| Description | A Nonevolutionary Screening Approach for DNA Aptamers
Abstract:
Oligonucleotide aptamers are single-stranded sequences that exhibit high affinity and specificity for a particular non-nucleotide target. To date, aptamer studies typically entail (1) an evolutionary-based screening approach and (2) a focus on biological, non-nucleotide targets such as proteins. This evolutionary screening approach called "Systematic Evolution of Ligands by Exponential Enrichment" (SELEX) employs a pool of approximately 1015 random sequences which is continuously enriched with amplified copies of “winning” sequences or adsorbates from prior selection rounds. SELEX has revolutionized the discovery of numerous DNA and RNA-based aptamers for a variety of targets and dominated the field for over two decades as a screening approach; however, SELEX itself is a labor-intensive process with pitfalls such as its propensity to introduce amplification-based contaminants and bias into the screening library. Here, we have developed a nonevolutionary screening approach to identify single-stranded DNA aptamers for a model material target, namely gold. Following aptamer selection against our gold-based target (e.g. planar crystalline gold, gold nanospheres, gold nanorods) we then evaluate sequences to identify base segment consensus as well as secondary structure elements such as hairpins, internal loops, and multi-branched loops to reveal any shared structural patterns among identified aptamer sequences for a given gold target. Lastly, in a separate post-screening assay, we rank our aptamer sequences in terms of their frequency as a bound species using next generation sequencing. As aptamers continue to be pursued as potential ligands or capture agents in the broader community, we continue to adapt our unconventional screening approach to hopefully enable faster and easier aptamer identification for a rich range of challenging biological targets as well as infrequently studied material targets. Bio:
Valeria Milam received her B.S. in Materials Science and Engineering with Honors from the University of Florida in 1993. She specialized in metallurgy and also received a minor in Portuguese. For her doctoral studies at UIUC, she explored the phase behavior, structure and properties of nanoparticle-microsphere suspensions and reported a novel colloidal stabilization mechanism called nanoparticle “haloing.” Her postdoctoral work at the University of Pennsylvania focused on DNA-mediated colloidal assembly. She joined the faculty at Georgia Tech in July 2004 as an assistant professor in the School of Materials Science & Engineering and was promoted to associate professor in July 2011. Current research efforts in the Milam group focus on oligonucleotides (1) as isothermal colloidal assembly and disassembly tools and (2) as synthetic ligands called aptamers that bind in a strong, but noncovalent manner to nonnucleotide targets. Her honors include a Georgia Cancer Coalition Distinguished Scholar Award, CETL/BP Teaching Award, AFRL Summer Faculty Fellowship, NSF CAREER, and 3M Nontenured Faculty Award. Molecular Engineering and Sciences Seminar Series This weekly seminar brings together students, faculty and invited guests from various disciplines across campus to explore current trends in molecular engineering and nanotechnology. It is a forum for active interdisciplinary discussions. These talks are open to the public and attract a diverse audience of students and faculty. |
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