Lu X J, El Hassan M A, Hunter C A
Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.
J Mol Biol. 1997 Oct 31;273(3):668-80. doi: 10.1006/jmbi.1997.1346.
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. In 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.
我们展示了一个用于分析双螺旋核酸结构的全新通用程序SCHNAaP。该程序使用数学上严谨且完全可逆的程序来计算结构参数：采用剑桥大学工程系螺旋计算方案（CEHS）来确定局部螺旋参数，并使用类似程序来确定全局螺旋参数。这些参数构成了一套完整的符合核酸结构参数定义和命名法“剑桥协议”的集合。除了两种标准的沃森-克里克碱基对之外，该程序还能处理错配碱基对和化学修饰碱基。程序还包括对糖-磷酸骨架构象的分析。生成了每个二核苷酸步相对于步中点三联体的标准化碱基堆积图。结构被归类为四个多态家族（A/B、Z、W或R）之一，尽管W-DNA和R-DNA（两种假设结构类型）尚未通过实验观察到。
