Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

European Journal of Biochemistry

Volumn 269, Issue 12, 2002, Pages 2821-2830

  Wu, Peng ^a,b   Nakano, Shu Ichi ^a   Sugimoto, Naoki ^a  

^a KONAN UNIVERSITY   (Japan)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Enthalpy entropy compensation; Heat capacity change; Temperature dependent thermodynamics; The NN model parameters

Indexed keywords

DNA; DOUBLE STRANDED DNA; RNA;

ARTICLE; BASE PAIRING; COMPLEX FORMATION; DNA BASE COMPOSITION; DNA HELIX; DNA RNA HYBRIDIZATION; DNA STRUCTURE; ENERGY; ENTHALPY; ENTROPY; EXTRACTION; HEAT TOLERANCE; MELTING POINT; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PARAMETER; PRIORITY JOURNAL; RNA STRUCTURE; TEMPERATURE; TEMPERATURE DEPENDENCE; THERMODYNAMICS; THERMOSTABILITY;

BASE PAIRING; DNA, SINGLE-STRANDED; ENTROPY; HEAT; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; RNA; TEMPERATURE; THERMODYNAMICS;

EID: 0036318088     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.02970.x     Document Type: Article

References (65)

1. Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein
2. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
3. On finding all suboptimal foldings of an RNA molecule
4. Prediction of common secondary structures of RNAs: A genetic algorithm approach
5. Accessing genetic information with high-density DNA arrays
6. Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms
7. Isolation and characterization of microplasminogen. A low molecular weight form of plasminogen
8. Mutation detection and single-molecule counting using isothermal rolling-circle amplification
9. DNA amplification by the polymerase chain reaction
10. Purification, cloning, and synthesis of a novel salivary antithrombin from the mosquito Anopheles albimanus
11. DNA chips survey an entire genome
12. DNA chips: An array of possibilities
13. Measuring the thermodynamics of RNA secondary structure formation
14. Thermodynamic analysis of biomolecular interactions
15. Thermal denaturation methods in the study of protein folding
16. Improved free-energy parameters for predictions of RNA duplex stability
17. Predicting DNA duplex stability from the base sequence
18. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
19. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
20. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
21. Thermodynamics and NMR of internal G·T mismatches in DNA
22. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
23. Thermodynamic parameters for DNA sequences with dangling ends
24. Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes
25. Stability and structure of RNA duplexes containing isoguanosine and isocytidine
26. The energetics of HMG box interactions with DNA: Thermodynamic description of the target DNA duplexes
27. 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
28. Heat capacity effects on the melting of DNA. 1. General aspects
29. Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects
30. Transition characteristics and thermodynamic analysis of DNA duplex formation: A quantitative consideration for the extent of duplex association
31. Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in four 40 base pair deoxyoligonucleotides
32. Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: Correlations of thermodynamic and structural data
33. Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides
34. Significant discrepancies between van't Hoff and calorimetric enthalpies
35. pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes
36. A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volume tric techniques
37. Significant discrepancies between van't Hoff and calorimetric enthalpies
38. Possible origin of differences between van't Hoff and calorimetric enthalpy estimates
39. Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
40. Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices
41. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes
42. Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability
43. Contribution of loops and nicks to the formation of DNA dumbbells: Melting behavior and ligand binding
44. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
45. Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs
46. 2 by two-dimensional NMR and simulated annealing
47. Thermodynamics of sequence-specific binding of PNA to DNA
48. Nucleic acid duplex stability: Influence of base composition on cation effects
49. Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect
50. Contribution of hydration and non-covalent interactions to the heat capacity effect on protein unfolding
51. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water
52. Thermodynamics of oligosaccharide binding to a monoclonal antibody specific for a Salmonella O-antigen point to hydrophobic interactions in the binding site
53. Thermodynamics and kinetics of dissociation of ligand-induced dimers of vancomycin antibiotics
54. Van't Hoff and calorimetric enthalpies from isothermal titration calorimetry: Are there significant discrepancies?
55. Thermodynamics of three-way multibranch loops in RNA
56. Long-range cooperativity in molecular recognition of RNA by oligodeoxynucleotides with multiple C5-(1-propynyl) pyrimidines
57. Improved nearest-neighbor parameters for predicting DNA duplex stability
58. Enthalpy-entropy compensation in DNA melting thermodynamics
59. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops
60. Theory of the melting transition of synthetic polynucleotides: Evaluation of the stacking free energy
61. Kinetic property of bulged helix formation: Analysis of kinetic behavior using nearest-neighbor parameters
62. Stability of ribonucleic acid double-stranded helices
63. Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest-neighbor stacking interactions in DNA
64. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
65. Improved free energies for G·C base-pairs