NUPARM AND NUCGEN - SOFTWARE FOR ANALYSIS AND GENERATION OF SEQUENCE-DEPENDENT NUCLEIC-ACID STRUCTURES

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids , by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and r ise) have been defined, which use geometry and coordinates of two succ essive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide step s. Intra basepair parameters, propeller, buckle, opening and the C6... C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation ill each of th e nucleotides. NUPARM can be used to analyse both DNA and RNA structur es, with single as well as double stranded helices. The NUCGEN softwar e generates double helical models with the backbone fixed in B-form DN A, but with appropriate modifications in the input data, it can also g enerate A-form DNA ar rd RNA duplex structures.