title: Molecular modeling and dynamics studies of HIV-1 kissing loop structures.
abstract: Recognition of an RNA loop by another RNA loop is involved in several biological functions. The dimerization of two copies of the HIV-1 genomic RNA is thought to be involved in several steps of the retroviral life cycle. It has been shown that the dimerization of the two HIV-1 RNA genomes is initiated by the so called kissing loop. The 9nt kissing loop consists of a palindromic 6nt sequence that forms Watson-Crick base-pairs at the kissing site in HIV-1. We report the results of our molecular modeling and dynamics studies on two major subtype isolates (MAL and LAI) of HIV-1 kissing loop structures. From our modeling studies, we conclude that the conformation of the loop in the monomer might be closer to the A-RNA-like conformation in order to form an initial kissing structure. This is achieved by the stacking interactions of the bases at the 3' end of the loop and by the intramolecular tertiary interactions of a single linker nucleotide. We discuss the effect of the loop size and the structural limitations on the formation of kissing loop structures. Also, we propose a possible mechanism to convert the kissing loop structure to a stable extended duplex structure without unwinding the stems.
authors.affiliation: Advanced Biomedical Computing Center, SAIC, NCI Frederick, MD 21702, USA. np47@georgetown.edu
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Pattabiraman
authors.forename: Hugo M
authors.initials: HM
authors.lastname: Martinez
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D001482:Base Composition; D020029:Base Pairing; D001483:Base Sequence; D019281:Dimerization; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D006860:Hydrogen Bonding; D007477:Ions; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D012964:Sodium / Q000378:metabolism; D055672:Static Electricity
chemical_list: D007477:Ions; D012367:RNA, Viral; D012964:Sodium