P. Bevilacqua

发表

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Y. Zhang, Yiliang Ding, Yin Tang, 2013, Nature.

Determination of in vivo RNA structure in low-abundance transcripts

Yiliang Ding, Yin Tang, C. Kwok, 2013, Nature Communications.

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study

D. Mathews, P. Bevilacqua, Mohammad Kayedkhordeh, 2018, Nucleic acids research.

Kinetic analysis of ribozyme cleavage

T. S. Brown, P. Bevilacqua, D. Chadalavada, 2003 .

Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections.

P. Bevilacqua, D. Chadalavada, 2009, Methods in enzymology.

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

Yin Tang, C. Kwok, P. Bevilacqua, 2015, Trends in biochemical sciences.

Bridging the gap between in vitro and in vivo RNA folding

D. Mathews, P. Bevilacqua, S. Assmann, 2016, Quarterly Reviews of Biophysics.

A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation.

Yiliang Ding, C. Kwok, P. Bevilacqua, 2013, Analytical biochemistry.

Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc).

P. Bevilacqua, Jing Liang, M. Nakano, 2002, Biochemistry.

Folding of a stable DNA motif involves a highly cooperative network of interactions.

P. Bevilacqua, E. Moody, Ellen M Moody, 2003, Journal of the American Chemical Society.

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

Sarah M. Assmann, Zhao Su, Philip C. Bevilacqua, 2017, Nucleic acids research.

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis

P. Bevilacqua, S. Assmann, D. Tack, 2019, bioRxiv.

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

Sarah M Assmann, Chun Kit Kwok, Philip C Bevilacqua, 2015, Nature Protocols.

Genome-Wide Analysis of RNA Secondary Structure.

Zhao Su, Sarah M Assmann, Laura E Ritchey, 2016, Annual review of genetics.

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

Philip C. Bevilacqua, D. Weissman, P. Bevilacqua, 2010, Nucleic acids research.

A brilliant disguise for self RNA: 5’-end and internal modifications of primary transcripts suppress elements of innate immunity

P. Bevilacqua, S. Nallagatla, Rebecca Toroney, 2008, RNA biology.

The double-stranded-RNA-binding motif: interference and much more

Michael B. Mathews, Bin Tian, Philip C. Bevilacqua, 2004, Nature Reviews Molecular Cell Biology.

Method for assigning double-stranded RNA structures.

T. S. Brown, P. Bevilacqua, 2005, BioTechniques.

Prospecting for aptamers in the human genome.

P. Bevilacqua, Peter C. Breen, Pallavi Thaplyal, 2012, Chemistry & biology.

Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.

B. Golden, P. Bevilacqua, N. Veeraraghavan, 2011, Biochemistry.

Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis.

B. Golden, P. Bevilacqua, D. Chadalavada, 2008, RNA.

and Biological Functions of RNA Hairpins

P. Bevilacqua, Joshua M Blose, 2008 .

Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites.

Daniel D. Seith, P. Bevilacqua, Jamie L. Bingaman, 2018, ACS catalysis.

A simple fluorescence method for pK(a) determination in RNA and DNA reveals highly shifted pK(a)'s.

P. Bevilacqua, Jennifer L. Wilcox, 2013, Journal of the American Chemical Society.

RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles

F. Major, P. Bevilacqua, S. Assmann, 2010, Nucleic acids research.

Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

C. Keating, P. Bevilacqua, F. Cakmak, 2020, Nature communications.

Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

C. Keating, P. Bevilacqua, F. Cakmak, 2020, Nature Communications.

The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting.

P. Bevilacqua, D. Chadalavada, E. A. Gratton, 2010, Biochemistry.

Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.

D. Mathews, P. Bevilacqua, Mohammad Kayedkhordeh, 2021, Methods in molecular biology.

Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms.

P. Bevilacqua, N. Yennawar, Kathleen A. Leamy, 2018, Biochemistry.

Protein Structure Is Related to RNA Structural Reactivity In Vivo.

Yin Tang, P. Bevilacqua, S. Assmann, 2016, Journal of molecular biology.

Thio Effects and an Unconventional Metal Ion Rescue in the Genomic HDV Ribozyme §

B. Golden, P. Bevilacqua, Pallavi Thaplyal, 2013 .

Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress

P. Bevilacqua, S. Assmann, R. Yamagami, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Single-nucleotide resolution of RNA strands in the presence of their RNA complements.

S. Ghosh, J. Arnold, C. Cameron, 1999, BioTechniques.

TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region.

P. Bevilacqua, P. Babitzke, A. Mcgraw, 2007, RNA.

Binding of the protein kinase PKR to RNAs with secondary structure defects: role of the tandem A-G mismatch and noncontiguous helixes.

T. Cech, P. Bevilacqua, C. Samuel, 1998, Biochemistry.

The GlcN6P cofactor serves multiple catalytic roles in the glmS ribozyme

P. Bevilacqua, N. Yennawar, Jamie L. Bingaman, 2017 .

Activation of PKR by RNA misfolding: HDV ribozyme dimers activate PKR.

P. Bevilacqua, Laurie A. Heinicke, 2012, RNA.

Mechanistic characterization of the 5'-triphosphate-dependent activation of PKR: lack of 5'-end nucleobase specificity, evidence for a distinct triphosphate binding site, and a critical role for the dsRBD.

P. Bevilacqua, J. Sokoloski, Rebecca Toroney, 2012, RNA.

RNA helical imperfections regulate activation of the protein kinase PKR: effects of bulge position, size, and geometry.

P. Bevilacqua, Laurie A. Heinicke, S. Nallagatla, 2011, RNA.

The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.

P. Bevilacqua, N. Yennawar, Jacob P Sieg, 2022, Biochemistry.

Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.

P. Bevilacqua, N. Yennawar, Kathleen A. Leamy, 2017, Biochemistry.

Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways

D. Turner, P. Bevilacqua, 2002, Current protocols in nucleic acid chemistry.

Amino Acid Specific Nonenzymatic Montmorillonite‐Promoted RNA Polymerization

P. Bevilacqua, C. Wesdemiotis, Nita Sahai, 2021 .

Charged nucleobases and their potential for RNA catalysis.

P. Bevilacqua, Jennifer L. Wilcox, Amarpreet Ahluwalia, 2011, Accounts of chemical research.

Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin.

P. Bevilacqua, J. M. Bevilacqua, 1998, Biochemistry.

Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics.

P. Bevilacqua, Jamie L. Bingaman, Kyle J. Messina, 2017, Methods.

Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate.

Martin Gruebele, Philip C Bevilacqua, Hairong Ma, 2004, Biochemistry.

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

P. Bevilacqua, R. Yamagami, Jamie L. Bingaman, 2018, Nature Communications.

Investigation of the pKa of the Nucleophilic O2' of the Hairpin Ribozyme.

P. Bevilacqua, Pengfei Li, A. Soudackov, 2021, The journal of physical chemistry. B.

Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+ Ions and the Hydrogen-Bonding Network in the Active Site

P. Bevilacqua, M. N. Ucisik, S. Hammes‐Schiffer, 2016, Biochemistry.

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

D. Turner, S. Kennedy, P. Bevilacqua, 2013, Biochemistry.

Bioreactor droplets from liposome-stabilized all-aqueous emulsions

Philip C Bevilacqua, C. Keating, P. Bevilacqua, 2014, Nature Communications.

RNA catalysis through compartmentalization.

Philip C Bevilacqua, C. Keating, P. Bevilacqua, 2012, Nature chemistry.

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates

C. Keating, P. Bevilacqua, R. Guth-Metzler, 2019, Nature Communications.

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility.

P. Bevilacqua, S. Showalter, N. Yennawar, 2016, Methods in enzymology.

Long Tracts of Guanines Drive Aggregation of RNA G-Quadruplexes in the Presence of Spermine.

P. Bevilacqua, Raghav R. Poudyal, Allison M Williams, 2021, Biochemistry.

Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry.

Philip C Bevilacqua, C. Keating, P. Bevilacqua, 2018, Biochemistry.

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg²⁺, Nucleotides, and RNA.

Philip C Bevilacqua, C. Keating, P. Bevilacqua, 2016, Langmuir : the ACS journal of surfaces and colloids.

RNA sequence and structure control assembly and function of RNA condensates

C. Keating, P. Bevilacqua, B. Portz, 2021, RNA.

Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles

C. Keating, P. Bevilacqua, Saehyun Choi, 2021, bioRxiv.

Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates.

Philip C Bevilacqua, C. Keating, P. Bevilacqua, 2019, ACS chemical biology.

Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.

B. Golden, P. Bevilacqua, N. Veeraraghavan, 2011, The journal of physical chemistry. B.

SYN BASES: THEIR PREVALENCE, RELEVANCE, AND UTILITY IN FUNCTIONAL RNA

P. Bevilacqua, S. Showalter, B. Garrison, 2009 .

Catalytic roles for proton transfer and protonation in ribozymes.

T. S. Brown, S. Nakano, P. Bevilacqua, 2004, Biopolymers.

Inverse Thio Effects in the Hepatitis Delta Virus Ribozyme Reveal that the Reaction Pathway Is Controlled by Metal Ion Charge Density

Sharon Hammes-Schiffer, Philip C. Bevilacqua, P. Bevilacqua, 2015, Biochemistry.

Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity.

R. Kierzek, P. Bevilacqua, Nathan A. Siegfried, 2010, Journal of the American Chemical Society.

A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme.

R. Kierzek, P. Bevilacqua, R. Yajima, 2007, Chemistry & biology.

Nucleobase catalysis in ribozyme mechanism.

P. Bevilacqua, R. Yajima, 2006, Current opinion in chemical biology.

Portability of the GN(R)A hairpin loop motif between RNA and DNA.

P. Bevilacqua, Joshua M Blose, K. Lloyd, 2009, Biochemistry.

Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2' OH groups.

D. Turner, P. Bevilacqua, 1991, Biochemistry.

Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails.

P. Bevilacqua, Xiaofeng Zheng, 2004, RNA.

Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR.

T. Cech, P. Bevilacqua, Philip C. Bevilacqua, 1996, Biochemistry.

Native Tertiary Structure and Nucleoside Modifications Suppress tRNA’s Intrinsic Ability to Activate the Innate Immune Sensor PKR

C. Cameron, P. Bevilacqua, Saikat Ghosh, 2013, PloS one.

Effect of loop sequence and loop length on the intrinsic fluorescence of G-quadruplexes.

C. Kwok, P. Bevilacqua, M. Sherlock, 2013, Biochemistry.

Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes.

M. Maroncelli, C. Kwok, P. Bevilacqua, 2016, The journal of physical chemistry. B.

Amyloid Precursor Protein Translation Is Regulated by a 3’UTR Guanine Quadruplex

C. Kwok, P. Bevilacqua, Brian P. Leung, 2015, PloS one.

A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation.

Yiliang Ding, C. Kwok, P. Bevilacqua, 2015, The Biochemical journal.

Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes.

C. Kwok, P. Bevilacqua, M. Sherlock, 2013, Angewandte Chemie.

Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity.

Sarah M Assmann, Philip C Bevilacqua, P. Bevilacqua, 2012, Journal of the American Chemical Society.

5'-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation

D. Turner, R. Kierzek, P. Bevilacqua, 1993 .

Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A.

C. Cameron, P. Bevilacqua, J. Boyer, 2010, Journal of molecular biology.

RNA dimerization promotes PKR dimerization and activation.

P. Bevilacqua, Xiaofeng Zheng, Laurie A. Heinicke, 2009, Journal of molecular biology.

Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure‐specific manner

P. Bevilacqua, S. Nallagatla, 2008, RNA.

Dynamics of a Group I Ribozyme Detected by Spectroscopic Methods

D. Turner, L. Profenno, P. Bevilacqua, 1996 .

Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5' cleavage site into a high free energy binding mode in the Tetrahymena ribozyme.

D. Turner, P. Bevilacqua, Y. Li, 1994, Biochemistry.

Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors.

Philip C. Bevilacqua, V. Misra, P. Bevilacqua, 2009, Journal of the American Chemical Society.

CsrA-Mediated Translational Activation of ymdA Expression in Escherichia coli

P. Bevilacqua, P. Babitzke, Anastasia H. Potts, 2020, mBio.

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

P. Bevilacqua, S. Assmann, E. Turro, 2019, Genome Biology.

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

P. Bevilacqua, S. Assmann, P. Babitzke, 2020, bioRxiv.

Regulation of innate immunity through RNA structure and the protein kinase PKR.

P. Bevilacqua, S. Nallagatla, Rebecca Toroney, 2011, Current opinion in structural biology.

RNA multimerization as an organizing force for liquid–liquid phase separation

P. Bevilacqua, S. Assmann, Hong-Li Chou, 2021, RNA.

Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.

P. Bevilacqua, R. Yamagami, R. Huang, 2019, Biochemistry.

Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR.

P. Bevilacqua, Ananya Anmangandla, Chelsea M Hull, 2016, ACS chemical biology.

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

P. Bevilacqua, J. Boyer, Christopher A. Strulson, 2014, RNA.

Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions.

P. Bevilacqua, R. Rambo, N. Yennawar, 2013, Biochemistry.

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Andrew J. Olson, D. Ware, P. Bevilacqua, 2022, Genome Biology.

Driving forces for nucleic acid pK(a) shifting in an A(+).C wobble: effects of helix position, temperature, and ionic strength.

P. Bevilacqua, Nathan A. Siegfried, Bernie O’Hare, 2010, Biochemistry.

Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions.

P. Bevilacqua, D. Chadalavada, Andrea L Cerrone-Szakal, 2007, RNA.

Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.

P. Bevilacqua, Joshua M Blose, 2008, Annual review of physical chemistry.

Insight into the functional versatility of RNA through model-making with applications to data fitting

P. Bevilacqua, Nathan A. Siegfried, Andrea L Cerrone-Szakal, 2007, Quarterly Reviews of Biophysics.

Folding cooperativity in RNA and DNA is dependent on position in the helix.

Philip C Bevilacqua, P. Bevilacqua, Nathan A. Siegfried, 2007, Biochemistry.

pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

P. Bevilacqua, Jennifer L. Wilcox, 2013, Biochemistry.

A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding.

P. Bevilacqua, P. Babitzke, H. Yakhnin, 2003, Journal of molecular biology.

Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis.

T. Cech, E. Podell, P. Bevilacqua, 1998, Biochemistry.

Exploring the energy landscape of a small RNA hairpin.

Martin Gruebele, Philip C Bevilacqua, Hairong Ma, 2006, Journal of the American Chemical Society.

Technique Development for Probing RNA Structure In Vivo and Genome-Wide.

P. Bevilacqua, S. Assmann, 2018, Cold Spring Harbor perspectives in biology.

Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA.

P. Bevilacqua, Chelsea M Hull, 2015, Journal of molecular biology.

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance

Yin Tang, P. Bevilacqua, S. Assmann, 2018, Proceedings of the National Academy of Sciences.

In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)

P. Bevilacqua, S. Assmann, P. Babitzke, 2018, RNA.

Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR.

P. Bevilacqua, Chelsea M Hull, 2016, Accounts of chemical research.

5'-Triphosphate-Dependent Activation of PKR by RNAs with Short Stem-Loops

C. Cameron, P. Bevilacqua, Xiaofeng Zheng, 2007, Science.

Probing RNA structure in vivo.

P. Bevilacqua, S. Assmann, David Mitchell, 2019, Current opinion in structural biology.

StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.

Yin Tang, Sarah M Assmann, David C Tack, 2018, Methods.

17 Thermodynamic Considerations for Evolution by RNA

Douglas H. Turner, Philip C. Bevilacqua, D. Turner, 1993 .

A simple molecular model for thermophilic adaptation of functional nucleic acids.

P. Bevilacqua, Joshua M Blose, S. Silverman, 2007, Biochemistry.

Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments.

P. Bevilacqua, N. Veeraraghavan, S. Hammes‐Schiffer, 2010, Journal of molecular biology.

RNA structure: A LASER-focused view into cells.

P. Bevilacqua, S. Assmann, 2018, Nature chemical biology.

Glyoxals as in vivo RNA structural probes of guanine base-pairing.

P. Bevilacqua, S. Assmann, P. Babitzke, 2018, RNA.

Upstream Flanking Sequence Assists Folding of an RNA Thermometer.

P. Bevilacqua, Elizabeth A. Jolley, Kathryn M. Bormes, 2022, Journal of Molecular Biology.

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

D. York, J. Piccirilli, P. Bevilacqua, 2019, ACS chemical biology.

PKR and the ribosome compete for mRNA.

P. Bevilacqua, Rebecca Toroney, 2009, Nature chemical biology.

Regulatory Mechanisms through RNA Conformational Switching and Dynamics.

P. Bevilacqua, B. Tolbert, 2022, Journal of molecular biology.

Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.

T. S. Brown, P. Bevilacqua, D. Chadalavada, 2004, Journal of molecular biology.

A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence.

P. Bevilacqua, Amy Diegelman‐Parente, 2002, Journal of molecular biology.

A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme.

S. Nakano, P. Bevilacqua, S. M. Knudsen, 2000, Journal of molecular biology.

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo

Anton Nekrutenko, Yin Tang, Sarah M. Assmann, 2015, Bioinform..

In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans

R. Gutell, P. Bevilacqua, J. Ferry, 2023, bioRxiv.

Prevalence of syn nucleobases in the active sites of functional RNAs.

P. Bevilacqua, Joshua E. Sokoloski, Stephanie A. Godfrey, 2011, RNA.

Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme.

B. Golden, P. Bevilacqua, P. Carey, 2009, Biochemistry.

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates

C. Keating, P. Bevilacqua, R. Guth-Metzler, 2019, Nature Communications.

The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2

P. Bevilacqua, Peter C. Forstmeier, McCauley O. Meyer, 2023, bioRxiv.

Raman crystallography of RNA.

B. Golden, P. Bevilacqua, P. Carey, 2009, Methods.

Cellular Small Molecules Contribute to Twister Ribozyme Catalysis.

P. Bevilacqua, Kyle J. Messina, 2018, Journal of the American Chemical Society.

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

P. Bevilacqua, Erica A. Frankel, 2017, Biochemistry.

Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme.

P. Bevilacqua, 2003, Biochemistry.

Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme.

B. Golden, P. Bevilacqua, Pallavi Thaplyal, 2013, Biochemistry.

Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism.

P. Bevilacqua, Abir Ganguly, S. Hammes‐Schiffer, 2011, The journal of physical chemistry letters.

Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid.

Philip C Bevilacqua, P. Bevilacqua, Nathan A. Siegfried, 2008, Journal of the American Chemical Society.

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme.

S. Nakano, P. Bevilacqua, D. Chadalavada, 2000, Science.

Rock, scissors, paper: How RNA structure informs function

P. Bevilacqua, S. Assmann, Hong-Li Chou, 2023, The Plant cell.

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Andrew J. Olson, D. Ware, P. Bevilacqua, 2022, Genome Biology.

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

P. Bevilacqua, R. Yamagami, Jamie L. Bingaman, 2018, Nature Communications.

Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting.

Philip C Bevilacqua, P. Bevilacqua, E. Moody, 2005, RNA.

Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

Sharon Hammes-Schiffer, Puja Goyal, Philip C. Bevilacqua, 2014, Journal of the American Chemical Society.

Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system.

Philip C Bevilacqua, P. Bevilacqua, P. Babitzke, 2003, Methods in enzymology.

Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods.

D. Turner, R. Kierzek, P. Bevilacqua, 1992, Science.

Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding.

P. Bevilacqua, Nathan A. Siegfried, 2009, Methods in enzymology.

Cooperative and anticooperative binding to a ribozyme.

D. Turner, P. Bevilacqua, K. Johnson, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer.

P. Bevilacqua, Joshua E. Sokoloski, Sarah E Dombrowski, 2012, Biochemistry.

Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.

S. Nakano, P. Bevilacqua, A. Cerrone, 2003, Biochemistry.

Assessing the Potential Effects of Active Site Mg2+ Ions in the glmS Ribozyme–Cofactor Complex

Sharon Hammes-Schiffer, Puja Goyal, David R. Stevens, 2016, The journal of physical chemistry letters.

Cooperative Interactions in the Hammerhead Ribozyme Drive pKa Shifting of G12 and Its Stacked Base C17.

C. Keating, P. Bevilacqua, Christopher A. Strulson, 2017, Biochemistry.

Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding interactions.

D. Turner, R. Kierzek, N. Sugimoto, 1989, Nucleic acids research.

Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions

P. Bevilacqua, R. Yamagami, N. Yennawar, 2019, Proceedings of the National Academy of Sciences.

An Integrated Picture of HDV Ribozyme Catalysis

B. Golden, P. Bevilacqua, P. Carey, 2013 .

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography.

B. Golden, P. Bevilacqua, P. Carey, 2007, Journal of the American Chemical Society.

Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons.

S. Nakano, P. Bevilacqua, 2007, Biochemistry.

Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart.

P. Bevilacqua, E. Moody, Ellen M Moody, 2004, Biochemistry.

Experimental approaches for measuring pKa's in RNA and DNA.

P. Bevilacqua, Pallavi Thaplyal, 2014, Methods in enzymology.

Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR.

P. Bevilacqua, X. Zheng, Xiaofeng Zheng, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs.

Philip C Bevilacqua, P. Bevilacqua, E. Moody, 2003, Journal of the American Chemical Society.

Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions.

Philip C Bevilacqua, P. Bevilacqua, J. M. Bevilacqua, 2002, Biochemistry.

Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library.

P. Bevilacqua, Z Shu, P C Bevilacqua, 1999, Biochemistry.

A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme.

B. Golden, P. Bevilacqua, P. Carey, 2009, Biochemistry.

The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots.

P. Bevilacqua, D. Chadalavada, S. E. Senchak, 2002, Journal of molecular biology.

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

David H Mathews, Sarah M Assmann, Philip C Bevilacqua, 2017, Nucleic acids research.

The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme.

Sharon Hammes-Schiffer, Philip C Bevilacqua, P. Bevilacqua, 2017, Nature chemical biology.

A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage.

B. Golden, P. Bevilacqua, E. Chase, 2010, Biochemistry.

Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications.

P. Bevilacqua, X. Zheng, 2001, Nucleic acids research.

Glyoxals as in vivo RNA structural probes of guanine base-pairing

P. Bevilacqua, S. Assmann, P. Babitzke, 2018, RNA.

In Vivo Genome-Wide RNA Structure Probing with Structure-seq.

P. Bevilacqua, S. Assmann, Laura E. Ritchey, 2019, Methods in molecular biology.

Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine.

R. Kierzek, P. Bevilacqua, E. Kierzek, 2003, Journal of the American Chemical Society.

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

P. Bevilacqua, S. Assmann, E. Turro, 2019, Genome Biology.

Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme.

B. Golden, P. Bevilacqua, Abir Ganguly, 2013, Biochemistry.

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism.

S. Nakano, P. Bevilacqua, David J. Proctor, 2001, Biochemistry.

Specificity of the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR for double-stranded RNA: insights from thermodynamics and small-angle X-ray scattering.

P. Bevilacqua, L. Pollack, Joshua M Blose, 2012, Biochemistry.

Evolution of PKR combats viral mimicry

P. Bevilacqua, Laurie A. Heinicke, Rebecca Toroney, 2009 .

Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change.

D. Turner, D. Mathews, P. Bevilacqua, 1995, Biochemistry.

MeltR software provides facile determination of nucleic acid thermodynamics.

Brent M. Znosko, P. Bevilacqua, Jacob P Sieg, 2023, Biophysics Reports.

Biological solution conditions and flanking sequence modulate LLPS of RNA G-quadruplex structures

P. Bevilacqua, Allison M Williams, Taylor M. Dickson, 2022, RNA.

RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles

P. Bevilacqua, P. Dallaire, Melissa A. Mullen, 2010, Nucleic Acids Research.

Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry.

P. Bevilacqua, Joshua E. Sokoloski, 2012, Methods in molecular biology.

P. Bevilacqua, Rebecca Toroney, Chelsea M Hull, 2012, RNA.

Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR.

P. Bevilacqua, Chelsea M Hull, 2016, Accounts of chemical research.

Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid.

P. Bevilacqua, Nathan A. Siegfried, Andrea L Cerrone-Szakal, 2008, Journal of the American Chemical Society.

Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme

P. Bevilacqua, E. Rosta, Pallavi Thaplyal, 2014, Journal of the American Chemical Society.

Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme.

R. Kierzek, P. Bevilacqua, Kyle J. Messina, 2019, Biochemistry.

Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA.

P. Bevilacqua, Chelsea M Hull, 2015, Journal of molecular biology.

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Yiliang Ding, Yin Tang, C. Kwok, 2013, Nature.

Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors.

V. Misra, P. Bevilacqua, N. Veeraraghavan, 2009, Journal of the American Chemical Society.

A simple fluorescence method for pK(a) determination in RNA and DNA reveals highly shifted pK(a)'s.

P. Bevilacqua, Jennifer L. Wilcox, 2013, Journal of the American Chemical Society.

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells

P. Bevilacqua, P. Babitzke, Elizabeth A. Jolley, 2023, Nucleic acids research.

RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

C. Keating, P. Bevilacqua, R. Yamagami, 2023, Science advances.

Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism.

F. Major, P. Bevilacqua, A. Mokdad, 2008, RNA.

Measuring the activity and structure of functional RNAs inside compartments formed by liquid-liquid phase separation.

P. Bevilacqua, Raghav R. Poudyal, McCauley O. Meyer, 2021, Methods in enzymology.

Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity.

P. Bevilacqua, Lauren N. McKinley, Reuben G Kern, 2023, Biochemistry.

Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.

S. Nakano, P. Bevilacqua, 2001, Journal of the American Chemical Society.

Determination of in vivo RNA structure in low-abundance transcripts

Yiliang Ding, Yin Tang, C. Kwok, 2013, Nature Communications.