The thermodynamics of DNA structural motifs

Annual Review of Biophysics and Biomolecular Structure

Volumn 33, Issue , 2004, Pages 415-440

  SantaLucia Jr , John ^a,b   Hicks, Donald ^b  

^a WAYNE STATE UNIVERSITY   (United States)

^b DNA Software Inc   (United States)

Author keywords

Hybridization; Nucleic acid folding; Oligonucleotides; Prediction; Secondary structure

Indexed keywords

DNA; INORGANIC SALT; MAGNESIUM; SODIUM;

ACCURACY; ALGORITHM; ANALYTIC METHOD; BASE PAIRING; BIOLOGY; BIOTECHNOLOGY; CATALYST; COMPETITIVE INHIBITION; COMPUTER PROGRAM; DATA ANALYSIS; DIAGNOSTIC PROCEDURE; DNA DETERMINATION; DNA HYBRIDIZATION; DNA PROBE; DNA SEQUENCE; DNA STRUCTURE; GENE TARGETING; GENOTYPE; IN VITRO STUDY; MODEL; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; NANOTECHNOLOGY; PARAMETER; PREDICTION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TECHNIQUE; THERMODYNAMICS;

ALGORITHMS; BASE PAIRING; DATABASES, FACTUAL; DNA; DNA PROBES; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 3042599013     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.32.110601.141800     Document Type: Review

References (97)

1. Allawi HT, SantaLucia J Jr. 1997. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 36:10581-94
2. Allawi HT, SantaLucia J Jr. 1998. Nearest-neighbor thermodynamics of internal A-C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435-44
3. Allawi HT, SantaLucia J Jr. 1998. Nearest-neighbor thermodynamics parameters for internal GA mismatches in DNA. Biochemistry 37:2170-79
4. Allawi HT, SantaLucia J Jr. 1998. Thermodynamics of internal C-T mismatches in DNA. Nucleic Acids Res. 26:2694-701
5. Antao VP, Lai SY, Tinoco I Jr. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19:5901-5
6. Antao VP, Tinoco I Jr. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 20:819-24
7. Astell CR, Chow MB, Ward DC. 1985. Sequence analysis of the termini of virion and replicative forms of minute virus of mice DNA suggests a modified rolling hairpin model for autonomous parvovirus DNA replication. J. Virol. 54:171-77
8. Blommers MJJ, Walters ALI, Haasnoot CAG, Aelen JMA, van der Marel GA, et al. 1989. Effects of base sequence on the loop folding in DNA hairpins. Biochemistry 28:7491-98
9. Bommarito S, Peyret N, SantaLucia J Jr. 2000. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28:1929-34
10. Bonnet G, Tyagi S, Libchaber A, Kramer FR. 1999. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA 96:6171-76
11. Breaker RR. 1997. DNA aptamers and DNA enzymes. Curr. Opin. Chem. Biol. 1:26-31
12. Breaker RR, Joyce FG. 1994. A DNA enzyme that cleaves RNA. Chem. Biol. 1:223-28
13. Breslauer KJ, Frank R, Blocker H, Marky LA. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83:3746-50
14. Buiser RG, DeStefano JJ, Mallaber LM, Fay PJ, Bambara RA. 1991. Requirements for the catalysis of strand transfer synthesis by retroviral DNA polymerases. J. Biol. Chem. 266:13103-9
15. Cuenoud B, Szostak JW. 1995. A DNA metalloenzyme with DNA ligase activity. Nature 375:611-19
16. 4GTATCC-3′, where X, Y = A, T, G, C. Biopolymers 30:829-45
17. Frank-Kamenetskii MD. 1971. Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration on sodium ions in solution. Biopolymers 10:2623-25
18. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, et al. 1986. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83:9373-77
19. Freier SM, Sugimoto N, Sinclair A, Alkema D, Neilson T, et al. 1986. Stability of XGCGCp, GCGCYp, and XGCGCYp helices: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry 25:3214-19
20. Furuichi T, Inouye S, Inouye M. 1987. Biosynthesis and structure of stable branched RNA covalently linked to the 5′ end of multicopy single-stranded DNA of Stigmatella aurantiaca. Cell 48:55-62
21. Gacy AM, Goellner G, Juranic N, Macura S, McMurray CT. 1995. Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81:533-40
22. Gibbons A, Amos M, Hodgson D. 1997. DNA computing. Curr. Opin. Biotechnol. 8:103-6
23. Goddard NL, Bonnet G, Krichevsky O, Libchaber A. 2000. Sequence dependent rigidity of single stranded DNA. Phys. Rev. Lett. 85:2400-3
24. Guckian KM, Schweitzer BA, Ren RX-F, Sheils CJ, Paris PL, et al. 1996. Experimental measurement of aromatic stacking affinities in the context of duplex DNA. J. Am. Chem.Soc. 118:8182-83
25. Haas S, Vingron M, Poustka A, Wiemann S. 1998. Primer design for large scale sequencing. Nucleic Acids Res. 26:3006-12
26. He L, Kierzek R, SantaLucia J Jr, Walter AE, Turner DH. 1991. Nearest neighbor parameters for GU mismatches: GU/UG is destabilizing in the contexts CGUG, UGUA, and AGUU, but stabilizing in GGUC. Biochemistry 30:11124-32
27. Held GA, Grinstein G, Tu Y. 2003. Modeling of DNA microarray data by using physical properties of hybridization. Proc. Natl. Acad. Sci. USA 100:7575-80
28. Higashitani N, Higashitani A, Horiuchi K. 1993. Nucleotide sequence of the primer RNA for DNA replication of filamentous bacteriophages. J. Virol. 67:2175-81
29. Hilbers CW, Haasnoot CAG, de Bruin SH, Joordens JJM, van der Marel GA, van Boom JH. 1985. Hairpin formation in synthetic oligonucleotides. Biochimie 67:685-95
30. Hirao I, Nishimura Y, Tagawa Y, Watanabe K, Miura K. 1992. Extraordinary stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. Nucleic Acid Res. 20:3891-96
31. Holmes CE, Hecht SM. 1993. Febleomycin cleaves a transfer RNA precursors and its "transfer DNA" analog at the same major site. J. Biol. Chem. 268:25909-13
32. Ikoku AS, Hearst JE. 1981. Identification of a structural hairpin in the filamentous chimeric phage M13Gori1. J. Mol. Biol. 151:245-59
33. Jacobson H, Stockmayer WH. 1950. Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18:1600-6
34. Kadrmas JL, Ravin AJ, Leontis NB. 1995. Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): Unpaired nucleotides can be stabilizing or destabilizing. Nucleic Acids Res. 23:2212-22
35. Ke S-H, Wartell RM. 1995. Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment. Biochemistry 34:4593-600
36. Khan AS, Roe BA. 1988. Aminoacylation of synthetic DNAs corresponding to Escherichia coli phenylalanine and lysine tRNAs. Science 241:74-79
37. Kieleczawa J, Dunn JJ, Studier FW. 1992. DNA sequencing by primer walking with strings of contiguous hexamers. Science 258:1787-91
38. Ladbury JE, Sturtevant JM, Leontis NB. 1994. The thermodynamics of formation of three-strand, DNA three-way junction complex. Biochemistry 33:6828-33
39. Lane MJ, Paner T, Kashin I, Faldasz BD, Li B, et al. 1997. The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick. Nucleic Acids Res. 25:611-17
40. LeBlanc DA, Morden KM. 1991. Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry 30:4042-47
41. Leontis NB, Kwok W, Newman JS. 1991. Stability and structure of three-way DNA junctions containing unpaired nucleotides. Nucleic Acids Res. 19:759-66
42. Li P, Kupfer KC, Davies CJ, Burbee D, Evans GA, Garner HR. 1997. PRIMO: a primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-85
43. Lilley DMJ, Hallam LR. 1984. Thermodynamics of the ColE1 cruciform: comparison between probing and topological experiments using single topoisomers. J. Mol. Biol. 180:179-200
44. Lim AC, Barton JK. 1993. Chemical probing of tDNA with transition metal complexes: a structural comparison of RNA and DNA. Biochemistry 32:11029-34
45. Longfellow CE, Kierzek R, Turner DH. 1990. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry 29:278-85
46. Lu M, Guo Q, Kallenbach NR. 1991. Effect of sequence on the structure of three-arm DNA junctions. Biochemistry 30:5815-20
47. Lu M, Guo Q, Marky LA, Seeman NC, Kallenbach NR. 1991. Thermodynamics of DNA branching. J. Mol. Biol. 223:781-89
48. Luo G, Taylor J. 1990. Template switching by reverse transcriptase during DNA synthesis. J. Virol. 64:4321-28
49. Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. 1999. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5:1458-69
50. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:911-40
51. Mathews DH, Turner DH. 2002. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry 41:869-80
52. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105-19
53. McKay SJ, Jones SJ. 2002. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics 18:1538-39
54. Morozov SY, Chernov BK, Merits A, Blinov VM. 1994. Computer-assisted predictions of the secondary structure in the plant virus single-stranded DNA genome. J. Biomol. Struct. Dyn. 11:837-47
55. Muragan R. 2002. Revised theory of DNA renaturation kinetics and its experimental verification. Biochem. Biophys. Res. Commun. 293:870-73
56. Nakano M, Moody EM, Liang J, Bevilacqua PC. 2002. Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc). Biochemistry 41:14281-92
57. Nazarenko I, Pires R, Lowe B, Obaidy M, Rashtchian A. 2002. Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes. Nucleic Acids Res. 30:2089-195
58. Okumoto Y, Ohmichi T, Sugimoto N. 2002. Immobilized small deoxyribozyme to distinguish RNA secondary structures. Biochemistry 41:2769-73
59. Owczarzy R, Vallone PM, Gallo FJ, Paner TM, Lane MJ, Benight AS. 1997. Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44:217-39
60. Owczarzy R, Vallone PM, Goldstein RF, Benight AS. 1999. Studies of DNA dumbbells. VII. Evaluation of the next-nearest neighbor sequence dependent interactions in duplex DNA. Biopolymers 52:29-56
61. Ozawa K, Kurtzman G, Young N. 1986. Replication of the B19 parvovirus in human bone marrow cell cultures. Science 233:883-86
62. Paner TM, Amaratunga M, Doktycz MJ, Benight AS. 1990. Analysis of melting transitions of the DNA hairpins formed from the oligomer sequence d[GGATAC(X)4GTATCC] (X = A, T, G, C). Biopolymers 29:1715-34
63. Paquette J, Nicoghosian K, Qi G, Beauchemin N, Cedergren R. 1990. The conformation of single-stranded nucleic acids tDNA versus tRNA. Eur. J. Biochem. 189:259-65
64. Petersheim M, Turner DH. 1983. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry 22: 256-63
65. Peyret N. 2000. Prediction of nucleic acid hybridization: parameters and algorithms. PhD thesis. Wayne State University, Detroit, MI. 352 pp.
66. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr. 1999. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 38:3468-77
67. Proutski V, Holmes EC. 1996. Primer-Master: a new program for the design and analysis of PCR primers. CABIOS 12:253-55
68. Riccelli PV, Merante F, Leung KT, Bortolin S, Zastawny RL, et al. 2001. Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. Nucleic Acids Res. 29:996-1004
69. Russel M. 1994. Mutants at conserved positions in gene IV, a gene required for assembly and secretion of filamentous phages. Mol. Microbiol. 14:357-69
70. Rychlik W, Rhoads ER. 1989. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing, and in vitro amplification of DNA. Nucleic Acids Res. 17:8543-51
71. Sambrook J, Fritsch EF, Maniatis T. 1989. Site-directed mutagenesis of cloned DNA, In Molecular Cloning: A Laboratory Manual, pp. 15.51-80. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
72. SantaLucia J Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95:1460-65
73. SantaLucia J Jr. 2000. The use of spectroscopic techniques in the study of DNA stability. In Spectrophotometry and Spectrofluorimetry: A Practical Approach, ed. MG Gore, pp. 329-56. Oxford, UK: Oxford Univ. Press
74. SantaLucia J Jr, Turner DH. 1997. Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44:309-19
75. Schutz E, von Ahsen N. 1999. Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. Biotechniques 27:1218-22
76. Seeman NC. 1999. DNA engineering and its application to nanotechnology. Trends Biotechnol. 17:437-43
77. Seeman NC. 2003. Biochemistry and structural DNA nanotechnology: an evolving symbiotic relationship. Biochemistry 42:7259-69
78. Senior M, Jones RA, Breslauer KJ. 1988. The influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry 27:3879-85
79. Senior MM, Jones RA, Breslauer KJ. 1988. Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc. Natl. Acad. Sci. USA 85:6242-46
80. Specthrie L, Bullitt E, Horiuchi K, Model P, Russel M, Makowski L. 1992. Construction of a microphage variant of filamentous bacteriophage. J. Mol. Biol. 228:720-24
81. Stull RA, Taylor LA, Szoka FC Jr. 1992. Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices. Nucleic Acids Res. 20:3501-8
82. Summers J, Mason WS. 1982. Replication of the genome of a hepatitis B-like virus by reverse transcription of an RNA intermediate. Cell 29:403-15
83. Tinoco I, Bustamante C. 1999. How RNA folds. J. Mol. Biol. 293:271-81
84. Turner DH. 1992. Bulges in nucleic acids. Curr. Opin. Struct. Biol. 2:334-37
85. Turner DH, Sugimoto N, Freier SM. 1988. RNA structure prediction. Annu. Rev. Biophys. Biophys. Chem. 17:167-92
86. Vallone PM, Paner T, Hilario J, Lane MJ, Faldasz BD, Benight AS. 1999. Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers 50:425-42
87. Varani G. 1995. Exceptionally stable nucleic acid hairpins. Annu. Rev. Biophys. Biomol. Struct. 24:379-404
88. von Ahsen N, Oellerich M, Armstrong VW, Schutz E. 1999. Application of a thermodynamic nearest-neighbor model to estimate nucleic acid stability and optimize probe design: prediction of melting points of multiple mutations of apolipoprotein B-3500 and factor V with a hybridization probe genotyping assay on the LightCycler. Clin. Chem. 45:2094-101
89. von Ahsen N, Oellerich M, Schutz E. 2000. DNA base bulge vs. unmatched end formation in probe-based diagnostic insertion/deletion genotyping: genotyping the UGTIAI (TA)(n) polymorphism by real-time fluorescence PCR. Clin. Chem. 46:1939-45
90. 2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin. Chem. 47:1956-61
91. Wang J-Y, Drlica K. 2003. Modeling hybridization kinetics. Math. Biosci. 183:37-47
92. White SA, Draper DE. 1989. Effects of single-base bulges on intercalator binding to small RNA and DNA hairpins and a ribosomal RNA fragment. Biochemistry 28:1892-97
93. Wu M, McDowell JA, Turner DH. 1995. A periodic table of tandem mismatches. Biochemistry 34:3204-11
94. Zhang L, Miles MF, Aldape KD. 2003. A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 21:818-21
95. Zieba K, Chu TM, Kupke DW, Marky LA. 1991. Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry 30:8018-26
96. Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52
97. Zuker M, Sankoff D. 1984. RNA secondary structures and their prediction. Bull. Math. Biol. 46:591-621