salt_correction: Corrections of melting temperature with salt ions

In TmCalculator: Melting Temperature of Nucleic Acid Sequences

Corrections of melting temperature with salt ions

Description

Corrections coefficient of melting temperature or entropy with different operations

Usage

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

Arguments

Na	Millimolar concentration of Na
K	Millimolar concentration of K
Tris	Millimolar concentration of Tris
Mg	Millimolar concentration of Mg
dNTPs	Millimolar concentration of dNTPs
method	Method to be applied including "Schildkraut2010", "Wetmur1991","SantaLucia1996", "SantaLucia1998-1", "SantaLucia1998-2","Owczarzy2004","Owczarzy2008". First fourth methods correct Tm, fifth method corrects deltaS, sixth and seventh methods correct 1/Tm. See details for the method description.
ntseq	Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.
ambiguous	Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

Details

The methods are:

1 Schildkraut C (2010) <doi:10.1002/bip.360030207>

2 Wetmur J G (1991) <doi:10.3109/10409239109114069>

3 SantaLucia J (1996) <doi:10.1021/bi951907q>

4 SantaLucia J (1998) <doi:10.1073/pnas.95.4.1460>

5 SantaLucia J (1998) <doi:10.1073/pnas.95.4.1460>

6 Owczarzy R (2004) <doi:10.1021/bi034621r>

7 Owczarzy R (2008) <doi:10.1021/bi702363u>

methods 1-4: Tm(new) = Tm(old) + correction

method 5: deltaS(new) = deltaS(old) + correction

methods 6+7: Tm(new) = 1/(1/Tm(old) + correction)

Author(s)

Junhui Li

References

Schildkraut C . Dependence of the melting temperature of DNA on salt concentration[J]. Biopolymers, 2010, 3(2):195-208.

Wetmur J G . DNA Probes: Applications of the Principles of Nucleic Acid Hybridization[J]. CRC Critical Reviews in Biochemistry, 1991, 26(3-4):3

Santalucia , J , Allawi H T , Seneviratne P A . Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, [J]. Biochemistry, 1996, 35(11):3555-3562.

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

Owczarzy R , You Y , Moreira B G , et al. Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions ofMelting Temperatures[J]. Biochemistry, 2004, 43(12):3537-3554.

Owczarzy R , Moreira B G , You Y , et al. Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations[J]. Biochemistry, 2008, 47(19):5336-5353.

Examples

ntseq <- c("acgtTGCAATGCCGTAWSDBSYXX")
salt_correction(Na=390, K=20, Tris=0, Mg=10, dNTPs=25, method="Owczarzy2008", ntseq)

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