Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy-Reference-Cited by-同舟云学术

Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy

Published:2023-04-24 Issue:1 Volume:74 Page:245-265
ISSN:0066-426X
Container-title:Annual Review of Physical Chemistry
language:en
Short-container-title:Annu. Rev. Phys. Chem.

Author:

Marcus Andrew H.¹²³⁴,Heussman Dylan¹²³,Maurer Jack¹²³,Albrecht Claire S.¹²⁴,Herbert Patrick¹²³,von Hippel Peter H.²³

Affiliation:

1. Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon, USA;

2. Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA

3. Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA

4. Department of Physics, University of Oregon, Eugene, Oregon, USA

Abstract

The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded–double-stranded DNA (ssDNA–dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA–dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2dimer probes. With the application of these methods, the (iCy3)2dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein–DNA complex assembly and function.

Publisher

Annual Reviews

Subject

Physical and Theoretical Chemistry,General Chemistry

Link

https://www.annualreviews.org/doi/pdf/10.1146/annurev-physchem-090419-041204

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