Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences.
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).
Hahn
C S
CS
Division of Biology, California Institute of Technology, Pasadena 91125.
Hahn
Y S
YS
Rice
C M
CM
Lee
E
E
Dalgarno
L
L
Strauss
E G
EG
Strauss
J H
JH
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
D012367:RNA, Viral