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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Publication Tags

These publication tags are generated from the output of this researcher. Click any tag below to view other Huck researchers working on the same topic.

Rna Catalysis Nucleotides Polymerization Bioreactors Catalytic Rna Genome Emulsions Dna Nucleic Acids Thermodynamics Polyamines Liposomes Compartments Chemistry Phase Separation Nucleic Acid Ph Value Messenger Rna Prebiotics Chlorides Polycationic Polymer Rna Structure Nucleotide Polymerization Reaction

Most Recent Publications

Single-cell probing of RNA structure

Elizabeth A. Jolley, Philip C. Bevilacqua, 2024, Nature Methods on p. 377-378

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

Jacob P. Sieg, Elizabeth A. Jolley, Melanie J. Huot, Paul Babitzke, Philip C. Bevilacqua, 2023, Nucleic Acids Research on p. 11298-11317

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

Allison M. Williams, Elizabeth A. Jolley, Michel Geovanni Santiago-Martínez, Cheong X.I.N. Chan, Robin R. Gutell, James Gregory Ferry, Philip C. Bevilacqua, 2023, RNA on p. 1610-1620

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 Assmann, H Chou, Philip C. Bevilacqua, 2023, Plant Cell on p. 1671-1707

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

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

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

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

Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity

L McKinley, R Kern, Sarah Assmann, Philip Bevilacqua, 2023, Biochemistry on p. 53-68

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

McCauley O. Meyer, Saehyun Choi, Christine Keating, Philip C. Bevilacqua, Ryota Yamagami, 2023, Methods in Enzymology on p. 81-126

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

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

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 RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance

Zhao Su, Yin Tang, Laura E. Ritchey, David C. Tack, Mengmeng Zhu, Philip C. Bevilacqua, Sarah M. Assmann, 2018, Proceedings of the National Academy of Sciences of the United States of America on p. 12170-12175

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

Fatma Pir Cakmak, Saehyun Choi, McCauley C.O. Meyer, Philip C. Bevilacqua, Christine D. Keating, 2020, Nature Communications

News Articles Featuring Philip Bevilacqua

Feb 15, 2024

Penn State chemist Eric Nacsa receives 2024 NSF CAREER Award

Eric Nacsa, assistant professor of chemistry, has been honored with a Faculty Early Career Development (CAREER) award from the U.S. National Science Foundation (NSF)

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Feb 15, 2024

Committee advances plan to rename Chemistry Building as 'Benkovic Building'

The Chemistry Building at the University Park campus will be renamed in honor of the careerlong scholarly impact of Stephen Benkovic, Atherton Professor of Chemistry

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Feb 14, 2024

Penn State biochemist Carsten Krebs named distinguished professor

Carsten Krebs, professor of chemistry and of biochemistry and molecular biology at Penn State, has been selected to receive the title of Distinguished Professor of Chemistry and Biochemistry and Molecular Biology

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Sep 26, 2023

Could RNA folding play a role in the origin of life?

New research in model protocells reveals naturally occurring chemical modifications to RNA molecules help them properly fold into functional structures.

Full Article

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.

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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.

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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.

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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.

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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.

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