A5053616792- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- Hepatitis C virus research
- Bacteriophages and microbial interactions
- Protein Structure and Dynamics
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- Advanced Fluorescence Microscopy Techniques
- Monoclonal and Polyclonal Antibodies Research
- Nanopore and Nanochannel Transport Studies
- HIV/AIDS drug development and treatment
- PARP inhibition in cancer therapy
- Various Chemistry Research Topics
- Field-Flow Fractionation Techniques
- Neurogenetic and Muscular Disorders Research
- Advanced Electron Microscopy Techniques and Applications
- Viral Infections and Immunology Research
- thermodynamics and calorimetric analyses
- Biochemical and Molecular Research
- Heat shock proteins research
- SARS-CoV-2 and COVID-19 Research
- Toxin Mechanisms and Immunotoxins
- Advanced MRI Techniques and Applications
University of Zurich
2017-2024
University of Kansas
2019-2024
National Institute of Standards and Technology
2010-2018
University of Colorado Boulder
2010-2018
Joint Institute for Laboratory Astrophysics
2010-2015
Significance The cell cytoplasm is a multicomponent solution that much more concentrated than typically sampled in conventional vitro studies. presence of cosolutes can strongly influence biomolecular folding due to “molecular-crowding” effects, which are poorly understood and yet crucial understand. In this study, the thermodynamics/kinetics “crowding” effects probed at single-molecule level for an isolated RNA tertiary interaction. We observe dramatic stabilization folded state and, first...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related CoVs encode 3 tandem macrodomains within nonstructural protein (nsp3). The first macrodomain, Mac1, is conserved throughout binds to hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated antiviral ADP-ribosylation, a posttranslational modification that part of the host response viral infections. essential for pathogenesis in multiple animal models CoV infection, implicating...
Abstract The association of biomolecules is the elementary event communication in biology. Most mechanistic information how interactions between binding partners form or break is, however, hidden transition paths, very short parts molecular trajectories from encounter two molecules to formation a stable complex. Here we use single-molecule spectroscopy measure path times for intrinsically disordered proteins that folded dimer upon binding. results reveal metastable complex electrostatically...
Abstract RNA chaperones are proteins that aid in the folding of nucleic acids, but remarkably, many these intrinsically disordered. How can function without a well-defined three-dimensional structure? Here, we address this question by studying hepatitis C virus core protein, chaperone promotes viral genome dimerization. Using single-molecule fluorescence spectroscopy, find positively charged disordered protein facilitates formation compact acid conformations acting as flexible macromolecular...
Mg 2+ is essential for the proper folding and function of RNA, though effect concentration on free energy, enthalpy, entropy landscapes RNA unknown. This work exploits temperature-controlled single-molecule FRET methods to address thermodynamics pathways by probing intramolecular docking/undocking kinetics ubiquitous GAAA tetraloop−receptor tertiary interaction as a [Mg ]. These measurements yield barrier standard state enthalpies, entropies, energies an transition, in particular, revealing...
Riboswitches represent a family of highly structured regulatory elements found primarily in the leader sequences bacterial mRNAs. They function as molecular switches capable altering gene expression; commonly, this occurs via conformational change element riboswitch that results from ligand binding aptamer domain. Numerous studies have investigated process, but little is known about structural changes element. A mechanistic description both processes essential for deeply understanding how...
Highlights•Structural features needed for a cobalamin-dependent regulatory switch are identified•Spatial relationship between receptor and domains is critical function•Translation initiation controlled by the kinetics of interdomain interaction•Efficient regulation translational riboswitch involves other cellular factorsSummaryRiboswitches mRNA elements regulating gene expression in response to direct binding metabolite. While these RNAs increasingly well understood with respect interactions...
The influential role of monovalent and divalent metal cations in facilitating conformational transitions both RNA DNA has been a target intense biophysical research efforts. However, organic neutrally charged cosolutes can also significantly alter nucleic acid transitions. For example, highly soluble small molecules such as trimethylamine N-oxide (TMAO) urea are occasionally utilized by organisms to regulate cellular osmotic pressure. Ensemble studies have revealed that these so-called...
We combine single-molecule Förster resonance energy transfer (single-molecule FRET) experiments with extensive all-atom molecular dynamics (MD) simulations (>100 μs) to characterize the conformational ensembles of single-stranded (ss) DNA and RNA in solution. From MD explicit dyes attached nucleic acids via flexible linkers, we calculate FRET efficiencies fluorescence anisotropy decays. find that dispersion-corrected water models alleviate problem overly abundant interactions between...
Abstract Risdiplam is the first approved small-molecule splicing modulator for treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 SMN2 pre-mRNA: (i) 5′-splice site and (ii) an upstream purine (GA)-rich site. Importantly, sequence this GA-rich significantly enhanced potency analogues. In report, we unambiguously determined a known analogue, SMN-C2, binds to single-stranded RNA sequence-specific manner....
Cations have long been associated with formation of native RNA structure and are commonly thought to stabilize the tertiary contacts by favorably interacting electrostatic potential RNA, giving rise an "ion atmosphere". A significant amount information regarding thermodynamics structural transitions in presence ion atmosphere has accumulated suggests stabilization is dominated entropic terms. This work provides analysis how RNA-cation interactions affect entropy enthalpy transition....
ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, binds to hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that part of the host response viral infections. essential for pathogenesis in multiple animal models CoV...
The ribonucleoprotein telomerase is an RNA-dependent DNA polymerase that catalyzes the repetitive addition of a short, species-specific, sequence to ends linear eukaryotic chromosomes. single RNA component contains both template for synthesis and functionally critical pseudoknot motif, which can also exist as less stable hairpin. Here we use minimal version human study this hairpin–pseudoknot structural equilibrium using temperature-controlled single-molecule fluorescence resonance energy...
Studying RNA-ligand interactions and quantifying their binding thermodynamics kinetics are of particular relevance in the field drug discovery. Here, we combined biochemical assays accelerated molecular simulations to investigate ligand dissociation RNA using theophylline-binding as a model system. All-atom Ligand Gaussian Molecular Dynamics method (LiGaMD) have captured repetitive theophylline caffeine RNA. Theophylline's free energy kinetic rate constants align with our experimental data,...
The 3' end of the hepatitis C virus genome is terminated by a highly conserved, 98 nt sequence called 3'X. This untranslated structural element thought to regulate several essential RNA-dependent processes associated with infection. 3'X has two proposed conformations comprised either three or stem-loop structures that result from different base-pairing interactions within first 55 nt. Here, we used single-molecule Förster resonance energy transfer spectroscopy monitor conformational status...
Abstract The conformational dynamics of single-stranded nucleic acids are fundamental for acid folding and function. However, their elementary chain have been difficult to resolve experimentally. Here we employ a combination single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, nanophotonic enhancement determine the ensembles rapid short in solution. To interpret experimental results terms end-to-end distance dynamics, utilize hierarchical...