Nucleolin-G-quadruplex interactions, with an emphasis on genome derived sequences

Fong, Casey
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McGown, Linda Baine
Wang, Xing
Linhardt, Robert J.
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The discovery of new DNA aptamers is an arduous process. The primary approach is the Systematic Evolution of Ligands by Exponential Enrichment (SELEX), where many different DNA sequences are screened against a specific target. These targets can vary in size from small molecules to entire cells. Our lab utilizes a novel genome inspired approach, where potential G-quadruplex forming sequences are identified from chromosomal regions, then incubated with human cell extract and screened for selective protein binding. In the past, our group has examined G-quadruplex forming sequences from the ERBB2, c-MYC, VEGF, and RB proximal promoters. The protein nucleolin (NCL) was found to associate with all of them in vitro and in vivo, and the literature has shown that NCL has the propensity to associate with G-quadruplex forming sequences across the human genome. NCL is a protein of particular interest, as it is found on the cell surface of many cancers but is absent in most normal tissues, making the protein a potential biomarker and drug target. This thesis is concerned with creating and testing recombinant NCL to study its G4 interactions, as well as the preparation of a ChIP-exo Illumina Library to identify all of NCL’s genomic binding sites at high resolution in a BT474 cancer cell line. Hopefully this will lead to the discovery of new potential G4 forming sequences that can serve as NCL targeting aptamers.
In recent years, there has been a growing interest in DNA aptamers for both laboratory and clinical applications, finding uses as biosensors, affinity reagents and pharmaceuticals. Aptamers are single stranded oligonucleotides that exhibit high specificity for a single molecular target through their unique, sequence dependent, secondary structures. Among aptamers, the G-quadruplex has been one of the most prominently featured secondary structures.
May 2017
School of Science
Dept. of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute, Troy, NY
Rensselaer Theses and Dissertations Online Collection
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