DNA Microarrays for Aptamer Identification and Structural Characterization
Abstract
Aptamers are ideal recognition elements, but integrating aptamers onto a sensor platform has two main challenges: (1) aptamers are selected in solution and, as such, their sequences are not optimized to function when immobilized onto a surface, and (2) the initial aptamer selection process is time consuming. Alternatively, oligonucleotide microarrays are attractive tools for aptamer selection and sensor applications and offer several advantages over solution-based selection. First, selection is performed with oligonucleotides immobilized on a substrate, thus binding is not affected by proximity to the sensor surface. Another advantage is that arrays are commercially available and contain upwards of a million unique sequences which can be tested in a single experiment, greatly reducing the time-frame of selection. While the initial library is composed of fewer sequences than solution-based methods, in silico selection provides an optimization step on the starting pool to increase the probability of identifying sequences with strong ligand binding. Therefore, we will improve the efficiency of aptamer selection in a microarray experimental setting using oligonucleotide libraries enriched by pre-screening the potential landscape of binders in silico. This work focuses on identification of specific, high-affinity binders for target molecules including biomarkers and chemical warfare agents for future applications in sensors.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 01, 2012
- Accession Number
- ADA597207
Entities
People
- Jennifer A. Martin
- Jorge C. Benavides
- Joshua A Hagen
- Nancy Kelley-Loughnane
- Yaroslav Chushak
Organizations
- National Research Council