Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)

被引:63
作者
Lu, XJ
ElHassan, MA
Hunter, CA
机构
[1] UNIV SHEFFIELD,DEPT CHEM,KREBS INST BIOMOLEC RES,SHEFFIELD S3 7HF,S YORKSHIRE,ENGLAND
[2] UNIV CAMBRIDGE,DEPT ENGN,CAMBRIDGE CB2 1PZ,ENGLAND
关键词
DNA conformation; step parameters; base-pair parameters; global helical parameters; base-stacking diagrams;
D O I
10.1006/jmbi.1997.1346
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
We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical parameters. These parameters form a complete set that conforms to the ''Cambridge Accord'' on definitions and nomenclature of nucleic acid structure parameters. Ln addition to the two standard Watson-Crick base-pairs, the program handles mismatched base-pairs and chemically modified bases. An analysis of the sugar-phosphate backbone conformation is included. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated, Structures are classified as one of the four polymorphic families, A/B, Z, W or R, although W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally. (C) 1997 Academic Press Limited.
引用
收藏
页码:668 / 680
页数:13
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