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Full-Text Articles in Engineering
Pursuing Excitonic Energy Transfer With Programmable Dna-Based Optical Breadboards, Divita Mathur, Sebastián A. Díaz, Niko Hildebrandt, Ryan D. Pensack, Bernard Yurke, Austin Biaggne, Lan Li, Joseph S. Melinger, Mario G. Ancona, William B. Knowlton, Igor L. Medintz
Pursuing Excitonic Energy Transfer With Programmable Dna-Based Optical Breadboards, Divita Mathur, Sebastián A. Díaz, Niko Hildebrandt, Ryan D. Pensack, Bernard Yurke, Austin Biaggne, Lan Li, Joseph S. Melinger, Mario G. Ancona, William B. Knowlton, Igor L. Medintz
Materials Science and Engineering Faculty Publications and Presentations
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex …
Exciton Delocalization In A Fully Synthetic Dna-Templated Bacteriochlorin Dimer, Olga A. Mass, Devan R. Watt, Lance K. Patten, Ryan D. Pensack, Jeunghoon Lee, Daniel B. Turner, Bernard Yurke, William B. Knowlton
Exciton Delocalization In A Fully Synthetic Dna-Templated Bacteriochlorin Dimer, Olga A. Mass, Devan R. Watt, Lance K. Patten, Ryan D. Pensack, Jeunghoon Lee, Daniel B. Turner, Bernard Yurke, William B. Knowlton
Materials Science and Engineering Faculty Publications and Presentations
A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment–protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments—secured by noncovalent bonding to a protein template—enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC …
High-Sensitivity Electronic Stark Spectrometer Featuring A Laser-Driven Light Source, J. S. Huff, K. M. Duncan, C. J. Van Galen, M. S. Barclay, W. B. Knowlton, B. Yurke, P. H. Davis, D. B. Turner, R. J. Stanley, R. D. Pensack
High-Sensitivity Electronic Stark Spectrometer Featuring A Laser-Driven Light Source, J. S. Huff, K. M. Duncan, C. J. Van Galen, M. S. Barclay, W. B. Knowlton, B. Yurke, P. H. Davis, D. B. Turner, R. J. Stanley, R. D. Pensack
Materials Science and Engineering Faculty Publications and Presentations
We report developmental details of a high-sensitivity Stark absorption spectrometer featuring a laser-driven light source. The light source exhibits intensity fluctuations of ∼0.3% over timescales ranging from 1 min to 12 h, minimal drift (≤ 0.1%/h), and very little 1/f noise at frequencies greater than 200 Hz, which are comparable to or better than an arc-driven light source. Additional features of the spectrometer include balanced detection with multiplex sampling, which yielded lower noise in A, and constant wavelength or wavenumber (energy) spectral bandpass modes. We achieve noise amplitudes of ∼7 × 10−4 and ∼6 × 10−6 …
Leveraging Steric Moieties For Kinetic Control Of Dna Strand Displacement Reactions, Drew Lysne, Tim Hachigian, Chris Thachuk, Jeunghoon Lee, Elton Graugnard
Leveraging Steric Moieties For Kinetic Control Of Dna Strand Displacement Reactions, Drew Lysne, Tim Hachigian, Chris Thachuk, Jeunghoon Lee, Elton Graugnard
Materials Science and Engineering Faculty Publications and Presentations
DNA strand displacement networks are a critical part of dynamic DNA nanotechnology and are proven primitives for implementing chemical reaction networks. Precise kinetic control of these networks is important for their use in a range of applications. Among the better understood and widely leveraged kinetic properties of these networks are toehold sequence, length, composition, and location. While steric hindrance has been recognized as an important factor in such systems, a clear understanding of its impact and role is lacking. Here, a systematic investigation of steric hindrance within a DNA toehold-mediated strand displacement network was performed through tracking kinetic reactions of …
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 …
Tunable Electronic Structure Via Dna-Templated Heteroaggregates Of Two Distinct Cyanine Dyes, Jonathan S. Huff, Matthew S. Barclay, Azhad U. Chowdhury, Lance K. Patten, Simon K. Roy, Aaron Sup, Austin Biaggne, Lan Li, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Daniel B. Turner, Ryan D. Pensack
Tunable Electronic Structure Via Dna-Templated Heteroaggregates Of Two Distinct Cyanine Dyes, Jonathan S. Huff, Matthew S. Barclay, Azhad U. Chowdhury, Lance K. Patten, Simon K. Roy, Aaron Sup, Austin Biaggne, Lan Li, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Daniel B. Turner, Ryan D. Pensack
Materials Science and Engineering Faculty Publications and Presentations
Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates─aggregates of chemically distinct dyes─rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to …
Molecular Dynamics Simulations Of Cyanine Dimers Attached To Dna Holliday Junctions, Austin Biaggne, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke, Lan Li
Molecular Dynamics Simulations Of Cyanine Dimers Attached To Dna Holliday Junctions, Austin Biaggne, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday …
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 …
Characterizing Mode Anharmonicity And Huang–Rhys Factors Using Models Of Femtosecond Coherence Spectra, Matthew S. Barclay, Jonathan S. Huff, Ryan D. Pensack, Paul H. Davis, William B. Knowlton, Bernard Yurke, Jacob C. Dean, Paul C. Arpin, Daniel B. Turner
Characterizing Mode Anharmonicity And Huang–Rhys Factors Using Models Of Femtosecond Coherence Spectra, Matthew S. Barclay, Jonathan S. Huff, Ryan D. Pensack, Paul H. Davis, William B. Knowlton, Bernard Yurke, Jacob C. Dean, Paul C. Arpin, Daniel B. Turner
Materials Science and Engineering Faculty Publications and Presentations
Femtosecond laser pulses readily produce coherent quantum beats in transient–absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck–Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang–Rhys factors and anharmonicity values. We discuss the extracted Huang–Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from …
Data-Driven And Multiscale Modeling Of Dna-Templated Dye Aggregates, Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, William B. Knowlton, Bernard Yurke, Lan Li
Data-Driven And Multiscale Modeling Of Dna-Templated Dye Aggregates, Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules …
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 …
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 …
First-Principles Studies Of Substituent Effects On Squaraine Dyes, German Barcenas, Austin Biaggne, Olga A. Mass, Christopher K. Wilson, Ryan D. Pensack, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, Lan Li
First-Principles Studies Of Substituent Effects On Squaraine Dyes, German Barcenas, Austin Biaggne, Olga A. Mass, Christopher K. Wilson, Ryan D. Pensack, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be …
Substituent Effects On The Solubility And Electronic Properties Of The Cyanine Dye Cy5: Density Functional And Time-Dependent Density Functional Theory Calculations, Austin Biaggne, William B. Knowlton, Bernard Yurke, Jeunghoon Lee, Lan Li
Substituent Effects On The Solubility And Electronic Properties Of The Cyanine Dye Cy5: Density Functional And Time-Dependent Density Functional Theory Calculations, Austin Biaggne, William B. Knowlton, Bernard Yurke, Jeunghoon Lee, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of …
Availability: A Metric For Nucleic Acid Strand Displacement Systems, Xiaoping Olson, Shohei Kotani, Jennifer E. Padilla, Natalya Hallstrom, Sara Goltry, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard
Availability: A Metric For Nucleic Acid Strand Displacement Systems, Xiaoping Olson, Shohei Kotani, Jennifer E. Padilla, Natalya Hallstrom, Sara Goltry, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard
Materials Science and Engineering Faculty Publications and Presentations
DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and …
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 …
Enhanced Dna Sensing Via Catalytic Aggregation Of Gold Nanoparticles, Herbert M. Huttanus, Elton Graugnard, Bernard Yurke, William B. Knowlton, Wan Kuang, William L. Hughes, Jeunghoon Lee
Enhanced Dna Sensing Via Catalytic Aggregation Of Gold Nanoparticles, Herbert M. Huttanus, Elton Graugnard, Bernard Yurke, William B. Knowlton, Wan Kuang, William L. Hughes, Jeunghoon Lee
Materials Science and Engineering Faculty Publications and Presentations
A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkagefrom only one target DNA strand, catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gelelectrophoresis was performed to compare DNA hybridization reactions …
Operation Of A Dna-Based Autocatalytic Network In Serum, Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes
Operation Of A Dna-Based Autocatalytic Network In Serum, Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes
Materials Science and Engineering Faculty Publications and Presentations
The potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of DNA-based chemical amplifiers that can operate in bodily fluids. As a first step toward this goal, we have tested the operation of a DNA-based autocatalytic network in human serum and mouse serum. With the addition of sodium dodecyl sulfate to prevent degradation by nuclease activity, the network was found to operate successfully with both DNA and RNA catalysts.
Programmable Periodicity Of Quantum Dot Arrays With Dna Origami Nanotubes, Hieu Bui, Craig Onodera, Carson Kidwell, Yerpeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, William L. Hughes
Programmable Periodicity Of Quantum Dot Arrays With Dna Origami Nanotubes, Hieu Bui, Craig Onodera, Carson Kidwell, Yerpeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, William L. Hughes
Materials Science and Engineering Faculty Publications and Presentations
To fabricate quantum dot arrays with programmable periodicity, functionalized DNA origami nanotubes were developed. Selected DNA staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of AFM images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.
Kinetics Of Dna And Rna Hybridization In Serum And Serum-Sds, Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes
Kinetics Of Dna And Rna Hybridization In Serum And Serum-Sds, Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes
Materials Science and Engineering Faculty Publications and Presentations
Cancer is recognized as a serious health challenge both in the United States and throughout the world. While early detection and diagnosis of cancer leads to decreased mortality rates, current screening methods require significant time and costly equipment. Recently, increased levels of certain micro-ribonucleic acids (miRNAs) in the blood have been linked to the presence of cancer. While blood-based biomarkers have been used for years in cancer detection, studies analyzing trace amounts of miRNAs in blood and serum samples are just the beginning. Recent developments in deoxyribonucleic acid (DNA) nanotechnology and DNA computing have shown that it is possible to …