STRUCTURE AND CONFORMATION OF HELICAL NUCLEIC-ACIDS - ANALYSIS PROGRAM (SCHNAAP)

We present a new versatile program, SCHNAaP, for the analysis of doubl e-helical nucleic acid structures. The program uses mathematically rig orous and fully reversible procedures for calculating the structural p arameters: the Cambridge University Engineering Department Helix compu tation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical pa rameters. These parameters form a complete set that conforms to the '' Cambridge Accord'' on definitions and nomenclature of nucleic acid str ucture parameters. Ln addition to the two standard Watson-Crick base-p airs, the program handles mismatched base-pairs and chemically modifie d bases. An analysis of the sugar-phosphate backbone conformation is i ncluded. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated, Structures are cl assified as one of the four polymorphic families, A/B, Z, W or R, alth ough W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally. (C) 1997 Academic Press Limited.