title: Structural and combinatorial constraints on base pairing in large nucleotide sequences.
abstract: In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the phi X 174 phage with over 5300 bases are discussed in the accompanying paper.
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003201:Computers; D004277:DNA, Single-Stranded; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012313:RNA; D012333:RNA, Messenger; D012343:RNA, Transfer
chemical_list: D004277:DNA, Single-Stranded; D012333:RNA, Messenger; D012313:RNA; D012343:RNA, Transfer