Author ORCID Identifier


Date of Award


Degree Type


Degree Name

Master of Science (MS)



First Advisor

Markus Germann

Second Advisor

Gregory Poon

Third Advisor

W. David Wilson


Ribonucleotide inclusion (rNMP) is the most prevalent form of DNA damage. The incorporation of a single RNP impacts the local structure and dynamics of the double-stranded DNA. Our previous work has shown that for an rG intrusion, the perturbation is strongly on the flanking nucleotide sequences. We have prepared a series of duplexed DNA oligonucleotides all containing a single rG or rC inclusion in different flanking sequence environments for enzymatic and structural studies. For the rG DNA substrates I have examined all possible nearest neighbor flanking sequence combinations. It was found that the reaction-efficiency-with RNase HII strongly depends on the flanking sequence by an up to 20-fold difference. NMR analysis was performed to determine the effects a ribonucleotide misincorporation has on a replication fork. The proximity of an RNP to a replication fork greatly distorts the fraction-south (fs) characteristics of the sugar residues and immediate phosphodiester backbone.


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