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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 …
Oblique Packing And Tunable Excitonic Coupling In Dna-Templated Squaraine Rotaxane Dimer Aggregates, Matthew S. Barclay, Christopher K. Wilson, Simon K. Roy, Olga A. Mass, Azhad U. Chowdhury, Jonathan S. Huff, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Ryan D. Pensack
Oblique Packing And Tunable Excitonic Coupling In Dna-Templated Squaraine Rotaxane Dimer Aggregates, Matthew S. Barclay, Christopher K. Wilson, Simon K. Roy, Olga A. Mass, Azhad U. Chowdhury, Jonathan S. Huff, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Ryan D. Pensack
Materials Science and Engineering Faculty Publications and Presentations
When molecules are aggregated such that their excited states form delocalized excitons, their spatial arrangement, or packing, can be coarsely controlled by templating and finely controlled by chemical substitution; however, challenges remain in controlling their packing on intermediate length scales. Here, we use an approach based on mechanically interlocked molecules to promote an elusive oblique packing arrangement in a series of three squaraine rotaxane dimers. We template the squaraine rotaxane dimers using DNA and observe two excitonically split bands of near-equal intensity in their absorption spectra – a distinct signature of oblique packing, validated by theoretical modeling of the experimental …
Boron-Implanted Silicon Substrates For Physical Adsorption Of Dna Origami, Sadao Takabayashi, Shohei Kotani, Juan Flores-Estrada, Elijah Spears, Jennifer E. Padilla, Lizandra C. Godwin, Elton Graugnard, Wan Kuang, William L. Hughes
Boron-Implanted Silicon Substrates For Physical Adsorption Of Dna Origami, Sadao Takabayashi, Shohei Kotani, Juan Flores-Estrada, Elijah Spears, Jennifer E. Padilla, Lizandra C. Godwin, Elton Graugnard, Wan Kuang, William L. Hughes
Materials Science and Engineering Faculty Publications and Presentations
DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alternative, we developed an ion implantation process that tailors the surface potential of silicon substrates to facilitate adsorption of DNA nanostructures …
Determining Hydrodynamic Forces In Bursting Bubbles Using Dna Nanotube Mechanics, Rizal F. Hariadi, Erik Winfree, Bernard Yurke
Determining Hydrodynamic Forces In Bursting Bubbles Using Dna Nanotube Mechanics, Rizal F. Hariadi, Erik Winfree, Bernard Yurke
Materials Science and Engineering Faculty Publications and Presentations
Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean’s environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension–driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates …
Dna-Mediated Excitonic Upconversion Fret Switching, Donald L. Kellis, Sarah M. Rehn, Brittany L. Cannon, Paul H. Davis, Elton Graugnard, Jeunghoon Lee, Bernard Yurke, William B. Knowlton
Dna-Mediated Excitonic Upconversion Fret Switching, Donald L. Kellis, Sarah M. Rehn, Brittany L. Cannon, Paul H. Davis, Elton Graugnard, Jeunghoon Lee, Bernard Yurke, William B. Knowlton
Materials Science and Engineering Faculty Publications and Presentations
Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via Förster resonant energy transfer (FRET), and subsequent charge separation or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy upconversion via upconversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based upconversion has been demonstrated, it suffers from low FRET …