title: Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences.
abstract: We have isolated a cDNA clone after reverse transcription of the genomic RNA of Asibi yellow fever virus whose structure suggests it was formed by self-priming from a 3'-terminal hairpin of 87 nucleotides in the genomic RNA. We have also isolated a clone from cDNA made to Murray Valley encephalitis virus RNA that also appears to have arisen by self-priming from a 3'-terminal structure very similar or identical to that of yellow fever. In addition, 3'-terminal sequencing of the S1 strain of dengue 2 RNA shows that this RNA is also capable of forming a 3'-terminal hairpin of 79 nucleotides. Furthermore, we have identified two 20-nucleotide sequence elements which are present in the 3' untranslated region of all three viruses; one of these sequence elements is repeated in Murray Valley encephalitis and dengue 2 RNA but not in yellow fever RNA. In all three viruses, which represent the three major serological subgroups of the mosquito-borne flaviviruses, the 3'-proximal conserved sequence element, which is found immediately adjacent to the potential 3'-terminal hairpin, is complementary to another conserved domain near the 5' end of the viral RNAs, suggesting that flavivirus RNAs can cyclize (calculated delta G less than -11 kcal; 1 kcal = 4.184 kJ).
authors.affiliation: Division of Biology, California Institute of Technology, Pasadena 91125.
authors.forename: C S
authors.initials: CS
authors.lastname: Hahn
authors.forename: Y S
authors.initials: YS
authors.lastname: Hahn
authors.forename: C M
authors.initials: CM
authors.lastname: Rice
authors.forename: E
authors.initials: E
authors.lastname: Lee
authors.forename: L
authors.initials: L
authors.lastname: Dalgarno
authors.forename: E G
authors.initials: EG
authors.lastname: Strauss
authors.forename: J H
authors.initials: JH
authors.lastname: Strauss
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D003500:Cyclization; D003716:Dengue Virus / Q000235:genetics; D005416:Flavivirus / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral; D015005:Yellow fever virus / Q000235:genetics
chemical_list: D012367:RNA, Viral