Understanding the local conformations of DNA at the level of individual nucleic acid
bases is important for the study of the mechanism of DNA sequence-dependent behavior.
Here we apply linear absorption, circular dichroism (CD), and fluorescence spectroscopy
to study the DNA local base conformation using 6-methyl Isoxanthopterin (6-MI) labeled
DNA. We interpret excitation–emission peak shift (EES) measurements of the 6-MI, both
as a ribonucleotide monophosphate in solution and as a site-specific substituent for guanine
in various DNA constructs, by implementing a simple two-state model. We show that the
spectroscopic properties of the 6-MI probe in DNA can be used to obtain detailed
information about local base conformations and conformational heterogeneity and
fluctuations. Based on these findings, we apply a simple theoretical model to calculate CD
of 6-MI substituted DNA constructs. We find that our model can be used to extract basesequence-
dependent information about the local conformation of the 6-MI probe as
modulated by the local base or base-pair environment. We next apply 6-MI to probe the
ligand insertion of small molecules to duplex DNA, further extending the potential of 6-
MI as a useful reporter of local nucleic acid base conformation. These studies served to
establish a new level of sophistication in qualitatively analyzing 6-MI structural behavior
in terms of local base stacking and unstacking conformations.
v
This dissertation contains previously published and unpublished co-authored
material.
| Identifer | oai:union.ndltd.org:uoregon.edu/oai:scholarsbank.uoregon.edu:1794/24545 |
| Date | 30 April 2019 |
| Creators | Ji, Huiying |
| Contributors | Marcud, Andrew |
| Publisher | University of Oregon |
| Source Sets | University of Oregon |
| Language | en_US |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Rights | All Rights Reserved. |
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