[The role of structural elements in dimerization of RNA fragments in avian retroviruses].
The slipped loop structure, earlier identified as an unusual DNA structure, was found to be a possible element of the RNA folding. In order to experimentally test this suggestion, model oligoribonucleotides capable of forming the SLS were synthesized. Treatment of the oligoribonucleotides with nuclease S1 and RNases specific for single- and double-stranded RNA demonstrated the steric possibility of SLS formation. To determine the possible functional role of SLS-RNA, various naturally occurring RNAs were screened in silico. Among the most interesting findings were dimerization initiation sites of avian retroviral genomic RNAs. Analysis of RNA from 31 viruses showed that formation of the intermolecular SLS during RNA dimerization is theoretically possible, competing with the formation of an alternative hairpin structure. Identification of the secondary structure of selected RNA dimers employing nuclease digestion techniques as well as covariance analysis of the retroviral RNA dimerization initiation site sequences were used to show that the alternative conformation (loop-loop interaction of two hairpins) is the most preferred. Alternative structures and conformational transitions in RNA dimerization mechanisms in avian retroviruses are discussed.
Beniaminov
A D
AD
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia. benson@imb.ac.ru
Ul'ianov
N B
NB
Samokhin
A B
AB
Ivanov
V I
VI
Doux
J
J
Miniat
E E
EE
D001355:Alpharetrovirus / Q000235:genetics*; D001483:Base Sequence; D019281:Dimerization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D012260:Ribonucleases / Q000737:chemistry / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000737:chemistry / Q000378:metabolism
D012367:RNA, Viral; D012260:Ribonucleases; D015719:Single-Strand Specific DNA and RNA Endonucleases