Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

Biophysical Journal

Volumn 82, Issue 5, 2002, Pages 2592-2609

  Lankaš, Filip ^a,c   Cheatham III, Thomas E ^b   Špačková, Nad'a ^a,d   Hobza, Pavel ^a   Langowski, Jörg ^c   Šponer, Jiří ^a  

^a J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

^b UNIVERSITY OF UTAH   (United States)

^c GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^d INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOADENINE THYMINE; ADENINE; CYTOSINE; DNA; GUANINE; INOSINE 5 METHYLCYTOSINE; PURINE DERIVATIVE; THYMINE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTALLOGRAPHY; DYNAMICS; ELASTICITY; ELECTRIC FIELD; ELECTRICITY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SIMULATION;

EID: 0036225151     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75601-4     Document Type: Article

References (121)

1. Poly (dA)·poly(dT) is a B-type double helix with a distinctively narrow minor groove
2. Heteronomous DNA
3. Recognition elements that determine affinity and sequence-specific binding to DNA of 2QN, a biosynthetic bis-quinoline analogue of echinomycin
4. The influence of the 2-amino group of guanine on DNA conformation-uranyl and DNAse-I probing of inosine diaminopurine substituted DNA
5. The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA
6. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
7. Molecular dynamics with coupling to an external bath
8. Nucleic acids: Theory and computer simulation, Y2K
9. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
10. From atomic to mesoscopic descriptions of the internal dynamics of DNA
11. The unusual conformation adopted by the adenine tracts in kinetoplast DNA
12. 5 tracts
13. Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution
14. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
15. Molecular dynamics simulation of nucleic acids
16. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
17. Molecular dynamics simulations of nucleic acids: Successes, limitations, and promise
18. Collective motion artifacts arising in long-duration molecular dynamics simulations
19. Sequence effects on local DNA topology
20. A bifurcated hydrogen-bonded conformation in the d(A.T) base-pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin
21. A second generation force field for the simulation of proteins; Nucleic acids, and organic molecules
22. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
23. Intrinsically bent DNA
24. DNA bending by adenine-thymine tracts
25. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
26. Sequence-specific binding of counterions to B-DNA
27. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature
28. Helix structure and molecular recognition by B-DNA
29. Sequence specificity of cured DNA
30. DNA curvature does not require bifurcated hydrogen bonds or pyrimidine methyl groups
31. The influence of exocyclic substituents of purine bases on DNA curvature
32. Crystal-lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract
33. A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend
34. High basepair opening rates in tracts of GC basepairs
35. The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
36. Structural equilibrium of DNA represented with different force fields
37. Constant-pressure molecular dynamics simulation: The Langevin piston method
38. Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: Ab initio/Langevin dipoles study
39. All-atom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data
40. The electrostatic contribution to DNA base-stacking interactions
41. The folding of centromeric DNA strands into intercalated structures: A physicochemical and computational study
42. DNA sequence-specific reading by ecinomycin: Role of hydrogen-bonding and stacking interactions
43. Bending and curvature calculations in B-DNA
44. B-DNA twisting correlates with base-pair morphology
45. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
46. Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects
47. n blocks
48. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
49. A premelting conformational transition in poly(dA)-poly(dT) coupled to daunomycin binding
50. Performance of empirical potentials (AMBER, CFF95, CFVV, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AMI, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results
51. Structure, energetics, and dynamics of the nucleic acid basepairs: Nonempirical ab initio calculations
52. Canonical dynamics: Equilibrium phase distributions
53. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
54. The curvature of dA tracts is temperature dependent
55. Comparison of simple potential functions for simulating liquid water
56. A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations
57. Chemical determinants of DNA bending at adenine-thymine tracts
58. DNA bending at adenine-thymine tracts
59. Minor groove functional groups are critical for the B-form conformation of duplex DNA
60. Molecular dynamic simulations of environment and sequence-dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results
61. Sequencedependent elastic properties of DNA
62. The dependence of the surface electrostatic potential of B-DNA on environmental factors
63. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
64. Defining the structure of irregular nucleic acids: Conventions and principles
65. Polymorphism of DNA double helices
66. structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
67. On the potential role of the amino nitrogen atom as a hydrogen acceptor in macromolecules
68. The physical basis of nucleic acid base stacking
69. Solution structure of an A-tract DNA bend
70. An all-atom empirical energy function for the simulation of nucleic acids
71. Physical characterization of a kinetoplast fragment with unusual properties
72. Bent helical structure in kinetoplast DNA
73. Bending and twisting elasticity of DNA
74. Base sequence effects in double-helical DNA. 3. Average properties of curved DNA
75. DNA structure: What's in charge?
76. Molecular dynamics simulations of B′-DNA: Sequence effects on A-tract-induced bending and flexibility
77. Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3'-A-tract junction
78. The structure of an oligo(dA)·oligo(dT) tract and its biological implications
79. The deformability of G-tracts: The crystal structure of a complete turn of an A/B-DNA intermediate
80. The structure of a stable intermediate in the A↔B DNA helix transition
81. A molecular dynamics method for simulations in the canonical ensemble
82. Elasticity theory of a twisted stack of plates
83. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
84. Influence of fluctuations on DNA curvature: A comparison of flexible and static wedge models of intrinsically bent DNA
85. Twenty years of DNA bending
86. TIT for TAT: The properties of inosine and adenosine in TATA box DNA
87. Sequence dependence of the helical repeat of DNA in solution
88. Sequence-dependent helical periodicity of DNA
89. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
90. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature
91. Molecular dynamics studies of DNA A-tract structure and flexibility
92. High-resolution NMR studies of A-containing and G-containing oligonucleotides
93. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: Stable trajectories on a nanosecond scale
94. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
95. Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G.A mismatch pairs
96. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale molecular dynamic simulations
97. Aromatic base stacking in DNA: From ab initio calculations to molecular dynamics simulations
98. Local conformational variations observed in B-DNA crystals do not improve base stacking. Computational analysis of base stacking in d(CATGGGC-CCATG)2 B[dharrow]A intermediate crystal structure
99. Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA. A quantum-chemical study
100. Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study
101. Different interstrand and intrastrand contributions to stacking account for roll variations at the alternating purinepyrimidine sequences in A-DNA and A-RNA
102. Theoretical analysis of the base stacking in DNA. Choice of the force field and comparison with oligonucleotide crystal structures
103. Close mutual contacts of the amino groups in DNA
104. Structures and energies of hydrogen-bonded DNA basepairs, a nonempirical study with inclusion of electron correlation
105. Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
106. 5): Effects of sequence polarity on DNA curvature
107. Unrestrained molecular dynamics simulations of [d(AT)(5)](2) duplex in aqueous solution: Hydration and binding of sodium ions in the minor groove
108. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine
109. Preferential counterion binding to A-tract DNA oligomers
110. A-tract bending: Insights into experimental structures by computational models
111. Helical periodicity of DNA, poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) in solution
112. An A-type double helix of DNA having B-type puckering of the deoxyribose rings
113. Crystal structures of A-DNA duplexes
114. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
115. Crystal-structure analysis of a complete turn of B-DNA
116. The locus of sequence-directed and protein-induced DNA bending
117. Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn
118. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA
119. A 5-nano-second molecular dynamics trajectory for B-DNA: Analysis of structure, motions, and solvation
120. Anisotropic flexibility of DNA and the nucleosomal structure