Resolving the discrepancies among nucleic acid conformational analyses

被引:82
作者
Lu, XJ [1 ]
Olson, WK [1 ]
机构
[1] Rutgers State Univ, Dept Chem, Wright Rieman Labs, Piscataway, NJ 08854 USA
关键词
nucleic acid conformational analysis; base-pair geometry; dimer step parameters; nucleic acid structure; conflicting rise values;
D O I
10.1006/jmbi.1998.2390
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
Growing interest in understanding the relationship between the global folding of nucleic acids and the sequence-dependent structure of individual base-pair steps has stimulated the development of new mathematical methods to define the geometry of the constituent base-pairs. Several approaches, designed to meet guidelines set by the nucleic acid community, permit rigorous comparative analyses of different three-dimensional structures, as well as allow for reconstruction of chain molecules at the base-pair level. The different computer programs, however, yield inconsistent descriptions of chain conformation. Here we report our own implementation of seven algorithms used to determine base-pair and dimer step parameters. Aside from reproducing the results of individual programs, we uncover the reasons why the different algorithms come to conflicting structural interpretations. The choice of mathematics has only a limited effect on the computed parameters, even in highly deformed duplexes. The results are much more sensitive to the choice of reference frame. The disparate schemes yield very similar conformational descriptions if the calculations are based on a common reference frame. The current positioning of reference frames at the inner and outer edges of complementary bases exaggerates the rise at distorted dimer steps, and points to the need for a carefully defined conformational standard. (C) 1999 Academic Press.
引用
收藏
页码:1563 / 1575
页数:13
相关论文
共 51 条
  • [1] Allen F. H., 1994, STRUCTURE CORRELATIO, V1, P71, DOI DOI 10.1002/9783527616091
  • [2] LEFT-HANDED DNA HELICES
    ARNOTT, S
    CHANDRASEKARAN, R
    BIRDSALL, DL
    LESLIE, AGW
    RATLIFF, RL
    [J]. NATURE, 1980, 283 (5749) : 743 - 745
  • [3] The structure of PurR mutant L54M shows an alternative route to DNA kinking
    Arvidson, DN
    Lu, F
    Faber, C
    Zalkin, H
    Brennan, RG
    [J]. NATURE STRUCTURAL BIOLOGY, 1998, 5 (06) : 436 - 441
  • [4] THE EFFECT OF MATHEMATICS AND COORDINATE SYSTEM ON COMPARABILITY AND DEPENDENCIES OF NUCLEIC-ACID STRUCTURE PARAMETERS
    BABCOCK, MS
    OLSON, WK
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 237 (01) : 98 - 124
  • [5] NUCLEIC-ACID STRUCTURE-ANALYSIS - MATHEMATICS FOR LOCAL CARTESIAN AND HELICAL STRUCTURE PARAMETERS THAT ARE TRULY COMPARABLE BETWEEN STRUCTURES
    BABCOCK, MS
    PEDNAULT, EPD
    OLSON, WK
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 237 (01) : 125 - 156
  • [6] NUCLEIC-ACID STRUCTURE-ANALYSIS - A USERS GUIDE TO A COLLECTION OF NEW ANALYSIS PROGRAMS
    BABCOCK, MS
    PEDNAULT, EPD
    OLSON, WK
    [J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1993, 11 (03) : 597 - 628
  • [7] BANSAL M, 1995, COMPUT APPL BIOSCI, V11, P281
  • [8] INTERACTION OF CLOSED CIRCULAR DNA WITH INTERCALATIVE DYES .I. SUPERHELIX DENSITY OF SV40 DNA IN PRESENCE AND ABSENCE OF DYE
    BAUER, W
    VINOGRAD, J
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1968, 33 (01) : 141 - &
  • [9] THE NUCLEIC-ACID DATABASE - A COMPREHENSIVE RELATIONAL DATABASE OF 3-DIMENSIONAL STRUCTURES OF NUCLEIC-ACIDS
    BERMAN, HM
    OLSON, WK
    BEVERIDGE, DL
    WESTBROOK, J
    GELBIN, A
    DEMENY, T
    HSIEH, SH
    SRINIVASAN, AR
    SCHNEIDER, B
    [J]. BIOPHYSICAL JOURNAL, 1992, 63 (03) : 751 - 759
  • [10] A SELF-CONSISTENT FORMULATION FOR ANALYSIS AND GENERATION OF NON-UNIFORM DNA STRUCTURES
    BHATTACHARYYA, D
    BANSAL, M
    [J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1989, 6 (04) : 635 - 653