Date of Award

2013

Document Type

Honors Thesis (Open Access)

Department

Colby College. Chemistry Dept.

Advisor(s)

Kevin P. Rice

Second Advisor

Julie Millard

Abstract

Recognition of structural features of DNA such as gaps, nicks and abasic sites is critical for many DNA-binding proteins, such as those involved in DNA damage repair. This study explores a novel strategy to model these protein-DNA interactions using phage display. Phage display has been commonly used to identity zinc fingers that bind to DNA sequences, but selection of peptides that binding to specific DNA structures has not been reported in the literature. A phage library of 109 variants was created based on one of three zinc finger domains of the DNA repair protein poly (ADP-ribose) polymerase I. The library, engineered at the DNA level using synthetic oligonucleotides and containing eight randomized codons in the “loop” region of the zinc finger, was cloned into a commercial T7 phagemid vector. Four rounds of selection against an immobilized nicked DNA target were carried out, the last of which resulted in 62% retention of phage. Sequencing of selected phage from this highly enriched library revealed convergence to a single 39-mer peptide, a truncated version of the designed 85-mer zinc finger. This peptide will be purified from transformed bacterial culture and its binding activity will be measured using fluorescence polarization. This project seeks to provide insight into the structure-function relationship of proteins that bind specific DNA structures and could possibly lead to a small peptide with diagnostic or therapeutic applications.

Keywords

genetics, biochemistry, proteins

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