chem_correct: Corrections of melting temperature with chemical substances

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

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 accepted empirical coefficients: 0.5, 0.6, 0.65, 0.675
formamide_factor	Coefficient of melting temperature (Tm) decrease per percent formamide. Default: 0.65 (empirical convention); accepted alternatives: 0.6, 0.72. Hutton (1977) reports 0.60, not the default 0.65.
pt_gc	Percentage of GC content in the sequence (0-100 This is used in molar formamide corrections.

Details

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

When formamide_unit$unit = "molar": Correction = (0.453 * GC/100 - 2.88) * formamide, from Blake & Delcourt (1996).

Author(s)

Junhui Li

References

von Ahsen N, Wittwer CT, Schutz E. Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin Chem 2001, 47:1956-1961.

Blake RD, Delcourt SG (1996). Thermodynamic effects of formamide on DNA stability. NAR 24:2095-2103. <doi:10.1093/nar/24.11.2095>

Hutton JR (1977). Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea. <doi:10.1093/nar/4.10.3537>

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)

TmCalculator documentation built on Oct. 5, 2026, 5:08 p.m.