A5027424609- Nanopore and Nanochannel Transport Studies
- Advanced biosensing and bioanalysis techniques
- Carbon Nanotubes in Composites
- RNA and protein synthesis mechanisms
- Lipid Membrane Structure and Behavior
- Mechanical and Optical Resonators
- Surfactants and Colloidal Systems
- DNA and Nucleic Acid Chemistry
- vaccines and immunoinformatics approaches
- Molecular Junctions and Nanostructures
- RNA Interference and Gene Delivery
- Chemical Synthesis and Analysis
- SARS-CoV-2 and COVID-19 Research
- Computational Drug Discovery Methods
- Nanoparticle-Based Drug Delivery
- Electrostatics and Colloid Interactions
- RNA Research and Splicing
- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Micro and Nano Robotics
- Atomic and Molecular Physics
- Electron and X-Ray Spectroscopy Techniques
- Advanced Chemical Physics Studies
- RNA regulation and disease
- Enzyme Structure and Function
The University of Texas at El Paso
2016-2025
University of Illinois Urbana-Champaign
2014-2017
University of California, Berkeley
2015
Urbana University
2015
University of Illinois Chicago
2006-2014
Max Planck Institute for Biophysical Chemistry
2013
University of Chicago
2012
New York University
1989-1992
Intercellular communication via chemical signaling proceeds with both spatial and temporal components, but analytical tools, such as microfabricated electrodes, have been limited to just a few probes per cell. In this work, we use nonphotobleaching fluorescent nanosensor array based on single-walled carbon nanotubes (SWCNTs) rendered selective dopamine study its release from PC12 neuroprogenitor cells at resolution exceeding 20,000 sensors This allows the dynamics of release, following K+...
Sulfonated cyclodextrins show nontoxic, broad-spectrum virucidal activity in vitro, ex vivo, and vivo.
Self-assembly of inorganic nanoparticles has been used to prepare hundreds different colloidal crystals, but almost invariably with the restriction that particles must be densely packed. Here, we show non-close-packed nanoparticle arrays can fabricated through selective removal one two components comprising binary superlattices. First, a variety superlattices were prepared at liquid-air interface, including several arrangements previously unknown. Molecular dynamics simulations revealed...
Close-packed nanoparticle monolayers have recently been shown to form mechanically robust, free-standing membranes. We report the first measurements of molecular transport through such ultrathin sheets, self-assembled from dodecanethiol-ligated gold nanocrystals. For aqueous solutions we find filtration coefficients 2 orders magnitude larger than those observed in polymer-based filters, sieving large solutes, and for smaller solutes a pronounced dependence rejection on being charged. These...
Noncovalent interactions between single-stranded DNA (ssDNA) oligonucleotides and single wall carbon nanotubes (SWNTs) have provided a unique class of tunable chemistries for variety applications. However, mechanistic insight into both the photophysical intermolecular phenomena underlying their utility is lacking, which results in obligate heuristic approaches producing ssDNA–SWNT based technologies. In this work, we present an ultrasensitive "turn-on" nanosensor neuromodulators dopamine...
Single-walled carbon nanotubes (SWCNTs) have unique photophysical properties and promise many novel applications. Their functionalization is crucial, but the organic phase around SWCNTs poorly understood. Noncovalent with single-stranded DNA (ssDNA) one of most used approaches to solubilize in water, variation ssDNA sequences leads major advances separation SWCNT chiralities SWCNT-based sensors. However, exact number adsorbed molecules on ssDNA/SWCNT complexes consequently surface coverage...
Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands many targets interest. Traditionally, generation such employs "early stage" incorporation building blocks into chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to starting from readily available material: genetically peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts displayed on phage...
Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to perturbations in the emitting motif. Optical sensors developed from single-stranded DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs) have started make useful contributions biological research. However, mechanisms underlying their function remained poorly understood. In this study, we combine experimental and computational approaches show...
Molecular assemblies of highly PEG-ylated phospholipids are important in many biomedical applications. We have studied sterically stabilized micelles (SSMs) self-assembled DSPE–PEG2000 pure water and isotonic HEPES-buffered saline solution. The observed SSM sizes 2–15 nm largely depend on the solvent lipid concentration used. critical micelle is 10 times higher than buffer, viscosity dispersion dramatically increases with concentration. To explain experimentally results, we performed...
We examine by semiclassical molecular dynamics simulations the possibility of driving nanoscale rotary motors electron tunneling. The model systems studied have a carbon nanotube shaft with covalently attached ``isolating'' stalks ending ``conducting'' blades. Periodic charging and discharging blades at two metallic electrodes maintains an electric dipole on that is rotated external field. Our demonstrate these can be efficient under load in presence noise defects.
Noncovalent polymer-single walled carbon nanotube (SWCNT) conjugates have gained recent interest due to their prevalent use as electrochemical and optical sensors, SWCNT-based therapeutics, for SWCNT separation. However, little is known about the effects of polymer-SWCNT molecular interactions on functional properties these conjugates. In this work, we show that complexed with related polynucleotide polymers (DNA, RNA) dramatically different fluorescence stability. Surprisingly, find a...
Abstract Many major degenerative disorders are associated with the formation of amyloid fibrils by proteins and peptides. Recent studies have extended repertoire amyloidogenic building blocks to non‐proteinaceous entities, including amino acids nucleobases. Here, based on high propensity tryptophan‐containing peptides form fibrils, we explored self‐assembly profile this acid. We discovered that tryptophan forms fibrillary assemblies a diameter 15–75 nm. These bind thioflavin T...
Abstract The formation of ordered amyloid fibrils by proteins and polypeptides is associated with human disorders. A recent extension the amyloidogenic building block family includes several small metabolites, which form assemblies structural functional similarities to well-established amyloids. Here we investigate whether generic polyphenolic inhibitors can also restrict metabolite fibrils. We reveal that epigallocatechin gallate tannic acid inhibit amyloid-like fibrillation adenine,...
DNA-wrapped single walled carbon nanotube (SWNT) conjugates have distinct optical properties leading to their use in biosensing and imaging applications. A critical limitation the development of DNA–SWNT sensors is current inability predict unique DNA sequences that confer a strong analyte-specific response these sensors. Here, near-infrared (nIR) fluorescence data sets for ∼100 conjugates, narrowed down by selective evolution protocol starting from pool ∼1010 candidates, are used train...
Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function DNA sequence based on whole SWNT fluorescence spectra. Our analysis reveals crucial role binding modes DNA-SWNTs serotonin, with smaller influence chirality. Regression ML models trained existing data sets predict change emission response ΔF/F, at over hundred...
In this study, we employed a novel approach to improve the serotonin-responsive ssDNA-wrapped single-walled carbon nanotube (ssDNA-SWCNT) nanosensors, combining directed evolution and machine learning-based prediction. Our iterative optimization process is aimed at sensitivity selectivity of ssDNA-SWCNT nanosensors. three rounds for higher serotonin sensitivity, substantially improved achieving remarkable 2.5-fold enhancement in fluorescence response compared original sequence. Following...
Integrins are transmembrane receptors that mediate cell-adhesion, signaling cascades and platelet-mediated blood clotting. Most integrins bind to the common short peptide Arg-Gly-Asp (RGD). The conformational freedom of RGD motif determines how strong which it binds. Here, we present a novel approach tune binding constants by confining motifs via noncovalent adsorption single-stranded DNA (ssDNA) anchors onto single-walled carbon nanotubes (SWCNTs). Semiconducting SWCNTs display fluorescence...
Double-stranded (ds) RNA is a key player in numerous biological activities cells, including interference, anti-viral immunity and mRNA transport. The class of proteins responsible for recognizing dsRNA termed double-stranded binding (dsRBP). However, little known about the molecular mechanisms underlying interaction between dsRBPs dsRNA. Here we examined four human dsRBPs, ADAD2, TRBP, Staufen 1 ADAR1 on six substrates that vary length secondary structure. We combined single molecule...
Abstract Single wall carbon nanotubes (SWCNTs) functionalized with (bio-)polymers such as DNA are soluble in water and sense analytes by analyte-specific changes of their intrinsic fluorescence. Such SWCNT-based (bio-)sensors translate the binding a molecule (molecular recognition) into measurable optical signal. This signal transduction is crucial for all types molecular sensors to achieve high sensitivities. Although there an increasing number sensors, yet no understanding observed SWCNT’s...
In this work, we describe a computational tool designed to determine the local dielectric constants (ε) of charge-neutral heterogeneous systems by analyzing dipole moment fluctuations from molecular dynamics (MD) trajectories. Unlike conventional methods, our can calculate for dynamically evolving selections molecules within defined region space, rather than fixed sets molecules. We validated approach computing TIP3P water nanospheres, achieving results consistent with literature values bulk...
PEGylated dendron coils (PDCs) were investigated as a novel potential nanocarrier platform. PDCs self-assembled into micelles at lower CMCs than linear copolymer counterparts by 1–2 orders of magnitude, due to the unique architecture dendrons. MD simulations also supported thermodynamically favourable self-assembly mediated
We explore microscopic principles governing the self-assembly of colloidal octylamine-coated platinum nanocubes solvated in toluene. Our experiments show that regular with an edge length lRC = 5.5 nm form supercrystals simple cubic packing, while slightly truncated lTC 4.7 tend to arrange fcc packing. model by averaged force fields and atomistic molecular dynamics simulations coupling forces between these nanocrystals. detailed analysis shows which for cubes has a lower density than is...