A5035373472- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Protein Structure and Dynamics
- DNA and Nucleic Acid Chemistry
- Bacteriophages and microbial interactions
- Viral Infections and Immunology Research
- Advanced biosensing and bioanalysis techniques
- Bacterial Genetics and Biotechnology
- Cell Image Analysis Techniques
- Machine Learning in Materials Science
- Chemical Synthesis and Analysis
- Telomeres, Telomerase, and Senescence
- Microbial Natural Products and Biosynthesis
- SARS-CoV-2 and COVID-19 Research
- Genomics and Phylogenetic Studies
- Copper Interconnects and Reliability
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Semiconductor materials and devices
- Enzyme Structure and Function
- Cancer-related gene regulation
- Viral gastroenteritis research and epidemiology
- Crystallography and molecular interactions
- Advancements in Photolithography Techniques
Stanford University
2014-2024
University of Nebraska–Lincoln
2020-2024
Howard Hughes Medical Institute
2024
University of Michigan
2011-2014
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
Abstract We introduce a toolset of program libraries collectively titled multipurpose atom‐typer for CHARMM (MATCH) the automated assignment atom types and force field parameters molecular mechanics simulation organic molecules. The includes utilities conversion multiple chemical structure file formats into graph. A general pattern‐matching engine using this graph has been implemented whereby types, charges, are achieved by comparison against customizable list fragments. While initially...
S-Adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong multiple distinct classes share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer remain undefined. A survey of high-resolution crystal structures reveals unconventional carbon–oxygen (CH···O) hydrogen bonds coordinate the AdoMet group in different irrespective their class,...
Significance The intricate structures of RNA molecules are crucial to their biological functions but have been difficult accurately characterize. Multidimensional chemical-mapping methods improve accuracy so far involved painstaking experiments and reliance on secondary-structure prediction software. A methodology called M2-seq now lifts these limitations. Mechanistic studies clarify the origin serendipitous M2-seq–like signals that were recently discovered not correctly explained also...
Abstract Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining is challenging because the information required to specify atomic structures thousands far exceeds that experimental measurements. We addressed this data gap dramatically simplified accelerated RNA ensemble determination by using structure prediction tools leverage growing database generate a conformation library. Refinement...
Small-molecule targeting of RNA stem loops in 5′-end SARS-CoV-2 reveals novel targets for viral inhibition.
Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety biological processes. However, direct determination 3D vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present method, Spatial 2'-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers defined lengths measure distances between nucleotides cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation,...
The propensity of backbone Cα atoms to engage in carbon-oxygen (CH···O) hydrogen bonding is well-appreciated protein structure, but side chain CH···O remains largely uncharacterized. extent which methyl groups proteins participate examined through a survey neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, were observed form stabilizing bonds within structure that are maintained correlated motion. Collectively, findings...
Structured RNAs and RNA complexes underlie biological processes ranging from control of gene expression to protein translation. Approximately 50% nucleotides within known structured are folded into Watson-Crick (WC) base pairs, sequence changes that preserve these pairs typically assumed higher-order structure binding macromolecule partners. Here, we report indirect effects the helix on tertiary stability are, in fact, significant but nevertheless predictable a simple computational model...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
Customized RNA synthesis is in demand for biological and biotechnological research. While chemical gel or chromatographic purification of costly difficult sequences longer than tens nucleotides, a pipeline primer assembly DNA templates, vitro transcription by T7 polymerase kit-based provides cost-effective fast alternative preparing molecules. Nevertheless, designing template primers that optimize cost avoid mispriming during chain reaction currently requires expert inspection, downloading...
Abstract Accurate computational methods of determining protein and nucleic acid p K a values are vital to understanding pH‐dependent processes in biological systems. In this article, we use the recently developed method constant pH molecular dynamics (CPHMD) explore calculation highly perturbed variants staphylococcal nuclease (SNase). Simulations were performed using replica exchange (REX) protocol for improved conformational sampling with eight temperature windows, yielded converged proton...
Abstract Multipurpose atom‐typer for CHARMM (MATCH), an atom‐typing toolset molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH‐generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies a series 457 small neutral molecules GBMV2, Generalized Born with smooth SWitching (GBSW), fast analytical continuum treatment solvation (FACTS) implicit solvent models. The quality associated...
Significance Telomerase synthesizes the telomeric DNA at 3′ ends of chromosomes and maintains genome integrity. RNA (TR) provides template for telomere-repeat synthesis within a template/pseudoknot (t/PK) domain that is essential activity. We investigated structure dynamics t/PK from medaka fish, which contain smallest vertebrate TR, using NMR modeling. Despite differences in length, sequence, predicted secondary with human remarkable similarities between subdomains, including one newly...
Abstract Structural plasticity is integral to RNA function; however, there are currently few methods quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy a powerful approach for resolving conformational ensembles but size-limited. Chemical probing well-suited large provides limited and kinetics information. Here, we integrate the two approaches visualize two-state ensemble central stem–loop 3 (SL3) of 7SK RNA, critical element function in transcription...
Abstract Structured RNAs often contain long-range tertiary contacts that are critical to their function. Despite the importance of contacts, methods measure thermodynamics low throughput or require specialized instruments. Here, we introduce a new quantitative chemical mapping method (qMaPseq) Mg2+-induced formation contact in high-throughput manner using standard biochemistry equipment. With qMaPseq, measured ΔG 98 unique tetraloop/tetraloop receptor (TL/TLR) variants one-pot reaction....
Chemical mapping is a broadly utilized technique for probing the structure and function of RNAs. The volume chemical data continues to grow as more researchers routinely employ this information experimental methods increase in throughput content. To create central location these data, we established an RNA database (RMDB) 5 years ago. RMDB, which available at http://rmdb.stanford.edu, now contains over 800 entries, involving 134 000 natural engineered RNAs, vitro cellulo. entries include...
Abstract The discovery and design of biologically important RNA molecules is dramatically outpacing three-dimensional structural characterization. To address this challenge, we present Ribosolve, a hybrid method integrating moderate-resolution cryo-EM maps, chemical mapping, Rosetta computational modeling, demonstrate its application to thirteen previously unknown 119-to 338-nucleotide protein-free RNA-only structures: full-length Tetrahymena ribozyme, hc16 ligase with without substrate, V....
RNA is rising in importance as a design medium for interrogating fundamental biology and developing therapeutic bioengineering applications. While there are several online servers of secondary structure, no tools available the rational 3D structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an tool RNA. This resource utilizes fixed-backbone to optimize sequence identity nucleobase conformations match desired backbone, analogous that underlie protein engineering. The...
Abstract The emerging field of RNA nanotechnology seeks to create nanoscale 3D machines by repurposing natural modules, but successes have been limited symmetric assemblies single repeating motifs. We present RNAMake, a suite that automates design molecules with complex folds. first challenged RNAMake the paradigmatic problem aligning tetraloop and sequence-distal receptor, previously only solved via symmetry. Single-nucleotide-resolution chemical mapping, native gel electrophoresis,...