Relationship of DNA structure to internal dynamics: Correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)2 and d(CGCTAGCG)2 with 13C order parameters implies conformational coupling in dinucleotide units

Journal of Molecular Biology

Volumn 307, Issue 2, 2001, Pages 525-540

  Isaacs, Richard J ^a   Spielmann, H Peter ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Helical parameter; NMR spectroscopy; Order parameter; Sequence dependent structure; Spin relaxation

Indexed keywords

CARBON 13; DNA;

ARTICLE; BASE PAIRING; DNA STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL;

EID: 0035937251     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4498     Document Type: Article

References (34)

1. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
2. Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures
3. Local variability and base sequence effects in DNA crystal structures
4. MARDIGRAS - A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure
5. Relaxation matrix analysis of 2D-NMR data
6. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
7. Mechanics of sequence-dependent stacking of bases in B-DNA
8. Principles of sequence-dependent flexure of DNA
9. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure
10. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
11. Two distinct modes of protein-induced bending in DNA
12. Sequence-dependent dynamics of TATA-Box binding sites
13. Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters
14. Sequence-dependent structural variation in B-DNA
15. Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using two-dimensional nuclear magnetic resonance methods
16. Sequence-dependent DNA structure. The role of base stacking interactions
17. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
18. Defining the structure of irregular nucleic acids: Conventions and principles
19. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
20. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
21. Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors
22. Sequence-dependent DNA structure: The role of the sugar-phosphate backbone
23. Sequence-dependent DNA structure: Tetranucleotide conformational maps
24. Conformational sub-states in B-DNA
25. DNA flexibility as a function of allomorphic conformation and of base sequence
26. Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
27. Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting
28. 13C NMR spectroscopy
29. 13C NMR spectroscopy
30. A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants
31. Systematic study of nuclear Overhauser effects vis-à-vis local helical parameters, sugar puckers, and glycosidic torsions in B DNA- insensitivity of NOE to local transitions in B DNA oligonucleotides due to internal structural compensations
32. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers