Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element.
We have extracted from a random population of about 10(9) oligodeoxynucleotides a series of 21-mers that are able to bind to a folded DNA 76-mer used as a template for in vitro transcription of the TAR element of the retrovirus HIV-1, by the T7 RNA polymerase. Five aptastrucs, that is, aptamers able to bind to the structure, out of 15 analyzed sequences, share the consensus motif 5'-PyGGG(TG)PyC, complementary in part to a weak double-stranded region of the target. (The parentheses indicate that either T or G is missing in one of these aptastrucs.) A dissociation constant of about 3 microM was evaluated by electrophoretic mobility shift assay for the winner sequence. Interactions between the aptastruc and the target sequences involve more than Watson-Crick base pairing of the consensus octamer. The binding is chemistry dependent. Phosphorothioate oligodeoxyribonucleotides and 2'-O-methyl oligoribonucleotides derived from the selected aptastrucs exhibit a weak if any affinity for the target.
Boiziau
C
C
INSERM U 386, IFR Pathologies Infectieuses, Université Victor Segalen, Bordeaux, France.
Dausse
E
E
Mishra
R
R
Ducongé
F
F
Toulmé
J J
JJ
D001482:Base Composition; D001483:Base Sequence; D016384:Consensus Sequence; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D016376:Oligonucleotides, Antisense / Q000494:pharmacology*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D013698:Templates, Genetic; D014158:Transcription, Genetic / Q000187:drug effects*
D004279:DNA, Viral; D016376:Oligonucleotides, Antisense; D012367:RNA, Viral