TmCalculator (version 1.0.9)

chem_correct: Corrections of melting temperature with chemical substances

Description

Apply corrections to melting temperature calculations based on the presence of DMSO and formamide. These corrections are rough approximations and should be used with caution.

Usage

chem_correct(
  DMSO = 0,
  formamide_unit = list(value = 0, unit = "percent"),
  dmso_factor = 0.75,
  formamide_factor = 0.65,
  pt_gc = NULL
)

Arguments

DMSO

Percent DMSO concentration in the reaction mixture. Default: 0 DMSO can lower the melting temperature of nucleic acid duplexes.

formamide_unit

A list containing formamide concentration information: - value: numeric value of formamide concentration - unit: character string specifying the unit ("percent" or "molar") Default: list(value=0, unit="percent")

dmso_factor

Coefficient of melting temperature (Tm) decrease per percent DMSO. Default: 0.75 (von Ahsen N, 2001, PMID:11673362) Other published values: 0.5, 0.6, 0.675

formamide_factor

Coefficient of melting temperature (Tm) decrease per percent formamide. Default: 0.65 Literature reports values ranging from 0.6 to 0.72

pt_gc

Percentage of GC content in the sequence (0-100 This is used in molar formamide corrections.

Author

Junhui Li

Details

When formamide_unit$unit = "percent": Correction = - factor * percentage_of_formamide

When formamide_unit$unit = "molar": Correction = (0.453 * GC/100 - 2.88) * 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, 47:1956-1961.

Examples

# DMSO correction
chem_correct(DMSO = 3)

# Formamide correction (percent)
chem_correct(formamide_unit = list(value = 1.25, unit = "percent"), pt_gc = 50)

# Formamide correction (molar)
chem_correct(formamide_unit = list(value = 1.25, unit = "molar"), pt_gc = 50)