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Needle in the Haystack – DNA Aptamer Selection and Data Science Needs

February 10, 2021 at 11:00 AM to 12:00 PM

Data Science Distinguished Speaker Seminar Series  

Tile: Needle in the Haystack – DNA Aptamer Selection and Data Science Needs
Presented by: Dr. Maria DeRosa
Format: Online via Zoom

Abstract: Aptamers are short DNA or RNA-based molecular affinity agents that can form the basis of a variety of applications such as biosensors, drug delivery systems, and smart materials. Interest in these molecules stems from their remarkable ability to bind with high affinity and specificity to all sorts of targets, spanning from small organic molecules, to proteins or protein complexes, to the surfaces of viruses and entire cells. Aptamers are identified via a screening experiment known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). An initial pool of randomized oligonucleotides, presumably containing sequences with favorable structure for interacting with the target, are screened against the molecule of interest and binders are partitioned from non-binders in a series of selection rounds. High throughput sequencing of the enriched libraries and bioinformatics analysis yields a few hits that are characterized for their binding properties and may or may not move on to applications. While the experimental procedure of SELEX is well established and has undergone many optimizations, there remains a gap in our ability to mine the rich sequence data that is generated in these experiments. The goal of this presentation is to give an overview of aptamers, their discovery, and their potential applications, and to start a discussion on how data science can enable the growth of aptamer science.

About the Speaker: Dr. Maria DeRosa is a Full Professor in the Department of Chemistry at Carleton University. Her research examines a family of synthetic nucleic acids known as aptamers that can fold into 3D nanoscale structures capable of binding tightly to a specific molecular target. Her group is focused on developing a better understanding of how these systems work and using this information to design useful nanotechnology, such as biosensors, components for nanomedicine, or smart delivery devices. This research takes place in the LADDER (Laboratory for Aptamer Discovery and Development of Emerging Research), a facility funded jointly by the Canada Foundation for Innovation (CFI) Leaders Opportunity Fund and the Ontario Research Fund. Dr. DeRosa received her BSc and PhD in Chemistry from Carleton University in 1999 and 2003, respectively, and was awarded an Natural Sciences and Engineering Council of Canada (NSERC) Postdoctoral Fellowship to do research at the California Institute of Technology from 2004-2005. In 2005, she returned to Carleton as a faculty member in the Chemistry Department and the Institute of Biochemistry. She was a recipient of the John Charles Polanyi Research Award for new researchers in 2006, an Ontario Early Researcher Award in 2010, and a Capital Educators Award in 2015.

Seminar Moderator: Dr. Tracey P. Lauriault, Associate Professor, Critical Media and Big Data, School of Journalism and Communication, Carleton University

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