Sequence and secondary structural analysis of a novel class of RNA aptamers that inhibit reverse transcriptase
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[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] RNA aptamers are synthetic RNAs selected for their ability to bind a molecular target. Reverse Transcriptase (RT) is the major target of antiretroviral therapy used in the treatment of HIV. RNA aptamers were selected to bind to RT of HIV-1 subtype B. Previous work showed aptamers from this selection inhibited various RT enzymatic activities, and have also been shown to inhibit viral replication in cellular assays. Most of the aptamers from this selection have predicted pseudoknot structures. The aptamers were classified into Pseudoknot families. Family 1 Pseudoknots (F1Pk) have a conserved UCCG sequence in stem one. Family 2 Pseudoknots (F2Pk) aptamers have CYGG (Y is pyrimidine either C or U). Aptamer secondary structural families are correlated with inhibitory behavior. F2Pk aptamers inhibit a broader range of RT subtypes compared to F1Pk. In the present work we present results of a screen into the inhibitory behavior of a novel family of anti RT aptamer from a previously well- studied pool. We found a group of aptamers that inhibit RT from subtype B very well and have novel secondary structure. These aptamers fold into stem loops with a highly conserved UCAA bulge. Aptamers in the UCAA family inhibit RT very well in primer extension assays and have IC50 values as low as 1.6nM. This work highlights the diversity of RNA secondary structures that are able to bind to a single target.
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