Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations

Biophysical Journal

Volumn 81, Issue 1, 2001, Pages 352-370

  Feig, Michael ^a,c   Zacharias, Martin ^b   Montgomery Pettitt, B ^a  

^a University of Houston   (United States)

^b FRITZ LIPMANN INSTITUTE   (Germany)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; COAT PROTEIN;

ALPHA HELIX; ARTICLE; BASE MISPAIRING; COMPLEX FORMATION; DNA CONFORMATION; DNA STRUCTURE; FRAMESHIFT MUTATION; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; SIMULATION; TRANSLATION REGULATION; X RAY CRYSTALLOGRAPHY;

EID: 0034950462     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(01)75705-0     Document Type: Article

References (114)

1. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein
2. Asp anticodon hairpin
3. Simulations of the molecular dynamics of nucleic acids
4. A difference in the importance of bulged nucleotides and parent base pairs in the binding of transcription factor IIIA to Xenopus 5S RNA and 5S RNA genes
5. Recent progress in molecular dynamics simulations of DNA and protein-DNA complexes including solvent
6. Modeling of DNA via molecular dynamics simulation: Structure, bending, and conformational transitions
7. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles)
8. Proton NMR and structural features of a 24-nucleotide RNA hairpin
9. Crystal structure of a group I ribozyme domain: Principles of RNA packing
10. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions
11. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
12. 2 in the presence of hexaamminecobalt(III)
13. Molecular dynamics simulations highlights the structural differences among DNA:DNA, RNA: RNA, and DNA:RNA hybrid duplexes
14. Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics
15. Effect of backbone ζ torsion angle on low energy single base opening in B-DNA crystal structures
16. 11 complex as a bulge-specific probe for DNA
17. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
18. Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants
19. Base sequence and helix structure variation in B- and A-DNA
20. Definitions and nomenclature of nucleic acid structure parameters
21. 2. Comparison of results from NMR and crystallography
22. Molecular dynamics simulation study of DNA dodecamer d(CGCGAAT7CGCG) in solution: Conformation and hydration
23. The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
24. Microsatellite instability in inherited and sporadic neoplasms
25. Crystallographic water sites from a theoretical perspective
26. Structural equilibrium of DNA represented with different force fields
27. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
28. Sodium and chlorine ions as part of the DNA solvation shell
29. All-atom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data
30. The accommodation of noncomplementary bases in helical polyribonucleotides and deoxyribonucleic acids
31. Isolation of MutS beta from human cells and comparison of the mismatch repair specificities of the MutS beta and MutS alpha
32. Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence energy transfer
33. A preorganized active site in the crystal structure of the tetrahymena ribozyme
34. Solution structure of the donor site of a trans-splicing RNA
35. Extra-helical adenosine stacks into right-handed DNA: Solution conformation of the d(CGCAGAGCTCGCG) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra
36. Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: Possible relevance to the folding of single-stranded nucleic acids
37. Free energy analysis of the conformational preferences of A and B forms of DNA in solution
38. Comparison of simple potential functions for simulating liquid water
39. Three-dimensional structures of bulge-containing DNA fragments
40. The three-dimensional structure of a DNA duplex containing looped-out bases
41. Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes
42. Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution
43. Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: Extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution
44. Site-specific cleavage at a DNA bulge by neocarzinostatin chromophore via a novel mechanism
45. Characterization of a covalent monoadduct of neocarzinostatin chromophore at a DNA bulge
46. Structure refinement for a 24-nucleotide RNA hairpin
47. HhaI methyltransferase flips its target base out of the DNA helix
48. Biochemistry and genetics of eukaryotic mismatch repair
49. Mismatch repair: Mechanisms and relationship to cancer susceptibility
50. The DNA (cytosine-5) methyltransferases
51. Molecular dynamics simulation studies of a high resolution Z-DNA crystal
52. Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA
53. All-atom empirical force field for nucleic acids. II. Application to molecular dynamics simulations of DNA and RNA in solution
54. Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair
55. Crystal structure of 15-mer DNA duplex containing unpaired bases
56. Mechanisms and biological effects of mismatch repair
57. Mismatch repair in replication fidelity, genetic recombination, and cancer biology
58. 6G) is outside of the helix
59. NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA) · oligo(dT) tract
60. Ethidium ion binds more strongly to a DNA double helix with a bulged cytosine base than to a regular double helix
61. 2 via a hybrid relaxation matrix procedure
62. 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxynucleotide duplex
63. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates
64. Stacking free energy profiles for all 16 natural ribodinucleoside monophosphates in aqueous solution
65. Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes
66. Extra adenosine stacks into the selfcomplementary d(CGCAGAATTCGCG) duplex in solution
67. A "bulged" double helix in an RNA-protein contact site
68. Crystal structures of an A-form duplex with single-adenosine bulges and conformational basis for site-specific RNA self-cleavage
69. Conformation of the TAR RNA-arginine complex by NMR spectroscopy
70. Branch nucleophile selection in pre-mRNA splicing: Evidence for the bulged duplex model
71. Energetic coupling between DNA bending and base pair opening
72. The crystal structure of HaeIII methylase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing
73. DNA bending by the bulge defect
74. RNA binding site of R17 coat protein
75. n bulge loops in DNA duplexes: Intrahelical stacking of A, A-A, and A-A-A bulge loops
76. Ion transport in the gramicidin channel: Molecular dynamics study of single and double occupancy
77. Crystal structures of a series of RNA aptamers complexed to the same protein target
78. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
79. Conformations of the sugar-phosphate backbone in helical DNA crystal structures
80. NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein
81. Modeling solvent in biomolecular systems
82. Efficient Ewald electrostatic calculations for large systems
83. Frameshift mutations and the genetic code
84. Crystal structure of an adenine bulge in the RNA chain of a DNA · RNA hybrid, d(CTCCTCTTC) · r(gaagagagag)
85. Evidence for allosteric coupling between the ribosome and repressor binding sites of a translationally regulated mRNA
86. Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement
87. Bulges in nucleic acids
88. Crystal structure of an RNA bacteriophage coat protein-operator complex
89. The three dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence- specific protein-rNa interactions
90. Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG) · (CCGCCCAG). A model-building and NMR study
91. Extra thymidine stacks into the d(CTGGTGCGG) · d(CCGCCCAG) duplex. An NMR and model-building study
92. Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments
93. Atomic model of a pyrimidine dimerspecific excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition
94. Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases
95. Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution
96. Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC-T mismatch by simulation
97. Binding of 9-aminoacridine to bulged-base DNA oligomers from a frameshift hot spot
98. Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization
99. Role of a bulged a residue in a specific RNA protein interaction
100. Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn
101. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
102. A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions, and solvation
103. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
104. Bulge-induced bends in RNA: Quantification by transient electric birefringence
105. Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions
106. Physical studies of 5S RNA variants at position 66
107. Sequence-dependent bending of DNA and phasing of nucleosomes