RAPID-SELEX for RNA aptamers.
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new...
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doaj-949f08f9820941de9703269298f9f2952020-11-25T02:06:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01812e8266710.1371/journal.pone.0082667RAPID-SELEX for RNA aptamers.Kylan SzetoDavid R LatulippeAbdullah OzerJohn M PaganoBrian S WhiteDavid ShallowayJohn T LisHarold G CraigheadAptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX approach. High-throughput sequencing of the enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5 × 10(15) sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance.http://europepmc.org/articles/PMC3869713?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kylan Szeto David R Latulippe Abdullah Ozer John M Pagano Brian S White David Shalloway John T Lis Harold G Craighead |
spellingShingle |
Kylan Szeto David R Latulippe Abdullah Ozer John M Pagano Brian S White David Shalloway John T Lis Harold G Craighead RAPID-SELEX for RNA aptamers. PLoS ONE |
author_facet |
Kylan Szeto David R Latulippe Abdullah Ozer John M Pagano Brian S White David Shalloway John T Lis Harold G Craighead |
author_sort |
Kylan Szeto |
title |
RAPID-SELEX for RNA aptamers. |
title_short |
RAPID-SELEX for RNA aptamers. |
title_full |
RAPID-SELEX for RNA aptamers. |
title_fullStr |
RAPID-SELEX for RNA aptamers. |
title_full_unstemmed |
RAPID-SELEX for RNA aptamers. |
title_sort |
rapid-selex for rna aptamers. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2013-01-01 |
description |
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX approach. High-throughput sequencing of the enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5 × 10(15) sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance. |
url |
http://europepmc.org/articles/PMC3869713?pdf=render |
work_keys_str_mv |
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