salt_correct: Corrections of melting temperature with salt concentration

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

Corrections of melting temperature with salt concentration

Description

Apply corrections to melting temperature calculations based on salt concentrations. Different correction methods are available for various experimental conditions.

Usage

salt_correct(
  Na = 0,
  K = 0,
  Tris = 0,
  Mg = 0,
  dNTPs = 0,
  method = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
    "SantaLucia1998-2", "Owczarzy2004", "Owczarzy2008"),
  input_seq,
  ambiguous = FALSE
)

Arguments

Na	Millimolar concentration of sodium ions. Default: 0
K	Millimolar concentration of potassium ions. Default: 0
Tris	Millimolar concentration of Tris buffer. Default: 0
Mg	Millimolar concentration of magnesium ions. Default: 0
dNTPs	Millimolar concentration of deoxynucleotide triphosphates. Default: 0
method	Method for calculating salt concentration corrections to the melting temperature. Available options: - "Schildkraut2010": Updated salt correction method - "Wetmur1991": Classic salt correction method - "SantaLucia1996": DNA-specific salt correction - "SantaLucia1998-1": Improved DNA salt correction - "SantaLucia1998-2": Alternative DNA salt correction (requires input_seq) - "Owczarzy2004": Comprehensive salt correction (requires input_seq) - "Owczarzy2008": Updated comprehensive salt correction (requires input_seq) Note: Setting to NA disables salt correction
input_seq	Sequence (5' to 3') of one strand of the nucleic acid duplex. Can be provided as either: - A character string (e.g., "ATGCG") - A path to a FASTA file containing the sequence(s) Required for methods: "SantaLucia1998-2", "Owczarzy2004", and "Owczarzy2008"
ambiguous	Logical. If TRUE, ambiguous bases are taken into account when computing the G and C content. The function handles various ambiguous bases (S, W, M, K, R, Y, V, H, D, B) by proportionally distributing their contribution to GC content based on their possible nucleotide compositions.

Details

Different correction methods are available for various experimental conditions:

- Schildkraut2010: Updated salt correction method that accounts for monovalent and divalent cations - Wetmur1991: Classic salt correction method for monovalent cations - SantaLucia1996: DNA-specific salt correction - SantaLucia1998-1: Improved DNA salt correction - SantaLucia1998-2: Alternative DNA salt correction (requires sequence information) - Owczarzy2004: Comprehensive salt correction including effects of divalent cations (requires sequence information) - Owczarzy2008: Updated comprehensive salt correction (requires sequence information)

Author(s)

Junhui Li

References

Schildkraut C, Lifson S. Dependence of the melting temperature of DNA on salt concentration. Biopolymers. 1965;3(2):195-208.

Wetmur JG. DNA Probes: Applications of the Principles of Nucleic Acid Hybridization. Critical Reviews in Biochemistry and Molecular Biology. 1991;26(3-4):227-259.

SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences. 1998;95(4):1460-1465.

Owczarzy R, Moreira BG, Manthey JA, et al. Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry. 2008;47(19):5336-5353.

Examples

salt_correct(Na = 50, Mg = 1.5, method = "Owczarzy2008", 
               input_seq = "ATGCGATGCG")

TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.