Philip Bevilacqua

Co-Director, Center for RNA Molecular Biology; Distinguished Professor of Chemistry and Biochemistry & Molecular Biology

Philip Bevilacqua

Research Summary

RNA folding in vivo and genome-wide; RNA regulation of gene expression; Ribozyme Mechanism; roles RNA may have played in the emergence of life on early earth

Huck Affiliations

Links

Publication Tags

Rna Catalytic Rna Catalysis Ions Dna Viruses Nucleotides Acids Fluorescence Enzymes Hepatitis Delta Virus Bioreactors Emulsions Metals Messenger Rna Liposomes Molecular Dynamics Magnesium Free Energy Polyanions Diphosphates Lewis Acids Nucleophiles Crystal Structure Catalytic Domain

Most Recent Papers

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

Joseph A. Waldron, David C. Tack, Laura E. Ritchey, Sarah L. Gillen, Ania Wilczynska, Ernest Turro, Philip C. Bevilacqua, Sarah M. Assmann, Martin Bushell, John Le Quesne, 2019, Genome biology

Small molecule rescue and glycosidic conformational analysis of the twister ribozyme

Kyle J. Messina, Ryszard Kierzek, Matthew A. Tracey, Philip C. Bevilacqua, 2019, Biochemistry on p. 4857-4868

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

Kathleen A. Leamy, Ryota Yamagami, Neela H. Yennawar, Philip C. Bevilacqua, 2019, Proceedings of the National Academy of Sciences of the United States of America on p. 23075-23082

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

Ryota Yamagami, Ruochuan Huang, Philip C. Bevilacqua, 2019, Biochemistry on p. 3971-3979

Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates

Raghav R. Poudyal, Christine D. Keating, Philip C. Bevilacqua, 2019, ACS chemical biology on p. 1243-1248

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

David Mitchell, Andrew J. Renda, Catherine A. Douds, Paul Babitzke, Sarah M. Assmann, Philip C. Bevilacqua, 2019, RNA on p. 147-157

StructureFold2

David Tack, Yin Tang, Laura E. Ritchey, Sarah Mary Assmann, Philip C. Bevilacqua, 2018, Methods on p. 12-15

Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites

Daniel D. Seith, Jamie L. Bingaman, Andrew J. Veenis, Aileen C. Button, Philip C. Bevilacqua, 2018, ACS Catalysis on p. 314-327

Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding

Jamie L. Bingaman, Inanllely Y. Gonzalez, Bo Wang, Philip C. Bevilacqua, 2017, Biochemistry on p. 4313-4317

Structure-seq2

Laura E. Ritchey, Zhao Su, Yin Tang, David C. Tack, Sarah M. Assmann, Philip C. Bevilacqua, 2017, Nucleic acids research on p. e135

Most-Cited Papers

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

Bart R. Anderson, Hiromi Muramatsu, Subba R. Nallagatla, Philip C. Bevilacqua, Lauren H. Sansing, Drew Weissman, Katalin Karikó, 2010, Nucleic acids research on p. 5884-5892

RNA catalysis through compartmentalization

Christopher A. Strulson, Rosalynn C. Molden, Christine Dolan Keating, Philip C. Bevilacqua, 2012, Nature Chemistry on p. 941-946

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

Jui Hui Chen, Rieko Yajima, Durga M. Chadalavada, Elaine Chase, Philip C. Bevilacqua, Barbara L. Golden, 2010, Biochemistry on p. 6508-6518

Bioreactor droplets from liposome-stabilized all-aqueous emulsions

Daniel C. Dewey, Christopher A. Strulson, David N. Cacace, Philip C. Bevilacqua, Christine Dolan Keating, 2014, Nature communications

Determination of in vivo RNA structure in low-abundance transcripts

Chun Kit Kwok, Yiliang Ding, Yin Tang, Sarah M. Assmann, Philip C. Bevilacqua, 2013, Nature communications

Charged nucleobases and their potential for RNA catalysis

Jennifer L. Wilcox, Amarpreet K. Ahluwalia, Philip C. Bevilacqua, 2011, Accounts of Chemical Research on p. 1270-1279

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

Narayanan Veeraraghavan, Abir Ganguly, Jui Hui Chen, Philip C. Bevilacqua, Sharon Hammes-Schiffer, Barbara L. Golden, 2011, Biochemistry on p. 2672-2682

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

Jason D. Tubbs, David E. Condon, Scott D. Kennedy, Melanie Hauser, Philip C. Bevilacqua, Douglas H. Turner, 2013, Biochemistry on p. 996-1010

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

Abir Ganguly, Pallavi Thaplyal, Edina Rosta, Philip C. Bevilacqua, Sharon Hammes-Schiffer, 2014, Journal of the American Chemical Society on p. 1483-1496

A simple fluorescence method for pK<sub>a</sub> determination in RNA and DNA reveals highly shifted pK<sub>a</sub>'s

Jennifer L. Wilcox, Philip C. Bevilacqua, 2013, Journal of the American Chemical Society on p. 7390-7393