of Nucleic Acid Sequences

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)

TmCalculator documentation built on March 18, 2022, 6:10 p.m.