Local Nucleic Acid Base Conformation Study by Guanine Fluorescent Analogue 6- Methyl Isoxanthopterin (6-MI) Labeled DNA
| dc.contributor.advisor | Marcud, Andrew | |
| dc.contributor.author | Ji, Huiying | |
| dc.date.accessioned | 2019-04-30T21:14:12Z | |
| dc.date.available | 2019-04-30T21:14:12Z | |
| dc.date.issued | 2019-04-30 | |
| dc.description.abstract | 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 v This dissertation contains previously published and unpublished co-authored material. | en_US |
| dc.identifier.uri | https://hdl.handle.net/1794/24545 | |
| dc.language.iso | en_US | |
| dc.publisher | University of Oregon | |
| dc.rights | All Rights Reserved. | |
| dc.subject | Fluorescence spectroscopy | en_US |
| dc.subject | Local base conformation of DNA | en_US |
| dc.subject | Theoretical circular dichroism calculation | en_US |
| dc.title | Local Nucleic Acid Base Conformation Study by Guanine Fluorescent Analogue 6- Methyl Isoxanthopterin (6-MI) Labeled DNA | |
| dc.type | Electronic Thesis or Dissertation | |
| thesis.degree.discipline | Department of Chemistry and Biochemistry | |
| thesis.degree.grantor | University of Oregon | |
| thesis.degree.level | doctoral | |
| thesis.degree.name | Ph.D. |
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