Calculate the melting temperature using empirical formulas based on GC content with different options
Tm_GC(
ntseq,
ambiguous = FALSE,
userset = NULL,
variant = c("Primer3Plus", "Chester1993", "QuikChange", "Schildkraut1965",
"Wetmur1991_MELTING", "Wetmur1991_RNA", "Wetmur1991_RNA/DNA", "vonAhsen2001"),
Na = 0,
K = 0,
Tris = 0,
Mg = 0,
dNTPs = 0,
saltcorr = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
"Owczarzy2004", "Owczarzy2008"),
mismatch = TRUE,
DMSO = 0,
fmd = 0,
DMSOfactor = 0.75,
fmdfactor = 0.65,
fmdmethod = c("concentration", "molar"),
outlist = TRUE
)
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.
A vector of four coefficient values. Usersets override value sets.
Empirical constants coefficient with 8 variant: Chester1993, QuikChange, Schildkraut1965, Wetmur1991_MELTING, Wetmur1991_RNA, Wetmur1991_RNA/DNA, Primer3Plus and vonAhsen2001
Millimolar concentration of Na, default is 0
Millimolar concentration of K, default is 0
Millimolar concentration of Tris, default is 0
Millimolar concentration of Mg, default is 0
Millimolar concentration of dNTPs, default is 0
Salt correction method should be chosen when provide 'userset'. Options are "Schildkraut2010", "Wetmur1991","SantaLucia1996","SantaLucia1998-1","Owczarzy2004","Owczarzy2008". Note that "SantaLucia1998-2" is not available for this function.
If 'True' (default) every 'X' in the sequence is counted as mismatch
Percent DMSO
Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar").
Coeffecient of Tm decreases per percent DMSO. Default=0.75 von Ahsen N (2001) <PMID:11673362>. Other published values are 0.5, 0.6 and 0.675.
Coeffecient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72.
"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar
output a list of Tm and options or only Tm value, default is TRUE.
Empirical constants coefficient with 8 variant:
Chester1993: Tm = 69.3 + 0.41(Percentage_GC) - 650/N
QuikChange: Tm = 81.5 + 0.41(Percentage_GC) - 675/N - Percentage_mismatch
Schildkraut1965: Tm = 81.5 + 0.41(Percentage_GC) - 675/N + 16.6 x log[Na+]
Wetmur1991_MELTING: Tm = 81.5 + 0.41(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch
Wetmur1991_RNA: Tm = 78 + 0.7(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch
Wetmur1991_RNA/DNA: Tm = 67 + 0.8(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch
Primer3Plus: Tm = 81.5 + 0.41(Percentage_GC) - 600/N + 16.6 x log[Na+]
vonAhsen2001: Tm = 77.1 + 0.41(Percentage_GC) - 528/N + 11.7 x log[Na+]
Marmur J , Doty P . Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.[J]. Journal of Molecular Biology, 1962, 5(1):109-118.
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):33.
Untergasser A , Cutcutache I , Koressaar T , et al. Primer3--new capabilities and interfaces[J]. Nucleic Acids Research, 2012, 40(15):e115-e115.
von Ahsen N, Wittwer CT, Schutz E , et al. Oligonucleotide melting temperatures under PCR conditions: deoxynucleotide Triphosphate and Dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin Chem 2001, 47:1956-1961.
# NOT RUN {
ntseq <- c("ATCGTGCGTAGCAGTACGATCAGTAG")
out <- Tm_GC(ntseq,ambiguous=TRUE,variant="Primer3Plus",Na=50,mismatch=TRUE)
out
out$Tm
out$Options
# }
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