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

被引:15
作者
Isaacs, RJ
Spielmann, HP [1 ]
机构
[1] Univ Kentucky, Dept Mol & Cellular Biochem, Lexington, KY 40536 USA
[2] Univ Kentucky, Dept Chem, Lexington, KY 40536 USA
[3] Univ Kentucky, Kentucky Ctr Struct Biol, Lexington, KY 40536 USA
基金
美国国家科学基金会;
关键词
spin relaxation; order parameter; helical parameter; NMR spectroscopy; sequence-dependent structure;
D O I
10.1006/jmbi.2001.4498
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with H-1 NMR spectroscopy by utilizing distance restraints from total relaxation matrix analysis of NOESY cross-peak intensities in restrained molecular dynamics calculations. The root-mean-square deviation of the coordinates for the ensemble of structures was 0.13 Angstrom for UM and 0.49 Angstrom for CTSYM, with crystallographic equivalent R-c=0.41 and 0.39 and sixth-root residual R-x=0.11 and 0.10 for UM and CTSYM, respectively. Both UM and CTSYM. are B-form with straight helical axes and show sequence-dependent variations in conformation. The internal dynamics of UM and CTSYM were previously determined by analysis of C-13 relaxation parameters in the context of the Lipari & Szabo model-free formalism. Helical parameters for the two DNA oligomers were examined for linear correlations with the order parameters (S-2) of groups of C-13 spins in base-pairs and dinucleotide units of UM and CTSYM. Correlations were found for six interstrand base-pair parameters tip, y-displacement, inclination, buckle and stretch with various combinations of S-2 for atoms in Watson-Crick base-pairs and for two inter-base-pair parameters, rise and roll with various combinations of S-2 for atoms in dinucleotides. The correlations for the interstrand base-pair helical parameters indicate that the conformations of the deoxyribose residues of each strand are dynamically coupled. Also, the inter-base-pair separation has a profound effect on the local internal motions available to the DNA, supporting the idea that rise is a principal degree of freedom for DNA conformational variability. The correlations indicate collective atomic motions of spins that may represent specific motional modes in DNA, and that base sequence has a predictable effect on the relative order of groups of spins both in the bases and in the deoxyribose ring of the DNA backbone. These observations suggest that an important functional outcome of DNA base sequence is the modulation of both the conformation and dynamic behavior of the DNA backbone. (C) 2001 Academic Press.
引用
收藏
页码:525 / 540
页数:16
相关论文
共 34 条
[1]  
Abseher R, 1998, PROTEINS, V31, P370
[2]   NUCLEIC-ACID STRUCTURE-ANALYSIS - MATHEMATICS FOR LOCAL CARTESIAN AND HELICAL STRUCTURE PARAMETERS THAT ARE TRULY COMPARABLE BETWEEN STRUCTURES [J].
BABCOCK, MS ;
PEDNAULT, EPD ;
OLSON, WK .
JOURNAL OF MOLECULAR BIOLOGY, 1994, 237 (01) :125-156
[3]   LOCAL VARIABILITY AND BASE SEQUENCE EFFECTS IN DNA CRYSTAL-STRUCTURES [J].
BHATTACHARYYA, D ;
BANSAL, M .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1990, 8 (03) :539-572
[4]   RELAXATION MATRIX ANALYSIS OF 2D-NMR DATA [J].
BORGIAS, BA ;
GOCHIN, M ;
KERWOOD, DJ ;
JAMES, TL .
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 1990, 22 :83-100
[5]   MARDIGRAS - A PROCEDURE FOR MATRIX ANALYSIS OF RELAXATION FOR DISCERNING GEOMETRY OF AN AQUEOUS STRUCTURE [J].
BORGIAS, BA ;
JAMES, TL .
JOURNAL OF MAGNETIC RESONANCE, 1990, 87 (03) :475-487
[6]  
Brooks C. L., 1988, PROTEINS THEORETICAL
[7]   PRINCIPLES OF SEQUENCE-DEPENDENT FLEXURE OF DNA [J].
CALLADINE, CR ;
DREW, HR .
JOURNAL OF MOLECULAR BIOLOGY, 1986, 192 (04) :907-918
[8]   MECHANICS OF SEQUENCE-DEPENDENT STACKING OF BASES IN B-DNA [J].
CALLADINE, CR .
JOURNAL OF MOLECULAR BIOLOGY, 1982, 161 (02) :343-352
[9]   STRUCTURE OF A B-DNA DODECAMER .2. INFLUENCE OF BASE SEQUENCE ON HELIX STRUCTURE [J].
DICKERSON, RE ;
DREW, HR .
JOURNAL OF MOLECULAR BIOLOGY, 1981, 149 (04) :761-786
[10]   Two distinct modes of protein-induced bending in DNA [J].
El Hassan, MA ;
Calladine, CR .
JOURNAL OF MOLECULAR BIOLOGY, 1998, 282 (02) :331-343