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": Schildkraut & Lifson (1965); historical identifier - "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: Schildkraut & Lifson (1965) monovalent correction; the name is historical - 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: Sodium correction from Owczarzy et al. (2004) (requires sequence information) - Owczarzy2008: Updated comprehensive salt correction (requires sequence information)

For methods other than Owczarzy2008, the sodium-equivalent magnesium adjustment follows von Ahsen et al. (2001); it is separate from the original monovalent formulas.

Owczarzy2008 is piecewise. Which of its three forms applies is decided by the ratio R = \sqrt{[Mg^{2+}]_{free}} / [Mon], where [Mon] is the total monovalent concentration in molar and the free magnesium is what is left after chelation by dNTPs (K_a = 3 \times 10^4 M^{-1}). Below 0.22 the monovalent term alone applies; between 0.22 and 6 a competing form whose coefficients are themselves functions of [Mon]; at 6 and above the divalent-dominated form, in which [Mon] drops out of the expression entirely. A solution with magnesium and no monovalent cation at all therefore has a defined correction rather than none.

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.

SantaLucia J Jr, Allawi HT, Seneviratne PA (1996). Improved nearest-neighbor parameters for predicting DNA duplex stability. <doi:10.1021/bi951907q>

Owczarzy R et al. (2004). Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. <doi:10.1021/bi034621r>

von Ahsen N, Wittwer CT, Schutz E (2001). Oligonucleotide melting temperatures under PCR conditions. <doi:10.1093/clinchem/47.11.1956>

Examples

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

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