Article
Optics
Bashir Fotouhi, Vahid Faramarzi, Vahid Ahmadi
Summary: We propose a new DNA sequencing concept based on nonradiative Forster resonant energy transfer (FRET) from a donor quantum dot (QD) to an acceptor molecule. The FRET mechanism combined with the nanopore-based DNA translocation is suggested as a novel concept for sequencing DNA molecules. The method shows high sensitivity to DNA and can determine unknown DNA nucleobases based on the signal-to-noise ratio.
Article
Chemistry, Physical
Haoyang Li, Simin Cao, Sanjun Zhang, Jinquan Chen, Jianhua Xu, Jay R. Knutson
Summary: Ultrafast Forster Resonance Energy Transfer (FRET) between tyrosine (Tyr) and tryptophan (Trp) residues in monellin protein was investigated using picosecond and femtosecond time-resolved fluorescence spectroscopy. The energy transfer between Tyr and Trp in monellin was observed at certain excitation wavelengths, causing changes in emission spectra and indicating excited state reactions. This FRET signature may overlap with conventional patterns in heterogeneous systems, resulting in mixed spectra showing both positive and negative sides.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Bei Liu, Orrin J. Stone, Michael Pablo, J. Cody Herron, Ana T. Nogueira, Onur Dagliyan, Jonathan B. Grimm, Luke D. Lavis, Timothy C. Elston, Klaus M. Hahn
Summary: The approach utilizes binder/tag to study the conformation of individual proteins during single particle tracking in living cells, allowing for the tracking of protein trajectory and conformation, and providing highly specific biosensors.
Article
Chemistry, Analytical
Tai Ye, Dongdong Zhu, Liling Hao, Min Yuan, Hui Cao, Xiuxiu Wu, Fengqin Yin, Fei Xu
Summary: By adjusting the programmable aptamer density on the surface of gold nanoparticles, kanamycin fluorescence aptasensors were created, which showed a low detection limit and good recovery in milk samples. This surface density regulation strategy holds promise in other aptamer-based interfacial recognition and sensing.
Article
Biology
Thomas G. W. Graham, John Joseph Ferrie, Gina M. Dailey, Robert Tjian, Xavier Darzacq
Summary: Single-molecule imaging is a powerful tool for studying biochemical processes in live cells, but tracking single molecules and detecting their interactions simultaneously remains challenging. This study describes a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which allows the detection of protein-protein interactions in live cells using two different labeled protein complexes in proximity.
Article
Biochemistry & Molecular Biology
Boris I. Godoy, Nicholas A. Vickers, Sean B. Andersson
Summary: Single Particle Tracking (SPT) is a powerful method for studying biomolecular dynamics in living cells, revealing trajectories of individual particles and motion model parameters. However, existing algorithms assume constant parameters, while this study proposes an estimation algorithm to determine time-varying parameters in systems that switch between different linear models of motion.
Article
Chemistry, Analytical
Pengfei Zhang, Rui Wang, Zijian Wan, Xinyu Zhou, Guangzhong Ma, Jayeeta Kolay, Jiapei Jiang, Shaopeng Wang
Summary: The article introduces a total internal reflection-based evanescent scattering microscopy technique that can detect single proteins without labeling and provides a high-precision measurement method for protein binding kinetics.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Teliang Zhang, Xueliang Wang, Youjun Zeng, Songfeng Huang, Xiaoqi Dai, Weifu Kong, Qian Liu, Jiajie Chen, Junle Qu, Yonghong Shao
Summary: Surface plasmon resonance microscopy (SPRM) is widely used in biological fields for its high spatial resolution and label-free detection. In this study, a home-built SPRM system based on total internal reflection (TIR) was utilized to study the imaging of a single nanoparticle. By using a ring filter and deconvolution algorithm, the parabolic tail of the nanoparticle image was removed, achieving a spatial resolution of 248 nm. Additionally, specific binding between human IgG antigen and goat anti-human IgG antibody was successfully measured using TIR-based SPRM, demonstrating its capability in imaging sparse nanoparticles and monitoring biomolecular interactions.
Article
Chemistry, Analytical
Xin Xie, Yaoyao Zhang, Lingjun Zhang, Jiangen Zheng, Yingzhou Huang, Huanbao Fa
Summary: Plasmonic metal-organic framework (MOF) nanoparticles exhibit excellent catalytic performance in both liquid and gaseous phases, with the MOF shell showing antioxidant properties in H2O2 solution. The presence of an organic porous nanoshell allows for effective capture of gaseous molecules, leading to plasmon-driven interfacial catalytic reactions only occurring in plasmonic AgNP@ZIF-8 nanoparticles in the gaseous phase.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Frank Mieskes, Evelyn Ploetz, Fabian Wehnekamp, Virgile Rat, Don C. Lamb
Summary: Feedback-based single-particle tracking is a powerful technique for studying particle behavior with high spatiotemporal resolution. This study demonstrates the new modalities available when performing 3D orbital tracking with a second detection channel, including dual-color tracking, tracking interacting particles, and monitoring spectral signature.
Review
Developmental Biology
Alan P. Boka, Apratim Mukherjee, Mustafa Mir
Summary: This article provides an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), covering the basics, motivation, key technologies, and data analysis of SMT experiments. It aims to enable readers to critically analyze single-molecule studies and inspire the application of SMT to their own work by explaining the trade-offs involved in optimizing parameters.
Article
Chemistry, Multidisciplinary
Ju Lu, Shenfei Zong, Zhuyuan Wang, Chen Chen, Yizhi Zhang, Hong Wang, Yiping Cui
Summary: This article introduces a dual-labeled graphene quantum dot-based Forster resonance energy transfer nanoprobe suitable for single-molecule localization microscopy imaging, demonstrating fluorescence intensity fluctuations and excellent blinking behavior under specific excitation conditions, with great potential for super-resolution imaging in cells.
Review
Biochemistry & Molecular Biology
Nitesh Kumar Podh, Sheetal Paliwal, Partha Dey, Ayan Das, Shruti Morjaria, Gunjan Mehta
Summary: Single-molecule imaging in live yeast cells has become a powerful tool for researchers to quantitatively measure cellular activities in real time, with significant progress made in recent years to provide important references for studying biological processes. Different labs have tailored imaging setups and data analysis pipelines to estimate biophysical parameters for various biological processes, reflecting a rich variety of experimental experiences.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Hannah Messenger, Daniel Madrid, Anuj Saini, Lydia Kisley
Summary: This study focuses on single-molecule fluorescence microscopy using turn-on dyes to investigate interfaces relevant to analytical and bioanalytical chemistry. Monte Carlo simulations are used to determine the influence of dye diffusion on accurately locating reaction sites. The findings demonstrate the importance of modeling in designing single-molecule microscopy experiments to understand interfaces in analytical chemistry.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Sina Jazani, Lance W. Q. Xu, Ioannis Sgouralis, Douglas P. Shepherd, Steve Presse
Summary: Single-molecule tracking provides new insights into biology, but observing trajectories and interactions in dense environments is challenging. This study proposes a computational tool for tracking multiple fluorescent molecules in three dimensions at submillisecond or faster time scales, addressing the need for high-speed tracking in densely labeled environments.
Article
Multidisciplinary Sciences
Connor J. Thompson, Vinh H. Vu, Deborah E. Leckband, Daniel K. Schwartz
Summary: Cadherin transmembrane proteins play important roles in intercellular adhesion and tissue morphogenesis. Experimental evidence shows mutual cooperativity between lateral cis and adhesive trans interactions, leading to the assembly of large intermembrane junctions. This cooperativity is primarily due to allostery and provides insights into how weak cis and trans interactions work together to create strong cell adhesions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Raphael Sarfati, Christopher P. Calderon, Daniel K. Schwartz
Summary: Although there is no comprehensive theory to describe transport behavior within porous environments, experimental results show that the diffusion of nanoparticles is more effective in fluctuating porous matrices compared to static ones, due to the enhancing effects of matrix fluctuations on the diffusion coefficient and cooperative gate-opening motions between matrix particles and nanoparticle probes.
Article
Chemistry, Analytical
Daniel F. Kienle, Daniel K. Schwartz
Summary: In this study, the diffusion of small charged molecules in anisotropic polyelectrolyte multilayers was tracked in three dimensions using single-molecule fluorescence localization and Forster resonance energy transfer. The results showed a significantly slower diffusion in the surface-normal direction compared to lateral diffusion, which was hypothesized to be related to the periodic distribution of charge in the multilayer.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Multidisciplinary
Andres F. Chaparro Sosa, Riley M. Bednar, Ryan A. Mehl, Daniel K. Schwartz, Joel L. Kaar
Summary: The efficiency of ligation reactions plays a crucial role in maintaining the activity and structure of enzymes on solid surfaces. Limiting enzyme exploration of surfaces may overcome the challenge of enzyme inactivation during integration. Increasing the rate constant of surface ligation reactions can enhance the probability of immobilization with reactive surface sites.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Nanoscience & Nanotechnology
Hector Sanchez-Moran, James S. Weltz, Daniel K. Schwartz, Joel L. Kaar
Summary: "The long-term goal of biotechnology is to develop design rules for stabilizing enzymes when immobilized to materials. By investigating the stabilization of lipases immobilized on PEGMA and SBMA copolymer brush surfaces, it was found that the stability of the lipases at elevated temperatures depended on the fraction of PEGMA in the brush layer. This understanding can lead to the rational tuning of enzyme-material interfaces for reliable ruggedization of enzymes under extreme conditions."
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Physical
Zachary Blanchette, Jing Zhang, Sadegh Yazdi, Michael B. Griffin, Daniel K. Schwartz, J. Will Medlin
Summary: Modification of supported metal catalysts with self-assembled monolayers (SAMs) can improve site accessibility and reactivity. SAM-first catalysts show higher rates and similar TOF and selectivity compared to metal-first catalysts. Reduced site blocking and smaller particle sizes contribute to the improved activity of SAM-first catalysts.
CATALYSIS SCIENCE & TECHNOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Albert Velasco Abadia, Katie M. Herbert, Timothy J. White, Daniel K. Schwartz, Joel L. Kaar
Summary: This study reports the fabrication of biocatalytic liquid crystal elastomers (LCEs) that respond to urea and undergo shape transformations. By immobilizing urease within chemically responsive LCE networks, the presence of urea triggers the generation of ammonia, leading to disruption of the supramolecular network and reduction of liquid crystalline order in the films. This reduction in order results in a strain response at the macroscopic level. Local control of the mechanical response is achieved by spatially patterning the enzyme on the film surface.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Connor J. Thompson, Daniel F. Kienle, Daniel K. Schwartz
Summary: This study investigates the surface diffusion of proteins confined between two symmetric lipid bilayer membranes in a planar constrained microenvironment. The results show that the surface diffusion varies non-monotonically with confinement height, reaching a maximum at around 750 nm. Simulations validate the experimental findings and suggest that confinement enhancement of surface diffusion is limited to cases where the adsorbate exhibits weak surface sticking.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Nanoscience & Nanotechnology
Ezra A. Baghdady, Daniel K. Schwartz, Will Medlin
Summary: This article investigates the influence of Pd/silica catalyst surface wettability on the rate of hydrocarbon reduction with formic acid. The study finds that modifying the surface with short chain alkyl silanes increases the reaction rate, while modifying it with sulfonate and C18 alkyl silanes decreases the reaction rate. The article discusses the relationship between catalyst interfacial activity and the relative affinity of reagents to Pd active sites. Furthermore, the study also discovers that changing the catalyst surface wettability can lead to a transition from a transport-limited to a kinetic-limited reaction regime.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Kaixuan Lyu, Hongbo Chen, Jing Gao, Jing Jin, Hengchong Shi, Daniel K. Schwartz, Dapeng Wang
Summary: Using different timescales for single-molecule tracking, we discovered that the kinetics of protein desorption is more complex than previously thought. We observed a transition in the surface residence time distribution of adsorbed proteins from power law to exponential behavior over a large range of timescales. These findings provide new insights into the complexities of protein adsorption and desorption.
Article
Chemistry, Physical
Benjamin Greydanus, J. Will Medlin, Daniel K. Schwartz
Summary: The adsorption strengths of organic compounds on metal surfaces are crucial for catalytic reactions, but they can be altered by the presence of solvent in liquid-phase reactions. This study investigates the effect of metal composition on binding strengths in a liquid environment by using the motion of active particles in water to probe the adsorption energies of an organic adsorbate on a range of metal surfaces.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Nanoscience & Nanotechnology
Zachary Blanchette, Daniel K. Schwartz, J. Will Medlin
Summary: Controlling reactant adsorption on catalyst surfaces is crucial for reaction activity and selectivity. This study used thiol self-assembled monolayers (SAMs) to control activity and selectivity via steric effects. The successful deposition of homogeneous low-density SAMs on the metal surface was demonstrated, and the SAM density significantly influenced reaction activity and selectivity. The low-density SAMs improved reaction rates and showed potential for size-selective reaction control.
ACS APPLIED NANO MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Evan A. Bisirri, Thaiesha A. Wright, Daniel K. Schwartz, Joel L. Kaar
Summary: Protein-polymer conjugation is a useful approach to improve protein stability and performance, but polymer-polymer interactions can also affect the properties of polymer-modified proteins. This study demonstrates that by adjusting the ratio of polymers, the productivity of lipase can be optimized, although this may lead to a trade-off between activity and stability.
Article
Electrochemistry
Francisco W. S. Lucas, Nathanael C. Ramos, Daniel K. Schwartz, J. Will Medlin, Adam Holewinski
Summary: Thiolate self-assembled monolayers (SAMs) are commonly used to modify surface properties, including catalytic activity. It is shown that irreversible changes to the metal surface, caused by the formation and removal of thiolate SAMs, can lead to significant changes in catalytic properties, regardless of specific interactions with reactants.
ELECTROCHIMICA ACTA
(2023)
Article
Physics, Multidisciplinary
Ohad Vilk, Erez Aghion, Tal Avgar, Carsten Beta, Oliver Nagel, Adal Sabri, Raphael Sarfati, Daniel K. Schwartz, Matthias Weiss, Diego Krapf, Ran Nathan, Ralf Metzler, Michael Assaf
Summary: Anomalous diffusion or transport, characterized by the nonlinear relationship between mean-squared displacement and measurement time, is widely observed in nature. Using data from various empirical systems, a method is employed to detect the individual origins of anomalous diffusion and transport. The method identifies three primary effects: long-range correlations, fat-tailed probability density of increments, and nonstationarity. The decomposition of real-life data allows for nontrivial behavioral predictions and resolves open questions in single-particle tracking and movement ecology.
PHYSICAL REVIEW RESEARCH
(2022)