TmCalculator (version 1.0.0)

Tm_NN: Calculate melting temperature using nearest neighbor thermodynamics

Description

Calculate melting temperature using nearest neighbor thermodynamics

Usage

Tm_NN(ntseq, ambiguous = FALSE, comSeq = NULL, shift = 0, nn_table = "DNA_NN4", 
tmm_table = "DNA_TMM1", imm_table = "DNA_IMM1",de_table = "DNA_DE1", dnac1 = 25,
dnac2 = 25, selfcomp = FALSE, Na = 50, K = 0, Tris = 0, Mg = 0, dNTPs = 0, saltcorr = 5)

Arguments

ntseq

The primer/probe sequence as string or vector of characters

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

comSeq

Complementary sequence. The sequence of the template/target in 3'->5' direction

shift

Shift of the primer/probe sequence on the template/target sequence, default=0. for example: when shift=0, the first nucleotide base at 5` end of primer align to first one at 3` end of template. When shift=-1, the secound nucleotide base at 5` end of primer align to first one at 3` end of template. When shift=1, the first nucleotide base at 5` end of primer align to secound one at 3` end of template. The shift parameter is necessary to align primer/probe and template/target if they have different lengths or if they should have dangling ends.

nn_table

Thermodynamic NN values, eight tables are implemented. For DNA/DNA hybridizations: DNA_NN1,DNA_NN2,DNA_NN3,DNA_NN4

For RNA/RNA hybridizations: RNA_NN1,RNA_NN2,RNA_NN3

For RNA/DNA hybridizations: R_DNA_NN1

tmm_table

Thermodynamic values for terminal mismatches. Default: DNA_TMM1

imm_table

Thermodynamic values for internal mismatches, may include insosine mismatches. Default: DNA_IMM1

de_table

Thermodynamic values for dangling ends: DNA_DE1(default),RNA_DE1

dnac1

Concentration of the higher concentrated strand [nM]. Typically this will be the primer (for PCR) or the probe. Default=25.

dnac2

Concentration of the lower concentrated strand [nM].

selfcomp

Sequence self-complementary, default=False. If 'True' the primer is thought binding to itself, thus dnac2 is not considered.

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

saltcorr

Type of salt correction. Default=5.

Details

DNA_NN1: Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>

DNA_NN2: Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>

DNA_NN3: Allawi H (1998) <doi:10.1093/nar/26.11.2694>

DNA_NN4: SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>

RNA_NN1: Freier S (1986) <doi:10.1073/pnas.83.24.9373>

RNA_NN2: Xia T (1998) <doi:10.1021/bi9809425>

RNA_NN3: Chen JL (2012) <doi:10.1021/bi3002709>

R_DNA_NN1: Sugimoto N (1995)<doi:10.1016/S0048-9697(98)00088-6>

DNA_TMM1: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>

DNA_IMM1: Peyret N (1999) <doi:10.1021/bi9825091> & Allawi H T (1997) <doi:10.1021/bi962590c> & Santalucia N (2005) <doi:10.1093/nar/gki918>

DNA_DE1: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>

RNA_DE1: Turner D H (2010) <doi:10.1093/nar/gkp892>

References

Breslauer K J , Frank R , Blocker H , et al. Predicting DNA duplex stability from the base sequence.[J]. Proceedings of the National Academy of Sciences, 1986, 83(11):3746-3750.

Sugimoto N , Nakano S , Yoneyama M , et al. Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes[J]. Nucleic Acids Research, 1996, 24(22):4501-5.

Allawi, H. Thermodynamics of internal C.T mismatches in DNA[J]. Nucleic Acids Research, 1998, 26(11):2694-2701.

Hicks L D , Santalucia J . The thermodynamics of DNA structural motifs.[J]. Annual Review of Biophysics & Biomolecular Structure, 2004, 33(1):415-440.

Freier S M , Kierzek R , Jaeger J A , et al. Improved free-energy parameters for predictions of RNA duplex stability.[J]. Proceedings of the National Academy of Sciences, 1986, 83(24):9373-9377.

Xia T , Santalucia , J , Burkard M E , et al. Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs,[J]. Biochemistry, 1998, 37(42):14719-14735.

Chen J L , Dishler A L , Kennedy S D , et al. Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters[J]. Biochemistry, 2012, 51(16):3508-3522.

Bommarito S, Peyret N, Jr S L. Thermodynamic parameters for DNA sequences with dangling ends[J]. Nucleic Acids Research, 2000, 28(9):1929-1934.

Turner D H , Mathews D H . NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure[J]. Nucleic Acids Research, 2010, 38(Database issue):D280-D282.

Sugimoto N , Nakano S I , Katoh M , et al. Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes[J]. Biochemistry, 1995, 34(35):11211-11216.

Allawi H, SantaLucia J: Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 1997, 36:10581-10594.

Santalucia N E W J . Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes[J]. Nucleic Acids Research, 2005, 33(19):6258-67.

Peyret N , Seneviratne P A , Allawi H T , et al. Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches, [J]. Biochemistry, 1999, 38(12):3468-3477.

Examples

Run this code
# NOT RUN {
ntseq <- c("AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC")
Tm_NN(ntseq, ambiguous = FALSE, comSeq = NULL, shift = 0, nn_table = "DNA_NN4",
tmm_table = "DNA_TMM1", imm_table = "DNA_IMM1",de_table = "DNA_DE1", dnac1 = 25,
dnac2 = 25, selfcomp = FALSE, Na = 50, K = 0, Tris = 0, Mg = 0, dNTPs = 0, saltcorr = 5)
# }

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