Article
Chemistry, Multidisciplinary
Moustapha A. Y. Nour, Alexandra V. Kulikova, Joseph Wanjohi, Ahmed A. El-Deeb
Summary: This article presents a new method for RNA cleavage using DNAzyme threshold gates, which can accurately distinguish cancer cells from healthy cells by increasing the number of marker recognition modules. It has potential applications in cancer diagnostics and DNA nanorobots.
Article
Chemistry, Multidisciplinary
Cuizheng Zhang, Victoria E. Paluzzi, Ruojie Sha, Natasha Jonoska, Chengde Mao
Summary: This article demonstrates the feasibility of implementing logic gates, the basic computation operations, in large ensembles of engineered 3D DNA crystals. The outputs are observed through the formation of macroscopic crystals, pointing to a new direction for constructing complex 3D crystal architectures and DNA-based biosensors with easy readouts.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Mike Filius, Sung Hyun Kim, Ivo Severins, Chirlmin Joo
Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.
Article
Chemistry, Multidisciplinary
Aaron T. Blanchard, Zi Li, Elizabeth C. Duran, Catherine E. Scull, J. Damon Hoff, Keenan R. Wright, Victor Pan, Nils G. Walter
Summary: DNA-based FluoroCubes were developed as a solution to photobleaching in fluorescence microscopy. These compact FluoroCubes, coupled with up to 6 fluorescent dyes, exhibit enhanced photostability up to 50 times and emit a higher number of photons up to 40 times compared to single dyes. The study addresses the mechanism behind the improved photostability and confirms the compatibility of FluoroCubes with FRET and dark quenching applications.
Article
Chemistry, Multidisciplinary
Divita Mathur, Katherine E. Rogers, Sebastian A. Diaz, Megan E. Muroski, William P. Klein, Okhil K. Nag, Kwahun Lee, Lauren D. Field, James B. Delehanty, Igor L. Medintz
Summary: DNA nanostructures have shown potential in biomedicine, but their intracellular interactions, especially cytosolic stability, are still largely unknown. This study bypassed endocytic uptake to evaluate DNA structural stability directly in live cells, finding that a tetrahedron structure remained intact for at least 1 hour postinjection, while a DNA crosshair degraded rapidly within 20 minutes. The results can inform the design of future DNA nanostructures where programmable degradation rates may be required.
Article
Chemistry, Physical
We-Hyo Soe, Paula de Mendoza, Antonio M. Echavarren, Christian Joachim
Summary: A specifically designed molecule functions as a digital full adder on a gold surface, with 3 inputs and 2 outputs. By interacting with aluminum atoms, classical digits are converted to quantum information, eliminating the need for a solid-state digital full adder cascade-like architecture. The results are influenced by quantum level repulsion and nonlinear magnetic effects intrinsic to the molecule.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Aoze Han, Liwei Zhang, Miaocheng Zhang, Cheng Liu, Rongrong Wu, Yixin Wei, Ronghui Dan, Xingyu Chen, Ertao Hu, Yerong Zhang, Yi Tong, Lei Liu
Summary: In this study, biocompatible memristive devices based on amyloid-gold nanoparticle hybrids were investigated, demonstrating excellent electrical performance, reliable reproducibility, and successful modulation of synaptic behavior. The results offer insights into the utilization of biomolecular materials for advanced memristive devices.
Article
Chemistry, Multidisciplinary
Xiaokang Zhang, Yuan Liu, Bin Wang, Shihua Zhou, Peijun Shi, Ben Cao, Yanfen Zheng, Qiang Zhang, Kirilov Kasabov Nikola
Summary: The rise of DNA nanotechnology is driving the development of molecular security devices and bringing about important changes in information security technology. However, developing a secure and reliable access control strategy remains a challenge.
Article
Multidisciplinary Sciences
Guolong Zhu, Mark Hannel, Ruojie Sha, Feng Zhou, Matan Yah Ben Zion, Yin Zhang, Kyle Bishop, David Grier, Nadrian Seeman, Paul Chaikin
Summary: This study extends the programmability of DNA oligonucleotides to the micrometer-colloidal scale, utilizing optical microscopy and holographic optical tweezers for real-time observations. The research team has designed a chemomechanical device based on DNA origami structures, demonstrating high energy storage/retrieval capability and remote activation. This work paves the way for easily designed micromechanical devices bridging the molecular and colloidal/cellular scales.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Junseong Ahn, Yongrok Jeong, Jimin Gu, Ji-Hwan Ha, Jiwoo Ko, Byeongmin Kang, Soon Hyoung Hwang, Jaeho Park, Sohee Jeon, Hwi Kim, Jun-Ho Jeong, Inkyu Park
Summary: The demand for nanophotonic devices has led to advancements in nanotransfer printing (nTP) technology. However, the current limitations of nTP are due to temperature, pressure, and chemical bonding requirements. In this study, a universal nTP technique was developed that utilizes covalent bonding-based adhesives to improve adhesion, along with plasma-based selective etching to weaken mold-material adhesion. The technique was evaluated on various substrates and successfully used to fabricate nanophotonic devices with high accuracy and reliability.
Article
Multidisciplinary Sciences
Mirna Rofail, Ahmed Younes
Summary: In this paper, DNA computing and reversible computing are combined to propose novel theoretical methods to implement reversible gates and circuits in DNA computers, aiming to enhance the capabilities and functionalities of DNA computers.
Review
Chemistry, Multidisciplinary
Zhixin Zhou, Daoqing Fan, Jianbang Wang, Yang Sung Sohn, Rachel Nechushtai, Itamar Willner
Summary: The reversible reconfiguration of tetrahedra nanostructures from monomer structures into dimer or trimer structures is triggered by K+-ion-stabilized G-quadruplexes or T-A center dot T triplexes. This signal-triggered dimerization/trimerization is used for developing multiplexed miRNA-sensing platforms and intracellular sensing and imaging of miRNAs.
Article
Biochemistry & Molecular Biology
Lydia Olejko, Anushree Dutta, Kosar Shahsavar, Ilko Bald
Summary: In this study, specific G-quadruplex structures formed by reversed human telomeric DNA in the presence of different cations were analyzed using circular dichroism spectroscopy and Forster resonance energy transfer. The results provide important insights into the formation of G-quadruplexes in different environments and the rational design of G-quadruplex-based applications in sensing and nanotechnology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Multidisciplinary
Jianjun Chen, Kexiu Rong
Summary: Colloidal quantum dots (CQDs) have emerged as a powerful platform for solution-processed photonic and optoelectronic devices, offering cost-effective synthesis and impressive photostability. Through novel material and structure engineering, CQD-based devices present appealing alternatives to costly semiconductor products and enable the construction of nanophotonic circuits for various applications. Further developments and challenges in CQD-based nanophotonic devices and circuits are also outlined.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Multidisciplinary
Tatiana A. Molden, Marcella C. Grillo, Dmitry M. Kolpashchikov
Summary: DNA-based computers have the potential to analyze complex biological markers for advancements in diagnostics and disease treatment, but limitations in integrating logic gates have hindered DNA processor development. The newly designed NAND gate in this study avoids stem-loop-folded DNA fragments and allows for reusable operations. Click chemistry was used to crosslink three NAND-gate-forming DNA strands, allowing for efficient production of gates, and two NAND gates can be combined to perform new logic functions.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Xiao Wang, Ruojie Sha, William B. Knowlton, Nadrian C. Seeman, James W. Canary, Bernard Yurke
Summary: A chiral dimer of an organic semiconductor was created by assembling an octamer of polyaniline with DNA. The dimer showed easy reconfiguration between its monomeric and dimeric forms. Experimental and theoretical studies were conducted to examine the dimer's geometry and the exciton coupling between its molecules. Protonic doping allowed for easy switching between different electronic states, and the dimer exhibited a Davydov splitting similar to DNA-dye systems with strong transition dipoles. This research provides a possible platform for studying the fundamental properties of organic semiconductors with DNAtemplated assemblies, which have potential applications in artificial light-harvesting systems and excitonic devices.
Article
Chemistry, Physical
Olga A. Mass, Christopher K. Wilson, German Barcenas, Ewald A. Terpetschnig, Olena M. Obukhova, Olga S. Kolosova, Anatoliy L. Tatarets, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee
Summary: This study investigates the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates templated by DNA Holliday Junction. It shows a strong correlation between squaraine hydrophobicity and the strength of excitonic coupling, with dimers of dichloroindolenine squaraine exhibiting the strongest coupling strength. The research provides insights into how dye structures affect excitonic coupling in dye aggregates templated by DNA, offering guidance for the design of exciton-based materials and devices.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Azhad U. Chowdhury, Sebastian A. Diaz, Jonathan S. Huff, Matthew S. Barclay, Matthew Chiriboga, Gregory A. Ellis, Divita Mathur, Lance K. Patten, Aaron Sup, Natalya Hallstrom, Paul D. Cunningham, Jeunghoon Lee, Paul H. Davis, Daniel B. Turner, Bernard Yurke, William B. Knowlton, Igor L. Medintz, Joseph S. Melinger, Ryan D. Pensack
Summary: By altering the spatial configuration of dyes on a DNA template, we can tune the energy transfer and quenching between molecular excitons. We find that heterodimers with different spatial configurations exhibit different optical properties, which is significant for various applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Jake Soares, Anil U. Mane, Devika Choudhury, Steven Letourneau, Steven M. Hues, Jeffrey W. Elam, Elton Graugnard
Summary: In this study, a thermal atomic layer etching (ALE) process for molybdenum disulfide (MoS2) was developed using MoF6 and H2O, which can remove both amorphous and crystalline MoS2 films deposited by atomic layer deposition. This process offers a low-temperature approach for high-volume manufacturing of devices.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
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
Summary: DNA is a re-configurable, biological information-storage unit, but there is still much to learn about its heterogeneous structural dynamics. In this study, femtosecond, two-dimensional electronic spectroscopy is used to probe local conformations in different DNA samples. The analysis reveals a strong excitation-emission correlation in only the double-stranded DNA-Cy5 complex, indicating inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this broadening is caused by a specific conformer found only in the double-stranded DNA-Cy5 complex. These insights will contribute to future studies on DNA's structural heterogeneity.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Nicholas D. Wright, Jonathan S. Huff, Matthew S. Barclay, Christopher K. Wilson, German Barcenas, Katelyn M. Duncan, Maia Ketteridge, Olena M. Obukhova, Alexander I. Krivoshey, Anatoliy L. Tatarets, Ewald A. Terpetschnig, Jacob C. Dean, William B. Knowlton, Bernard Yurke, Lan Li, Olga A. Mass, Paul H. Davis, Jeunghoon Lee, Daniel B. Turner, Ryan D. Pensack, Ryan D. Pensack
Summary: This study characterized the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating electron donating and/or electron withdrawing substituents. The results showed that the introduction of these substituents increased the static dipole moment difference (delta d) while maintaining a large transition dipole moment (mu). However, asymmetrically substituted dyes exhibited a significant nonradiative decay pathway that drastically reduced their excited-state lifetime (tau), indicating the need for strategies such as rigidifying the pi-conjugated network to ensure long tau.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Materials Science, Coatings & Films
Jake Soares, Steven Letourneau, Matthew Lawson, Anil U. Mane, Yu Lu, Yaqiao Wu, Steven M. Hues, Lan Li, Jeffrey W. Elam, Elton Graugnard
Summary: This study investigates the reactions of molybdenum hexafluoride and hydrogen sulfide with metal oxide substrates during nucleation, providing insights into the nucleation mechanism of MoS2. The deposition temperature was found to play a crucial role in film morphology and MoS2 content. These findings contribute to the development of surface preparation techniques for MoS2 deposition and its integration into device manufacturing.
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A
(2022)
Article
Chemistry, Physical
KatelynM. Duncan, Hannah M. Byers, Madaline E. Houdek, Simon K. Roy, Austin Biaggne, Matthew S. Barclay, Lance K. Patten, Jonathan S. Huff, Donald L. Kellis, Christopher K. Wilson, Jeunghoon Lee, Paul H. Davis, Olga A. Mass, Lan Li, Daniel B. Turner, John A. Hall, William B. Knowlton, Bernard Yurke, Ryan D. Pensack
Summary: In this study, the electronic structure and excited-state dynamics of monomers and aggregates of four asymmetric polymethine dyes templated via DNA were characterized. The asymmetric polymethine dye monomers exhibited large transition dipole moments (mu), appreciable static dipole moment differences (Delta d), and long excited-state lifetimes (tau(p)). Dye Dy 754 displayed the strongest propensity for aggregation and exciton delocalization, with promising values of the excitonic hopping parameter (J).
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Tim Hachigian, Drew Lysne, Elton Graugnard, Jeunghoon Lee
Summary: Biosensing using aptamers has gained attention due to their versatility in detecting different analytes in various fields. This study explored the kinetic behavior and performance of modified aptamer transducers (ATs) by altering the aptamer complementary elements (ACEs). The results showed that the ATs' performance correlated moderately with the predictions based on the ACE selection method, providing valuable insights into the dynamics of the duplexed aptamer domain and suggesting a high-throughput approach for developing ATs with improved sensitivity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Drew Lysne, Tim Hachigian, Chris Thachuk, Jeunghoon Lee, Elton Graugnard
Summary: DNA strand displacement networks are crucial to dynamic DNA nanotechnology and are widely used in chemical reaction networks. The precise kinetic control of these networks is important for various applications. Although the effects of factors such as toehold sequence, length, composition, and location are well understood, the impact of steric hindrance in these networks is not fully understood.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Materials Science, Coatings & Films
Jake Soares, Wesley Jen, John D. Hues, Drew Lysne, Jesse Wensel, Steven M. Hues, Elton Graugnard
Summary: New processes for precise high volume fabrication are needed for continual scaling in microelectronics. Area-selective atomic layer deposition (ASALD) can provide self-aligned material patterning and can correct edge placement errors in top-down patterning processes. 2D transition metal dichalcogenides also show potential in scaled microelectronic devices due to their high mobilities and few-atom thickness. In this study, ASALD of MoS2 thin films using MoF6 and H2S precursor reactants is reported, with selective deposition observed on common dielectric materials. The selectivity can be enhanced through atomic layer etching (ALE) steps during MoS2 growth, providing insight into the effectiveness of a supercycle ALD and ALE process.
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A
(2023)
Article
Instruments & Instrumentation
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
Summary: Developmental details of a high-sensitivity Stark absorption spectrometer with a laser-driven light source are reported. The spectrometer exhibits minimal intensity fluctuations, drift, and 1/f noise, with additional features of balanced detection and multiplex sampling. Measurements show low noise amplitudes.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Chemistry, Physical
Nicholas D. Wright, Jonathan S. Huff, Matthew S. Barclay, Christopher K. Wilson, German Barcenas, Katelyn M. Duncan, Maia Ketteridge, Olena M. Obukhova, Alexander I. Krivoshey, Anatoliy L. Tatarets, Ewald A. Terpetschnig, Jacob C. Dean, William B. Knowlton, Bernard Yurke, Lan Li, Olga A. Mass, Paul H. Davis, Jeunghoo Lee, Daniel B. Turner, Ryan D. Pensack
Summary: Molecular (dye) aggregates are a materials platform of interest in various fields, and this study characterizes the properties of certain asymmetric squaraine dyes and suggests strategies to enhance their interaction.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Katelyn M. Duncan, Donald L. Kellis, Jonathan S. Huff, Matthew S. Barclay, Jeunghoon Lee, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton, Ryan D. Pensack
Summary: This study investigates the electronic structure and excited-state dynamics of DNA-templated molecular aggregates. The researchers found a new nonradiative decay pathway in the dimers, which may facilitate singlet fission. This is of great significance in the fields of energy conversion and quantum information.
