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 Graduate Students

Huck Affiliations

Links

Publication Tags

Rna Nucleotides Genome Catalysis Thermodynamics Polymerization Catalytic Rna Bioreactors Rna Structure Climate Emulsions Dna Polyamines Arabidopsis Phase Separation Nucleic Acids Temperature Genes Liposomes Prediction Nucleic Acid Protein Ground State Molecular Dynamics Transcriptome

Most Recent Publications

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

The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability

Jacob P. Sieg, Lauren N. McKinley, Melanie J. Huot, Neela H. Yennawar, Philip C. Bevilacqua, 2022, Biochemistry on p. 2579-2591

Regulatory Mechanisms through RNA Conformational Switching and Dynamics

Philip C. Bevilacqua, Blanton S. Tolbert, 2022, Journal of Molecular Biology

Upstream Flanking Sequence Assists Folding of an RNA Thermometer

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

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

Allison M. Williams, Taylor M. Dickson, Claudia A. Lagoa-Miguel, Philip C. Bevilacqua, 2022, RNA on p. 1197-1209

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

Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua, 2022, Proceedings of the National Academy of Sciences of the United States of America

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

Saehyun Choi, McCauley C.O. Meyer, Philip C. Bevilacqua, Christine D. Keating, 2022, Nature Chemistry

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

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

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 Ritchey, Zhao Su, Sarah M. Assmann, 2016, Annual Review of Genetics on p. 235--266

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

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

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

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

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

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

Experimental approaches for measuring pK<sub>a</sub>'s in RNA and DNA

Pallavi Thaplyal, Philip C. Bevilacqua, 2014, Methods in enzymology on p. 189-219

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

Yiliang Ding, Chun Kit Kwok, Yin Tang, Philip C. Bevilacqua, Sarah M. Assmann, 2015, Nature Protocols on p. 1050-1066

News Articles Featuring Philip Bevilacqua

Aug 31, 2022

Boal recieves Early Career Award from Society of Biological Inorganic Chemistry

Amie Boal, professor of chemistry and of biochemistry and molecular biology, has been named a recipient of the 2022 Early Career Award from the International Society for Biological Inorganic Chemistry (SBIC), an organization dedicated to advancing research and promoting understanding of biological inorganic chemistry within academia, industry, and the general public

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Jun 13, 2022

Climate-associated genetic switches found in plants

Genetic variants that can act as switches directing structural changes in the RNA molecules that code for proteins in plants have been experimentally validated in plants for the first time. The changes to RNA structure can affect the molecule’s stability, how it interacts with other molecules, and how efficiently it can be translated into protein — all of which can impact its function and the traits of the plant.

Full Article

Aug 20, 2019

Penn State Chemistry Alum Recognized with Young Scientists Award

Kathleen Leamy has been awarded the 2019 Gordon Hammes Scholar Award, based on a 2018 article she co-authored with the Huck Institutes' Neela Yennawar and Phillip Bevilacqua.

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Apr 19, 2019

NIH Trainees Juan Cerda and Catherine Douds Receive NSF-GRFP Honorable Mentions

Juan Cerda and Catherine Douds, both members of NIH-sponsored training programs overseen by the Huck Institutes, were recognized for their promising research ideas.

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