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Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers
RNA aptamers that bind the reverse transcriptase (RT) of human immunodeficiency virus (HIV) compete with nucleic acid primer/template for access to RT, inhibit RT enzymatic activity in vitro, and suppress viral replication when expressed in human cells. Numerous pseudoknot aptamers have been identif...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586799/ https://www.ncbi.nlm.nih.gov/pubmed/23385524 http://dx.doi.org/10.1038/mtna.2012.62 |
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author | Whatley, Angela S Ditzler, Mark A Lange, Margaret J Biondi, Elisa Sawyer, Andrew W Chang, Jonathan L Franken, Joshua D Burke, Donald H |
author_facet | Whatley, Angela S Ditzler, Mark A Lange, Margaret J Biondi, Elisa Sawyer, Andrew W Chang, Jonathan L Franken, Joshua D Burke, Donald H |
author_sort | Whatley, Angela S |
collection | PubMed |
description | RNA aptamers that bind the reverse transcriptase (RT) of human immunodeficiency virus (HIV) compete with nucleic acid primer/template for access to RT, inhibit RT enzymatic activity in vitro, and suppress viral replication when expressed in human cells. Numerous pseudoknot aptamers have been identified by sequence analysis, but relatively few have been confirmed experimentally. In this work, a screen of nearly 100 full-length and >60 truncated aptamer transcripts established the predictive value of the F1Pk and F2Pk pseudoknot signature motifs. The screen also identified a new, nonpseudoknot motif with a conserved unpaired UCAA element. High-throughput sequence (HTS) analysis identified 181 clusters capable of forming this novel element. Comparative sequence analysis, enzymatic probing and RT inhibition by aptamer variants established the essential requirements of the motif, which include two conserved base pairs (AC/GU) on the 5′ side of the unpaired UCAA. Aptamers in this family inhibit RT in primer extension assays with IC(50) values in the low nmol/l range, and they suppress viral replication with a potency that is comparable with that of previously studied aptamers. All three known anti-RT aptamer families (pseudoknots, the UCAA element, and the recently described “(6/5)AL” motif) are therefore suitable for developing aptamer-based antiviral gene therapies. |
format | Online Article Text |
id | pubmed-3586799 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-35867992013-03-06 Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers Whatley, Angela S Ditzler, Mark A Lange, Margaret J Biondi, Elisa Sawyer, Andrew W Chang, Jonathan L Franken, Joshua D Burke, Donald H Mol Ther Nucleic Acids Original Article RNA aptamers that bind the reverse transcriptase (RT) of human immunodeficiency virus (HIV) compete with nucleic acid primer/template for access to RT, inhibit RT enzymatic activity in vitro, and suppress viral replication when expressed in human cells. Numerous pseudoknot aptamers have been identified by sequence analysis, but relatively few have been confirmed experimentally. In this work, a screen of nearly 100 full-length and >60 truncated aptamer transcripts established the predictive value of the F1Pk and F2Pk pseudoknot signature motifs. The screen also identified a new, nonpseudoknot motif with a conserved unpaired UCAA element. High-throughput sequence (HTS) analysis identified 181 clusters capable of forming this novel element. Comparative sequence analysis, enzymatic probing and RT inhibition by aptamer variants established the essential requirements of the motif, which include two conserved base pairs (AC/GU) on the 5′ side of the unpaired UCAA. Aptamers in this family inhibit RT in primer extension assays with IC(50) values in the low nmol/l range, and they suppress viral replication with a potency that is comparable with that of previously studied aptamers. All three known anti-RT aptamer families (pseudoknots, the UCAA element, and the recently described “(6/5)AL” motif) are therefore suitable for developing aptamer-based antiviral gene therapies. Nature Publishing Group 2013-02 2013-02-05 /pmc/articles/PMC3586799/ /pubmed/23385524 http://dx.doi.org/10.1038/mtna.2012.62 Text en Copyright © 2013 American Society of Gene & Cell Therapy http://creativecommons.org/licenses/by-nc-nd/3.0/ Molecular Therapy-Nucleic Acids is an open-access journal published by Nature Publishing Group. This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/ |
spellingShingle | Original Article Whatley, Angela S Ditzler, Mark A Lange, Margaret J Biondi, Elisa Sawyer, Andrew W Chang, Jonathan L Franken, Joshua D Burke, Donald H Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title | Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title_full | Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title_fullStr | Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title_full_unstemmed | Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title_short | Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers |
title_sort | potent inhibition of hiv-1 reverse transcriptase and replication by nonpseudoknot, “ucaa-motif” rna aptamers |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586799/ https://www.ncbi.nlm.nih.gov/pubmed/23385524 http://dx.doi.org/10.1038/mtna.2012.62 |
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