Open Access. Powered by Scholars. Published by Universities.®
- Discipline
Articles 1 - 7 of 7
Full-Text Articles in Entire DC Network
Tuning Between Quenching And Energy Transfer In Dna-Templated Heterodimer Aggregates, Azhad U. Chowdhury, Jonathan S. Huff, Matthew S. Barclay, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Ryan D. Pensack
Tuning Between Quenching And Energy Transfer In Dna-Templated Heterodimer Aggregates, Azhad U. Chowdhury, Jonathan S. Huff, Matthew S. Barclay, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Ryan D. Pensack
Materials Science and Engineering Faculty Publications and Presentations
Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble “transverse” and “adjacent” heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting …
Influence Of Hydrophobicity On Excitonic Coupling In Dna-Templated Indolenine Squaraine Dye Aggregates, Olga A. Mass, Christopher K. Wilson, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee
Influence Of Hydrophobicity On Excitonic Coupling In Dna-Templated Indolenine Squaraine Dye Aggregates, Olga A. Mass, Christopher K. Wilson, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee
Materials Science and Engineering Faculty Publications and Presentations
Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA …
Exciton Delocalization And Scaffold Stability In Bridged Nucleotide-Substituted, Dna Duplex-Templated Cyanine Aggregates, Simon K. Roy, Olga A. Mass, Donald L. Kellis, Christopher K. Wilson, John A. Hall, Bernard Yurke, William B. Knowlton
Exciton Delocalization And Scaffold Stability In Bridged Nucleotide-Substituted, Dna Duplex-Templated Cyanine Aggregates, Simon K. Roy, Olga A. Mass, Donald L. Kellis, Christopher K. Wilson, John A. Hall, Bernard Yurke, William B. Knowlton
Electrical and Computer Engineering Faculty Publications and Presentations
Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, …
Customizable Aptamer Transducer Network Designed For Feed-Forward Coupling, Tim Hachigian, Drew Lysne, Elton Graugnard, Jeunghoon Lee
Customizable Aptamer Transducer Network Designed For Feed-Forward Coupling, Tim Hachigian, Drew Lysne, Elton Graugnard, Jeunghoon Lee
Materials Science and Engineering Faculty Publications and Presentations
Solution-based biosensors that utilize aptamers have been engineered in a variety of formats to detect a range of analytes for both medical and environmental applications. However, since aptamers have fixed base sequences, incorporation of aptamers into DNA strand displacement networks for feed-forward signal amplification and processing requires significant redesign of downstream DNA reaction networks. We designed a novel aptamer transduction network that releases customizable output domains, which can then be used to initiate downstream strand displacement reaction networks without any sequence redesign of the downstream reaction networks. In our aptamer transducer (AT), aptamer input domains are independent of output domains …
Excited-State Lifetimes Of Dna-Templated Cyanine Dimer, Trimer, And Tetramer Aggregates: The Role Of Exciton Delocalization, Dye Separation, And Dna Heterogeneity, Jonathan S. Huff, Daniel B. Turner, Olga A. Mass, Lance K. Patten, Christopher K. Wilson, Simon K. Roy, Matthew S. Barclay, Bernard Yurke, William B. Knowlton, Paul H. Davis, Ryan D. Pensack
Excited-State Lifetimes Of Dna-Templated Cyanine Dimer, Trimer, And Tetramer Aggregates: The Role Of Exciton Delocalization, Dye Separation, And Dna Heterogeneity, Jonathan S. Huff, Daniel B. Turner, Olga A. Mass, Lance K. Patten, Christopher K. Wilson, Simon K. Roy, Matthew S. Barclay, Bernard Yurke, William B. Knowlton, Paul H. Davis, Ryan D. Pensack
Materials Science and Engineering Faculty Publications and Presentations
DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the …
Landscape Of Transcription In Human Cells, Jainab Khatun
Landscape Of Transcription In Human Cells, Jainab Khatun
Biology Faculty Publications and Presentations
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, …
A Genetic Algorithms Approach To Non-Coding Rna Gene Searches, Jennifer A. Smith
A Genetic Algorithms Approach To Non-Coding Rna Gene Searches, Jennifer A. Smith
Electrical and Computer Engineering Faculty Publications and Presentations
A genetic algorithm is proposed as an alternative to the traditional linear programming method for scoring covariance models in non-coding RNA (ncRNA) gene searches. The standard method is guaranteed to find the best score, but it is too slow for general use. The observation that most of the search space investigated by the linear programming method does not even remotely resemble any observed sequence in real sequence data can be used to motivate the use of genetic algorithms (GAs) to quickly reject regions of the search space. A search space with many local minima makes gradient decent an unattractive alternative. …