Philip Bevilacqua

Co-Director, Center for RNA Molecular Biology; Distinguished Professor of Chemistry and of Biochemistry and 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 Genome Ions Nucleotides Polymerization Bioreactors Climate Emulsions Ion Arabidopsis Polyamines Phase Separation Proteins Liquids Nucleic Acids Temperature Free Energy Spermine Rna Folding Viruses Prediction Liposomes Guanine

Most Recent Papers

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

Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua, Sarah M. Assmann, 2022, Genome Biology

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

S Choi, Philip Bevilacqua, C Keating, 2022, Nature Commun.

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

Philip C. Bevilacqua, Allison M. Williams, Hong Li Chou, Sarah M. Assmann, 2022, RNA on p. 16-26

RNA sequence and structure control assembly and function of RNA condensates

Raghav R. Poudyal, Jacob P. Sieg, Bede Portz, Christine D. Keating, Philip C. Bevilacqua, 2021, RNA on p. 1589-1601

Investigation of the pK<sub>a</sub> of the nucleophilic O2' of the hairpin ribozyme

Andrew J. Veenis, Pengfei Li, Alexander V. Soudackov, Sharon Hammes-Schiffer, Philip C. Bevilacqua, 2021, Journal of Physical Chemistry B on p. 11869-11883

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

Allison M. Williams, Raghav R. Poudyal, Philip C. Bevilacqua, 2021, Biochemistry on p. 2715-2726

Functional Roles of Chelated Magnesium Ions in RNA Folding and Function

Ryota Yamagami, Jacob P. Sieg, Philip C. Bevilacqua, 2021, Biochemistry on p. 2374-2386

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

Xiaofeng Zheng, Philip C. Bevilacqua, 2021, Nucleic Acids Research

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

Raghav R. Poudyal, McCauley O. Meyer, Philip C. Bevilacqua, 2021, on p. 307-327

Inverse RNA folding workflow to design and test ribozymes that include pseudoknots

Mohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, David H. Mathews, 2021, on p. 113-143

Most-Cited Papers

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

Yiliang Ding, Yin Tang, Chun Kit Kwok, Yu Zhang, Philip C. Bevilacqua, Sarah M. Assmann, 2014, Nature on p. 696-700

RNA catalysis through compartmentalization

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

Bioreactor droplets from liposome-stabilized all-aqueous emulsions

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

Genome-Wide Analysis of RNA Secondary Structure

Philip C. Bevilacqua, Laura E. Ritchey, Zhao Su, Sarah M. Assmann, 2016, Annual Review of Genetics on p. 235-266

The RNA structurome

Chun Kit Kwok, Yin Tang, Sarah M. Assmann, Philip C. Bevilacqua, 2015, Trends in Biochemical Sciences on p. 221-232

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

Raghav R. Poudyal, Rebecca M. Guth-Metzler, Andrew J. Veenis, Erica A. Frankel, Christine D. Keating, Philip C. Bevilacqua, 2019, Nature Communications on p. 490

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

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg<sup>2+</sup>, Nucleotides, and RNA

Erica A. Frankel, Philip C. Bevilacqua, Christine D. Keating, 2016, Langmuir on p. 2041-2049

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

Raghav Poudyal, Fatma Cakmak, Christine Keating, Philip Bevilacqua, 2018, Biochemistry on p. 2509-2519

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