Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye

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

doi:10.1063/5.0131795

Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye

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

Micron School of Materials Science and Engineering

Boise State University

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	American English
Article number	035101
Journal	The Journal of Chemical Physics
Volume	158
Issue number	3
DOIs	https://doi.org/10.1063/5.0131795
State	Published - 21 Jan 2023

Keywords

molecular dynamics
dye
flourescence spectrosopy
two-dimensional electronic spectroscopy
density functional theory
DNA nanotechnology
nucleobases

EGS Disciplines

Materials Science and Engineering

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10.1063/5.0131795

Probing DNA Structural Heterogeneity by Identifying ConformationaFinal published version, 8.77 MBLicense: Unspecified

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Barclay, M. S., Chowdhury, A. U., Biaggne, A., Huff, J. S., Wright, N. D., Davis, P. H., Li, L., Knowlton, W. B., Yurke, B., Pensack, R. D., & Turner, D. B. (2023). Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye. The Journal of Chemical Physics, 158(3), Article 035101. https://doi.org/10.1063/5.0131795

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title = "Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye",

abstract = "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.",

keywords = "molecular dynamics, dye, flourescence spectrosopy, two-dimensional electronic spectroscopy, density functional theory, DNA nanotechnology, nucleobases",

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

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doi = "10.1063/5.0131795",

language = "American English",

volume = "158",

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T1 - Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye

AU - Barclay, Matthew S.

AU - Chowdhury, Azhad U.

AU - Biaggne, Austin

AU - Huff, Jonathan S.

AU - Wright, Nicholas D.

AU - Davis, Paul H.

AU - Li, Lan

AU - Knowlton, William B.

AU - Yurke, Bernard

AU - Pensack, Ryan D.

AU - Turner, Daniel B.

PY - 2023/1/21

Y1 - 2023/1/21

N2 - 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.

AB - 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.

KW - molecular dynamics

KW - dye

KW - flourescence spectrosopy

KW - two-dimensional electronic spectroscopy

KW - density functional theory

KW - DNA nanotechnology

KW - nucleobases

UR - https://scholarworks.boisestate.edu/mse_facpubs/533

U2 - 10.1063/5.0131795

DO - 10.1063/5.0131795

M3 - Article

C2 - 36681650

SN - 0021-9606

VL - 158

JO - The Journal of Chemical Physics

JF - The Journal of Chemical Physics

IS - 3

M1 - 035101

ER -

Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye

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