Single-Round Patterned DNA Library Microarray Aptamer Lead Identification
Abstract
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 01, 2015
- Source ID
- 10.1155/2015/137489
Entities
People
- Jennifer A. Martin
- Jorge L. Chávez
- Joshua A Hagen
- Nancy Kelley-Loughnane
- Peter A Mirau
- Rajesh R Naik
- Yaroslav Chushak
Organizations
- Air Force Office of Scientific Research
- Air Force Research Laboratory
- Henry M. Jackson Foundation for the Advancement of Military Medicine