A5016954340- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- RNA Research and Splicing
- RNA modifications and cancer
- Protein Structure and Dynamics
- Nanopore and Nanochannel Transport Studies
- Advanced biosensing and bioanalysis techniques
- Electrostatics and Colloid Interactions
- Bacteriophages and microbial interactions
- X-ray Spectroscopy and Fluorescence Analysis
- Genomics and Chromatin Dynamics
- Advanced Electron Microscopy Techniques and Applications
- Advanced X-ray Imaging Techniques
- Biochemical and Molecular Research
- RNA Interference and Gene Delivery
- Mass Spectrometry Techniques and Applications
- Advanced NMR Techniques and Applications
- DNA Repair Mechanisms
- Quantum, superfluid, helium dynamics
- Atomic and Subatomic Physics Research
- X-ray Diffraction in Crystallography
- Solid-state spectroscopy and crystallography
- Rare-earth and actinide compounds
- Ion-surface interactions and analysis
Cornell University
2016-2025
Rutgers, The State University of New Jersey
2023
University of Minnesota
2017
Deutsches Elektronen-Synchrotron DESY
2017
Universität Hamburg
2017
Max Planck Institute for the Structure and Dynamics of Matter
2017
Center for Free-Electron Laser Science
2017
National Radio Astronomy Observatory
2005
University of California, Santa Cruz
2005
Stanford University
2002
Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize into relatively rigid structures, while flexible non-base-paired regions allow to undergo conformational changes required for function. To advance our understanding of folding dynamics it is critical know flexibility these un-base-paired how depends on counterions. Yet, information about nucleic acid polymer properties mainly derived from studies ssDNA. Here we...
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering validation, modelling for biomolecular small-angle (SAS) experiments. Biomolecular SAS has since continued to grow authors have increasingly adopted the guidelines. parallel, integrative/hybrid determination structures is a rapidly growing field that expanding scope structural biology. For contribute maximally this field, it essential ensure open access...
Approximately 17 years after the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic, world is currently facing COVID-19 pandemic caused by SARS corona virus 2 (SARS-CoV-2). According to most optimistic projections, it will take more than a year develop vaccine, so best short-term strategy may lie in identifying virus-specific targets for small molecule-based interventions. All coronaviruses utilize molecular mechanism called programmed -1 ribosomal frameshift (-1 PRF) control...
Time-resolved small-angle x-ray scattering was used to measure the radius of gyration cytochrome c after initiation folding by a pH jump. Submillisecond time resolution obtained with microfabricated diffusional mixer and synchrotron radiation. The results show that protein first collapses compact denatured structures before very fast native state.
We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide time-resolved picture of the global folding process Tetrahymena group I RNA over time window more than five orders magnitude. A substantial phase compaction is observed on low millisecond timescale, overall shape changes are largely complete within one second, earlier any known tertiary contacts formed. This finding indicates that forms nonspecifically collapsed intermediate then...
Counterion atmospheres condensed onto charged biopolymers strongly affect their physical properties and biological functions, but have been difficult to quantify experimentally. Here, monovalent divalent counterion around DNA double helices in solution are probed using small-angle x-ray scattering techniques. Modulation of the ion factors by anomalous (resonant) interchanging identities yields direct measurements signal due spatial correlation surrounding ions DNA. The quality data permit,...
Ever since the first atomic structure of an enzyme was solved, discovery mechanism and dynamics reactions catalyzed by biomolecules has been key goal for understanding molecular processes that drive life on earth. Despite a large number successful methods trapping reaction intermediates, direct observation ongoing possible only in rare exceptional cases.
Abstract Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam an X-ray free-electron laser over course experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability previous generations nozzles. demonstrate its use determine first room-temperature structure RNA polymerase II at high resolution, revealing new structural details. Moreover,...
Significance Cryptochromes (CRYs) are photosensors that play central roles in the circadian rhythms of plants and animals. CRYs related to photolyase DNA-repair enzymes, but instead binding DNA, insect bind a C-terminal tail (CTT) α-helix pocket holds light-sensing flavin molecule. There is no consensus on how light activates Drosophila CRY (dCRY). We show reduction anionic semiquinone by or chemicals releases CTT activate dCRY. The target dCRY, protein Timeless, contains sequence similar...
Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with substrate just prior being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds seconds, and (iii) convenient reaction initiation. outruns radiation damage using femtosecond pulses allowing...
Significance Nucleosomes are fundamental protein–DNA structures through which eukaryotes package and organize DNA inside the nucleus. disassembled to gain access critical information stored in DNA. Here, we describe a new experimental approach that characterizes kinetics of nucleosome disassembly synergy between conformation protein components. Using NaCl disrupt electrostatic interactions, identify kinetic pathways transient intermediates reveal how unwrapping dissociation linked this...
Knowledge of protein structure provides essential insight into function, enhancing our understanding diseases and enabling new treatment development. X-ray crystallography has been used to solve the structures more than 100 000 proteins; however, vast majority represent long-lived states that do not capture functional motions these molecular machines. Reactions triggered by addition a ligand can be most challenging detect with because difficulty synchronizing reactions create detectable...
Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase enzymatic cycle is observed with near-atomic resolution using most advanced X-ray source currently available: European XFEL (EuXFEL). high repetition rate EuXFEL combined our mix-and-inject technology enables ceftriaxone binding to
High-intensity, ``pink'' beam from an undulator was used in conjunction with microfabricated rapid-fluid mixing devices to monitor the early events protein folding time resolved small angle x-ray scattering. This Letter describes recent work on bovine $\ensuremath{\beta}$-lactoglobulin where collapse expanded a compact set of states directly observed millisecond scale. The role chain collapse, one initial stages folding, is not currently understood. characterization transient, vital...
We describe a microfluidic mixer that is well-suited for kinetic studies of macromolecular conformational change under broad range experimental conditions. The exploits hydrodynamic focusing to create thin jet containing the macromolecules interest. Kinetic reactions are triggered by molecular diffusion into from adjacent flow layers. ultimate time resolution these devices can be restricted premature contact between co-flowing solutions during process. Here, we design and characterization in...
Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating short strands mediated by ${\mathrm{Mg}}^{2+}$ ions. Solution small angle x-ray scattering data collected as a function of concentration enable model independent extraction the second virial coefficient. As [${\mathrm{Mg}}^{2+}$] increases, this coefficient turns from positive to negative reflecting transition repulsive attractive inter-DNA interaction....
A microfluidic mixer is applied to study the kinetics of calmodulin conformational changes upon Ca2+ binding. The device facilitates rapid, uniform mixing by decoupling hydrodynamic focusing from diffusive and accesses time scales tens microseconds. used in conjunction with multiphoton microscopy examine fast Ca2+-induced transitions acrylodan-labeled calmodulin. We find that kinetic rates two homologous globular domains differ more than an order magnitude. characteristic constants are...
The majority of charge-compensating ions around nucleic acids form a diffuse counterion "cloud" that is not amenable to investigation by traditional methods rely on rigid structural interactions. Although various techniques have been employed characterize the ion atmosphere acids, only anomalous small-angle X-ray scattering (ASAXS) provides information about spatial distribution ions. Here we present an experimentally straightforward extension ASAXS can be used count number acids.
The modulation of DNA accessibility by nucleosomes is a fundamental mechanism gene regulation in eukaryotes. nucleosome core particle (NCP) consists 147 bp wrapped around symmetric octamer histone proteins. dynamics packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including positioning sequence, variants modifications. Although structure intact has been studied crystallography at atomic resolution, little known about structures partially...