thermodynamic_nn_params: Thermodynamic Tables for Nucleic Acid Hybridization

In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration

Thermodynamic Tables for Nucleic Acid Hybridization

Description

A comprehensive collection of thermodynamic parameters used for calculating melting temperatures of nucleic acid duplexes. The dataset includes parameters for DNA/DNA, RNA/RNA, RNA/DNA and 2'-O-methylRNA/RNA hybridizations, plus parameters for mismatches, dangling ends, internal / bulge loops, GU wobble, CNG repeats, inosine, hydroxyadenine, azobenzene and locked nucleic acids (LNA).

Usage

thermodynamic_nn_params

Format

A named list of two-column matrices with colnames = c("left", "right") (left = \Delta H, right = \Delta S). Rownames are dinucleotide step keys such as "AT/TA", mismatch / dangling-end keys, or feature-specific keys (e.g. "CAG_4" for the (CAG)4 CNG entry).

Populated tables

DNA_NN_Breslauer_1986

DNA/DNA NN, Breslauer et al. (1986)

DNA_NN_Sugimoto_1996

DNA/DNA NN, Sugimoto et al. (1996)

DNA_NN_Allawi_1998

DNA/DNA Watson-Crick NN, Allawi & SantaLucia (1997), Table 1; legacy identifier

DNA_NN_SantaLucia_2004

DNA/DNA NN, SantaLucia & Hicks (2004)

RNA_NN_Freier_1986

RNA/RNA NN, Freier (1986)

RNA_NN_Xia_1998

RNA/RNA NN, Xia (1998)

RNA_NN_Chen_2012

RNA/RNA NN with GU, Chen / Serra (2012)

RNA_DNA_NN_Sugimoto_1995

RNA/DNA hybrid NN, Sugimoto (1995)

DNA_IMM_Peyret_1999

DNA internal mismatches, six sources (1997-2005); see tm_nn

DNA_TMM_Bommarito_2000

DNA terminal mismatch, SantaLucia & Peyret (2001), WO2001094611A2, Tables 2-3; legacy identifier

DNA_DE_Bommarito_2000

DNA single dangling end, Bommarito (2000)

RNA_DE_Turner_2010

RNA single dangling end, NNDB Turner 2004 compilation; database described in 2010

Registered placeholders (values TBD - populate from primary literature)

DNA_NN_AllSan_1997

Allawi & SantaLucia (1997) Biochemistry 36:10581

DNA_NN_SantaLucia_1996

SantaLucia et al. (1996) Biochemistry 35:3555

DNA_NN_Tanaka_2004

Tanaka et al. (2004) Biochemistry 43:7143

MeRNA_RNA_NN_Kierzek_2006

Kierzek et al. (2006) Biochemistry 45:581

DNA_RNA_IMM_Watkins_2011

Watkins et al. (2011) Nucleic Acids Res 39:1894

RNA_IMM_Lu_2006

Lu et al. (2006) Nucleic Acids Res 34:4912

RNA_IMM_Davis_Znosko_2007

Davis & Znosko (2007) Biochemistry 46:13425

RNA_IMM_Davis_Znosko_2008

Davis & Znosko (2008) Biochemistry 47:10178

DNA_TandemMM_AllSanPey

Allawi & SantaLucia (1997/1998); Peyret (1999)

RNA_TandemMM_Mathews_1999

Mathews et al. (1999) JMB 288:911

DNA_DE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

RNA_DE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

RNA_DE_Serra_2008

O'Toole / Serra (2006, 2008)

DNA_DDE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

RNA_DDE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

RNA_DDE_OToole_2005

O'Toole et al. (2005) Biochemistry 44:14914

RNA_DDE_OToole_2006

O'Toole et al. (2006) NAR 34:3338

DNA_LDE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

RNA_LDE_Ohmichi_2002

Ohmichi et al. (2002) JACS 124:10367

DNA_IL_SantaLucia_2004

SantaLucia & Hicks (2004)

RNA_IL_Lu_2006

Lu et al. (2006) NAR 34:4912

RNA_IL_Badhwar_2007

Badhwar et al. (2007) Biochemistry 46:14715

DNA_SBL_Tanaka_2007

Tan & Chen (2007) Biophys J 92:3615

DNA_SBL_SantaLucia_2004

SantaLucia & Hicks (2004)

RNA_SBL_Lu_2006

Lu et al. (2006) NAR 34:4912

RNA_SBL_Blose_2007

Blose et al. (2007) Biochemistry 46:15123

DNA_LBL_SantaLucia_2004

SantaLucia & Hicks (2004)

RNA_LBL_Lu_2006

Mathews (1999); Lu et al. (2006)

RNA_GU_Mathews_1999

Mathews & Turner (1999) JMB 288:911

RNA_GU_Chen_2012

Chen / Serra (2012)

DNA_CNG_Broda_2005

Broda et al. (2005) Biochemistry 44:13851 - rownames use paste0("C", N, "G_", n), e.g. "CAG_4".

DNA_INO_SantaLucia_2005

Watkins & SantaLucia (2005) NAR 33:6258

RNA_INO_Wright_2007

Wright et al. (2007) Biochemistry 46:4625

DNA_HA_Kawakami_2001

Kawakami / Sugimoto (2001) Biochemistry 40:14040

DNA_AZB_Asanuma_2005

Asanuma et al. (2005) Angew Chem Int Ed 44:2747

DNA_LNA_Owczarzy_2011

Owczarzy et al. (2011) Biochemistry 50:9352

DNA_LNA_McTigue_2004

McTigue et al. (2004) Biochemistry 43:5388

DNA_cLNA_Owczarzy_2011

Owczarzy et al. (2011) Biochemistry 50:9352

DNA_cLNA_MM_Owczarzy_2011

Owczarzy et al. (2011) Biochemistry 50:9352

To add the numeric values for any placeholder table, construct a matrix with two columns (\Delta H kcal/mol, \Delta S cal/(mol*K)) and the dinucleotide-step rownames described above, then assign it:

thermodynamic_nn_params$DNA_CNG_Broda_2005 <- new_table

Details

Coverage mirrors the rmelting (Bioconductor) vignette sections 4.2.1 - 4.4. Tables whose numeric values are not yet ported from primary literature are included in the list as NULL placeholders so that tm_nn can still dispatch on the table name; the corresponding contribution is silently skipped after a one-time package-startup notice.

Source

Various publications as cited above. See the installed extdata/tm_nn_reference_audit.md for the audit of runtime tables.

References

Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746> Sugimoto N (1996) <doi:10.1093/nar/24.22.4501> Allawi H T & SantaLucia J Jr (1997), Table 1 <doi:10.1021/bi962590c>; also SantaLucia (1998), Table 2 <doi:10.1073/pnas.95.4.1460> SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800> Freier S (1986) <doi:10.1073/pnas.83.24.9373> Xia T (1998) <doi:10.1021/bi9809425> Chen JL (2012) <doi:10.1021/bi3002709> Sugimoto N (1995) <doi:10.1021/bi00035a029> Bommarito S (2000) <doi:10.1093/nar/28.9.1929> Peyret N (1999) <doi:10.1021/bi9825091> Allawi H T & SantaLucia J (1997) <doi:10.1021/bi962590c> Watkins N E Jr & SantaLucia J Jr (2005) <doi:10.1093/nar/gki918> Allawi H T & SantaLucia J Jr (1998, G.A) <doi:10.1021/bi9724873> Allawi H T & SantaLucia J Jr (1998, A.C) <doi:10.1021/bi9803729> Allawi H T & SantaLucia J Jr (1998, C.T) <doi:10.1093/nar/26.11.2694> SantaLucia J Jr & Peyret N (2001), WO2001094611A2, Tables 2-3. https://patents.google.com/patent/WO2001094611A2/en Turner D H & Mathews D H (2010) <doi:10.1093/nar/gkp892> Tanaka F (2004) Biochemistry 43:7143 Kierzek E (2006) Biochemistry 45:581 Watkins N E (2011) Nucleic Acids Res 39:1894 Lu Z J (2006) Nucleic Acids Res 34:4912 Davis A R & Znosko B M (2007, 2008) Biochemistry Mathews D H (1999) <doi:10.1006/jmbi.1999.2700> Ohmichi T (2002) J Am Chem Soc 124:10367 O'Toole A S (2005, 2006) Biochemistry / Nucleic Acids Res Badhwar J (2007) Biochemistry 46:14715 Tan Z J & Chen S J (2007) Biophys J 92:3615 Blose J M (2007) Biochemistry 46:15123 Broda M (2005) <doi:10.1021/bi0501447> Wright D J (2007) Biochemistry 46:4625 Kawakami J / Sugimoto N (2001) <doi:10.1021/bi010918b> Asanuma H (2005) Angew Chem Int Ed 44:2747 McTigue P M (2004) Biochemistry 43:5388 Owczarzy R (2011) Biochemistry 50:9352

Examples

# Access DNA/DNA nearest neighbor parameters
thermodynamic_nn_params$DNA_NN_SantaLucia_2004

# Access DNA internal mismatch parameters
thermodynamic_nn_params$DNA_IMM_Peyret_1999

# See which tables are still placeholders (NULL)
names(Filter(is.null, thermodynamic_nn_params))

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