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Full-Text Articles in Engineering
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was …
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
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
Materials Science and Engineering Faculty Publications and Presentations
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 …