Corrections coefficient of melting temperature or entropy with different operations
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
)
Millimolar concentration of Na
Millimolar concentration of K
Millimolar concentration of Tris
Millimolar concentration of Mg
Millimolar concentration of dNTPs
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.
Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.
Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.
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)
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.
# NOT RUN {
ntseq <- c("acgtTGCAATGCCGTAWSDBSYXX")
salt_correction(Na=390, K=20, Tris=0, Mg=10, dNTPs=25, method="Owczarzy2008", ntseq)
# }
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