title: 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.
authors.affiliation: Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA ; The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Martin
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Mirau
authors.affiliation: Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA ; The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Chushak
authors.affiliation: Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA ; UES Inc., 4401 Dayton-Xenia Road, Dayton, Dayton, OH 45433, USA.
authors.forename: Jorge L
authors.initials: JL
authors.lastname: Chávez
authors.affiliation: Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA.
authors.forename: Rajesh R
authors.initials: RR
authors.lastname: Naik
authors.affiliation: Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Hagen
authors.affiliation: Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Kelley-Loughnane