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Ligand-Guided Selection (LIGS):A SELEX Variant to Identify Specific Aptamers Against Cell-surface Markers

November 8, 2017 @ 18:00 - 19:30


Westchester Local Section

Westchester Chemical Society

New York Section of the American Chemical Society





Refreshments   5:30 p.m.   Lecture     6:00 p.m.


Ligand-Guided Selection (LIGS):A SELEX Variant to Identify Specific Aptamers Against Cell-surface Markers


Prabodhika Mallikaratchy, Ph.D.

Assistant Professor of Chemistry

New Science Hall-Office S-4404/Lab S-4401

City University of New York-Lehman College

250 Bedford Park Blvd. West

Bronx, NY 10468


Nucleic Acid Aptamers (NAAs) are a class of molecules with significant potential in developing molecular tools in biomedical applications. Aptamers are selected using a screening method called Systematic Evolution Ligands by EXponential enrichment (SELEX). Recently, a number of SELEX approaches utilizing whole cells to evolve aptamers against cell-surface membrane proteins were introduced. To this end, we reported on a new variant of SELEX termed Ligand-Guided-Selection (LIGS) to identify highly specific aptamers against a predetermined epitope of a cell-surface target. Hallmark of LIGS is rooted in the ability to exploit the evolutionary selection step in SELEX as a strategy to evolve highly specific aptamers. The iterative process in conventional SELEX is designed to outcompete low-affinity binders through a competitive process whereby high affinity binders move on through the selection process. By introducing a naturally occurring stronger, highly specific bivalent binder, for example, an antibody (Ab) interacting with its cognate epitope, LIGS out-competes specific aptamers from a partially enriched SELEX pool against cells expressing the same epitope. Utilizing LIGS we have selected aptamers against membrane bound IgM (mIgM) expressed on B-cells and Cluster of differentiation 3 (CD3) expressed on T-cells. Based on the detailed validation studies conducted using one of the aptamers selected using LIGS, we will show that aptamers identified using LIGS can be optimized into higher affinity variants. In addition, we will show that LIGS generated aptamers show similar specificities to that of the secondary ligand utilized to out-compete the aptamers. Presentation will conclude with a short discussion on ongoing projects aimed at selecting DNA aptamers against CD3 molecule expressed on human T-cells at physiological temperatures.



Dr. Mallikaratchy obtained her undergraduate degree in chemistry from The Institute of Chemistry, Colombo, Sri Lanka in 2000, her M.S. in organic chemistry from the University of Louisiana, Monroe, LA in 2003, and her Ph.D in analytical biochemistry from the Center for Bio-Nano Interface, The University of Florida, Gainsville, FL in 2008. From 2008 to 2012, she was a research fellow at The Memorial Sloan-Kettering Cancer Center, in New York, NY. In 2012, she was appointed as Assistant Professor in the Department of Chemistry, PhD program in Chemistry and Biochemistry, at the Graduate Center of the City University of New York. There, she has worked to lay the groundwork to establish a new method for aptamer selection, resulting in a patent application and two peer-reviewed publications. Concurrently, she established her lab in the Department of Chemistry at Lehman College (CUNY). She has an extensive background in aptamer selection and manipulation of aptamers to develop molecular tools for disease detection and therapy. A number of aptamer selection methods have become available to select aptamers against cell-surface proteins; however, none of these methods has successfully identified aptamers specific to an antigen of a cell-surface receptor at its endogenous level and native conformation. Such precise targeting of known proteins will determine the success of molecular tools used for disease detection and therapy. Therefore, to select aptamers against the predetermined site of a cell-surface receptor in its native state, her group, for the first time, introduced a simple method called Ligand-guided Selection (LIGS), the subject of the current talk. She has received several awards (the 2008 Crow Stasch Awards for excellence in publications, University of Florida Recipient, the 2009 Lauri Strauss Leukemia Research Fellow award, the 2010-12 Lymphoma Research Foundation Research Fellow award, and the 2017 Junior Faculty Research Award-runner-up at CUNY). She is also a member of several professional associations.

 For more information, contact Paul Dillon:
E-Mail PaulWDillon2@hotmail.com

Phone 1-914-393-6940



November 8, 2017
18:00 - 19:30
Event Category:


ACS Paul Dillon


Westchester Community College
75 Grasslands Road
Valhalla, NY 10595 United States
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