Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

Barclay, Matthew S.; Chowdhury, Azhad U.; Biaggne, Austin; Huff, Jonathan S.; Wright, Nicholas D.; Davis, Paul H.; Li, Lan; Knowlton, William B.; Yurke, Bernard; Pensack, Ryan D.; Turner, Daniel B.

doi:10.1063/5.0131795

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

Journal Article · Wed Jan 18 00:00:00 EST 2023 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/5.0131795· OSTI ID:1909709

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Boise State Univ., ID (United States); Boise State University
Boise State Univ., ID (United States)
Boise State Univ., ID (United States); Center for Advanced Energy Studies, Idaho Falls, ID (United States)

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.

View Accepted Manuscript (DOE)

Research Organization:: Boise State Univ., ID (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division

Grant/Contract Number:: SC0020089

OSTI ID:: 1909709

Alternate ID(s):: OSTI ID: 1909749

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 3 Vol. 158; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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77 NANOSCIENCE AND NANOTECHNOLOGY
DNA nanotechnology
DNA structural heterogeneity
conformational subensembles
cyanine dye Cy5
density functional theory
femtosecond
fluorescence spectroscopy
inhomogeneous broadening
molecular dynamics
molecular dynamics simulations
nucleobases
two-dimensional electronic spectroscopy

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

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