Local Nucleic Acid Base Conformation Study by Guanine Fluorescent Analogue 6- Methyl Isoxanthopterin (6-MI) Labeled DNA
Datum
2019-04-30
Autor:innen
Zeitschriftentitel
ISSN der Zeitschrift
Bandtitel
Verlag
University of Oregon
Zusammenfassung
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This dissertation contains previously published and unpublished co-authored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.
Beschreibung
Schlagwörter
Fluorescence spectroscopy, Local base conformation of DNA, Theoretical circular dichroism calculation