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

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Rna Nucleotides Genome Catalysis Polymerization Bioreactors Rna Structure Climate Emulsions Dna Arabidopsis Polyamines Catalytic Rna Nucleic Acids Genes Temperature Thermodynamics Prediction Liposomes Nucleic Acid Chemistry Transcriptome Messenger Rna Chlorides Heat Shock Response

Most Recent Publications

Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis

Elizabeth A. Jolley, Helen Yakhnin, David Tack, Paul Babitzke, Philip C. Bevilacqua, 2023, RNA on p. 1365-1378

MeltR software provides facile determination of nucleic acid thermodynamics

Jacob P. Sieg, Sebastian J. Arteaga, Brent M. Znosko, Philip C. Bevilacqua, 2023, Biophysical Reports

Rock, scissors, paper: How RNA structure informs function

Sarah M. Assmann, Hong Li Chou, Philip C. Bevilacqua, 2023, Plant Cell on p. 1671-1707

Structure-seq of tRNAs and other short RNAs in droplets and in vivo

McCauley O. Meyer, Saehyun Choi, Christine D. Keating, Philip C. Bevilacqua, Ryota Yamagami, 2023,

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

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

Upstream Flanking Sequence Assists Folding of an RNA Thermometer

Elizabeth Jolley, Kathryn Bormes, Philip C. Bevilacqua, 2022, Journal of Molecular Biology on p. 13

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 on p. e2201237119

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

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

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

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

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

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

Jul 06, 2023

Penn State chemist Stephen Benkovic named Atherton Professor

Stephen Benkovic, Evan Pugh Professor and Holder of the Eberly Family Chair in Chemistry at Penn State, has been honored by Penn State with the title of Atherton Professor.

Full Article

Apr 20, 2023

Grad Students in Huck Labs Win Awards for Innovative Research

Two graduate students—one in the Huck's Neuroscience program and the other in the Eberly College of Science's BMMB program—have been named recipients of an award available to those working in Biochemistry and Molecular Biology labs. Both PIs are also part of the Huck.

Full Article

Apr 17, 2023

Structured Nucleic Acids Day, Robert Simpson and Sons Lecture set for April 18

A half-day symposium on structured (noncanonical) nucleic acids will be held on Tuesday, April 18, in Foster Auditorium, Paterno Library, Penn State University Park.

Full Article

Feb 23, 2023

Nobel Prize-winning Penn State alumnus Paul Berg dies

Penn State alumnus Paul Berg, who received the 1980 Nobel Prize in chemistry, died Feb. 15 at his home in Stanford, California, surrounded by loved ones. He was 96.

Full Article

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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