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Single-Round Patterned DNA Library Microarray Aptamer Lead Identification

A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increas...

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Autores principales: Martin, Jennifer A., Mirau, Peter A., Chushak, Yaroslav, Chávez, Jorge L., Naik, Rajesh R., Hagen, Joshua A., Kelley-Loughnane, Nancy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446497/
https://www.ncbi.nlm.nih.gov/pubmed/26075138
http://dx.doi.org/10.1155/2015/137489
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author Martin, Jennifer A.
Mirau, Peter A.
Chushak, Yaroslav
Chávez, Jorge L.
Naik, Rajesh R.
Hagen, Joshua A.
Kelley-Loughnane, Nancy
author_facet Martin, Jennifer A.
Mirau, Peter A.
Chushak, Yaroslav
Chávez, Jorge L.
Naik, Rajesh R.
Hagen, Joshua A.
Kelley-Loughnane, Nancy
author_sort Martin, Jennifer A.
collection PubMed
description A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface.
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spelling pubmed-44464972015-06-14 Single-Round Patterned DNA Library Microarray Aptamer Lead Identification Martin, Jennifer A. Mirau, Peter A. Chushak, Yaroslav Chávez, Jorge L. Naik, Rajesh R. Hagen, Joshua A. Kelley-Loughnane, Nancy J Anal Methods Chem Research Article A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface. Hindawi Publishing Corporation 2015 2015-05-14 /pmc/articles/PMC4446497/ /pubmed/26075138 http://dx.doi.org/10.1155/2015/137489 Text en Copyright © 2015 Jennifer A. Martin et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Martin, Jennifer A.
Mirau, Peter A.
Chushak, Yaroslav
Chávez, Jorge L.
Naik, Rajesh R.
Hagen, Joshua A.
Kelley-Loughnane, Nancy
Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title_full Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title_fullStr Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title_full_unstemmed Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title_short Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
title_sort single-round patterned dna library microarray aptamer lead identification
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446497/
https://www.ncbi.nlm.nih.gov/pubmed/26075138
http://dx.doi.org/10.1155/2015/137489
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