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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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | Journal of Analytical Methods in Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2015/137489 |
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| author | Jennifer A. Martin Peter A. Mirau Yaroslav Chushak Jorge L. Chávez Rajesh R. Naik Joshua A. Hagen Nancy Kelley-Loughnane |
| author_facet | Jennifer A. Martin Peter A. Mirau Yaroslav Chushak Jorge L. Chávez Rajesh R. Naik Joshua A. Hagen Nancy Kelley-Loughnane |
| author_sort | Jennifer A. Martin |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-28cc1a226c57447c99a25be1c9a626df |
| institution | Kabale University |
| issn | 2090-8865 2090-8873 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Analytical Methods in Chemistry |
| spelling | doaj-art-28cc1a226c57447c99a25be1c9a626df2025-02-03T07:23:55ZengWileyJournal of Analytical Methods in Chemistry2090-88652090-88732015-01-01201510.1155/2015/137489137489Single-Round Patterned DNA Library Microarray Aptamer Lead IdentificationJennifer A. Martin0Peter A. Mirau1Yaroslav Chushak2Jorge L. Chávez3Rajesh R. Naik4Joshua A. Hagen5Nancy Kelley-Loughnane6Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USAMaterials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USAHuman Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USAHuman Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USAMaterials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USAHuman Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USAHuman Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USAA 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.http://dx.doi.org/10.1155/2015/137489 |
| spellingShingle | Jennifer A. Martin Peter A. Mirau Yaroslav Chushak Jorge L. Chávez Rajesh R. Naik Joshua A. Hagen Nancy Kelley-Loughnane Single-Round Patterned DNA Library Microarray Aptamer Lead Identification Journal of Analytical Methods in Chemistry |
| 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 |
| url | http://dx.doi.org/10.1155/2015/137489 |
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