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DNA ligase is a commonly used enzyme in DNA repair and replication. Ligase activity requires Watson-Crick base pairs while mismatches within a duplex are not tolerated efficiently by the enzyme. Therefore, molecules that trigger the formation of stable non-Watson-Crick base pairs would be useful in the study of mismatched DNA ligation. Coralyne and Berberine are small intercalating molecules that bind homo-adenine DNA structures. These molecules bind to DNA by intercalation between two A-A base pairs to form stable secondary structures.
We hypothesize that intercalating molecules could have facilitated the assembly of oligonucleotides in a duplex system containing A:A mismatches. Subsequently, a protein ligase joins the backbones of the substrates aligned alongside a template strand. Our project uses T4 DNA ligase as the coupling reagent. Since enzymes have very complex structures, we investigated the proper oligonucleotide length, the potential interactions between intercalator and T4 DNA ligase, and the optimal reaction environment. Our primary objective in this project is to ascertain whether T4 DNA ligation in the presence of mismatches is enhanced by intercalating molecules.
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Yang, Jing, "LIGATION OF SHORT DNA STRANDS CONTAINING CONSECUTIVE MISMATCH A:A PAIRS" (2012). Senior Projects Spring 2012. 365.
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