DNA Oligomers Containing Alloxazine in Place of Thymine: Interactions Between DNA Strands

Downing, Jordan Noel

Undergraduate Honors Thesis

DNA Oligomers Containing Alloxazine in Place of Thymine: Interactions Between DNA Strands Public Deposited

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Citeable URL: https://scholar.colorado.edu/concern/undergraduate_honors_theses/s7526f233

Abstract

Single DNA strands combine to form a double helix structure following Watson-Crick base pairing rules, adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). However, by introducing a non-standard base called alloxazine into a DNA sequence, the residue can form both normal Watson-Crick base pairs to adenine, or new connections to another non-canonical residue. The number of bonds alloxazine forms depends on the oxidized/reduced state of the residue. A small amount of literature has focused on the base pairing properties of alloxazine. Our research, however, focused on the reduced form of alloxazine paired with a non-standard residue P (2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one). Very little research has been done on residue P, and, to our knowledge, no research has studied DNA samples containing both alloxazine and residue P. It has been previously established that DNA strands containing one or two alloxazine residues takes on the B-form like canonical (standard) DNA. Our research, however, aimed to seek whether the form of DNA changed when alloxazine base paired with residue P. Using dithionite, both the alloxazine in the DNA strands as well as the oxygen in solution were reduced, as reduced alloxazine preferentially forms hydrogen bonds with residue P. Using spectroscopy, we compared the Tm (melting temperature) values of DNA containing standard base pairs, alloxazine, residue P, and/or dithionite. This research provides important information in the fields of biotechnology and robotics. By controlling the interactions between DNA bases, the ability of molecular nanorobots to accomplish specific goals in molecular interactions and personalized medicine is far more achievable.

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