Sequence effects in the melting and renaturation of short DNA oligonucleotides: Structure and mechanistic pathways

Journal of Physics Condensed Matter

Volumn 21, Issue 3, 2009, Pages

  Sambriski, E J ^a   Ortiz, V ^a   De Pablo, J J ^a  

^a University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENERGY BARRIERS; FREE ENERGY; GENES; HEAT SHIELDING; IONIC STRENGTH; LIGHT WEIGHT ROLLING STOCK; NUCLEIC ACIDS; OLIGONUCLEOTIDES;

BASE PAIRS; CRITICAL SIZES; DNA-OLIGONUCLEOTIDES; DOUBLE-STRANDED DNAS; ENERGY PROFILES; FREE ENERGY BARRIERS; LANGEVIN DYNAMICS; LOW IONIC STRENGTHS; MECHANISTIC PATHWAYS; RANDOM SEQUENCES; RENATURATION; SIMULATION RESULTS; SPECIFIC CONTACTS; TRANSITION PATH SAMPLINGS; TRANSITION STATE; TRANSITION STATE ENSEMBLES;

DNA SEQUENCES;

EID: 63649094163     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/21/3/034105     Document Type: Article

References (55)

1. Wartell R M and Benight A S 1985 Thermal denaturation of DNA molecules: a comparison of theory with experiment Phys. Rep. 126 67-107
2. Hill T L 1959 Generalization of the one-dimensional Ising model applicable to helix transitions in nucleic acids and proteins J. Chem. Phys. 30 383-7
3. Lifson S and Zimm B H 1963 Simplified theory of the helix-coil transition in DNA based on a grand partition function Biopolymers 1 15-23
4. Marmur J, Rownd R and Schildkraut C L 1963 Denaturation and renaturation of deoxyribonucleic acid Prog. Nucleic Acid Res. 1 231-300
5. Rau D C and Klotz L C 1978 A unified theory of nucleation-rate-limited DNA renaturation kinetics Biophys. Chem. 8 41-51
6. Murugan R 2002 Sample size autocorrelation analysis of kinetic data: resolving reaction path heterogeneity J. Chem. Phys. 117 6372-7
7. Britten R J and Davidson R H 1976 Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation Proc. Natl Acad. Sci. USA 73 415-9
8. Rau D C and Klotz L C 1975 A more complete kinetic theory of DNA renaturation J. Chem. Phys. 62 2354-65
9. Marmur J and Doty P 1961 Thermal renaturation of deoxyribonucleic acids J. Mol. Biol. 3 585-94
10. Nygaard A P and Hall B D 1964 Formation and properties of RNA-DNA complexes J. Mol. Biol. 9 125-42
11. Marmur J and Lane D 1960 Strand separation and specific recombination in deoxyribonucleic acids: biological studies Proc. Natl Acad. Sci. USA 46 453-61
12. Subirana J A and Doty P 1966 Kinetics of renaturation of denaturated DNA. I. Spectrophotometric results Biopolymers 4 171-87
13. Thrower K J and Peacocke A R 1966 The kinetics of renaturation of DNA Biochim. Biophys. Acta 119 652-4
14. Wetmur J G 1976 Hybridization and renaturation kinetics of nucleic acids Annu. Rev. Biophys. Bioeng. 5 337-61
15. Saunders M and Ross P D 1960 A simple model of the reaction between polyadenylic acid and polyuridylic acid Biochem. Biophys. Res. Commun. 3 314-8
16. Kallenback N R, Crothers D M and Mortimer R G 1963 Interpretation of the kinetics of helix formation Biochem. Biophys. Res. Commun. 11 213-6
17. Murugan R 2003 A stochastic model on DNA renaturation kinetics Biophys. Chem. 104 535-41
18. Murugan R 2003 A theory on the origin of cooperativity in DNA renaturation kinetics Biophys. Chem. 106 173-8
19. Murugan R 2002 Revised theory on DNA renaturation kinetics and its experimental verification Biochem. Biophys. Res. Commun. 293 870-3
20. Matsuzawa Y, Yonezawa Y and Yoshikawa K 1996 Formation of nucleation center in single double-stranded DNA chain Biochem. Biophys. Res. Commun. 225 796-800
21. Yoshikawa K and Matsuzawa Y 1996 Nucleation and growth in single DNA molecules J. Am. Chem. Soc. 118 929-30
22. Saiki R K, Gelfand D H, Stoffel S, Scharf S J, Higuchi R, Horn G T, Mullis K B and Erlich H A 1988 Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science 239 487-91
23. Buck M J and Lieb J D 2004 ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments Genomics 83 349-60
24. Ramanathan A, Huff E J, Lamers C C, Potamousis K D, Forrest D K and Schwartz D C 2004 An integrative approach for the optical sequencing of single DNA molecules Anal. Biochem. 330 227-41
25. Knotts T A IV, Rathore N, Schwartz D C and dePablo J J 2007 A coarse grain model for DNA J. Chem. Phys. 126 084901
26. Sambriski E J, Schwartz D C and de Pablo J J 2009 Mesoscale model of DNA and its renaturation Biophys. J. at press
27. Hoang T X and Cieplak M 2000 Molecular dynamics of folding of secondary structures in G-type models of proteins J. Chem. Phys. 112 6851-62
28. Rau D C and Parsegian V A 1992 Direct measurement of the intermolecular forces between counterion-condensed DNA double helices: evidence for long range attractive hydration forces Biophys. J. 61 246-59
29. Rau D C and Persegian V A 1992 Direct measurement of temperature- dependent solvation forces between DNA double helices Biophys. J. 61 260-71
30. Kwok L W, Qiu X, Park H Y, Lamb J S, Andresen K and Pollack L 2006 Measuring inter-DNA potentials in solution Phys. Rev. Lett. 96 138101
31. Ha B-Y and Liu A J 1998 Charge oscillations and many-body effects in bundles of like-charged rods Phys. Rev. E 58 6281-6
32. Ha B-Y and Liu A J 1999 Counterion-mediated, non-pairwise-additive attractions in bundles of like-charged rods Phys. Rev. E 60 803-13
33. Lyubartsev A P, Martsinovski A A, Shevkunov S V and Vorontsov-Velyaminov P N 1992 New approach to Monte Carlo calculation of the free energy: method of expanded ensembles J. Chem. Phys. 96 1776-83
34. Wilding N B and Müller M 1994 Accurate measurements of the chemical potential of polymeric systems by Monte Carlo J. Chem. Phys. 101 4324-30
35. Escobedo F A and dePablo J J 1995 Monte Carlo simulation of the chemical potential of polymers in an expanded ensemble J. Chem. Phys. 103 2703-10
36. Escobedo F A and dePablo J J 1996 Expanded grand canonical and Gibbs ensemble Monte Carlo simulation of polymers J. Chem. Phys. 105 4391-4
37. dePablo J J, Yan Q and Escobedo F A 1999 Simulation of phase transitions in fluids Annu. Rev. Phys. Chem. 50 377-411
38. Shulz B J, Binder K, Müller M and Landau D P 2003 Avoiding boundary effects in Wang-Landau sampling Phys. Rev. E 67 067102
39. Rathore N, Knotts T A IV and dePablo J J 2003 Density of states simulations of proteins J. Chem. Phys. 118 4285-90
40. Rathore N and dePablo J J 2002 Monte Carlo simulation of proteins through a random walk in energy space J. Chem. Phys. 116 7225-30
41. Roux B 1995 The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 275-82
42. Souaille M and Roux B 2001 Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations Comput. Phys. Commun. 135 40-57
43. Ferrenberg A M and Swendsen R H 1988 New Monte Carlo technique for studying phase transitions Phys. Rev. Lett. 61 2635-8
44. Chopra M, Müller M and dePablo J J 2006 Order-parameter-based Monte Carlo simulation of crystallization J. Chem. Phys. 124 134102
45. Bolhuis P G, Chandler D, Dellago C and Geissler P L 2002 Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu. Rev. Phys. Chem. 53 291-318
46. Dellago C, Bolhuis P G and Geissler P L 2002 Transition path sampling Adv. Chem. Phys. 123 1-78
47. Owczarzy R, You Y, Moreira B G, Manthey J A, Huang L, Behlke M A and Walder J A 2004 Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures Biochemistry 43 3537-54
48. http://www.idtdna.com/analyzer/Applications/OligoAnalyzer
49. Garel T, Monthus C and Orland H 2001 A simple model for DNA denaturation Europhys. Lett. 55 132-8
50. Carlon E, Orlandini E and Stella A L 2002 Role of stiffness and excluded volume in DNA denaturation Phys. Rev. Lett. 88 198101
51. Kafri Y, Mukamel D and Peliti L 2000 Why is the DNA denaturation transition first-order? Phys. Rev. Lett. 85 4988-91
52. Holbrook J A, Capp M W, Saecker R M and Record M T Jr 1999 Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices Biochemistry 38 8409
53. Owczarzy R, Vallone P M, Gallo F J, Paner T M, Lane M J and Benight A S 1997 Predicting sequence-dependent melting stability of short duplex DNA oligomers Biopolymers 44 217-39
54. Goldar A and Sikorav J-L 2004 DNA renaturation at the water-phenol interface Eur. Phys. J. E 14 211-39
55. Stogryn A 1971 Equations for calculating the dielectric constant of saline water IEEE Trans. Microw. Theory Tech. 19 733-6