Research Summary
Biological chemistry of RNA, characterization of RNA catalysis and folding, characterization of the RNA-dependent regulation of human viral response and RNA folding in plants as a response to environmental stress.
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Recent Publications
Primitive Molecular Buffering by Low-Multivalency Coacervates
Choi, S., Liu, S. P., Meyer, M. O., Bevilacqua, P. C. & Keating, C. D., Aug 21 2025, In: Journal of Physical Chemistry B. 129, 33, p. 8368-8381 14 p.Research output: Contribution to journal › Article › peer-review
Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor
Fordjour, G. N. R., Ghosh, A., Ferry, J. G., Armache, J. P., Bevilacqua, P. C. & Murakami, K. S., Nov 2025, In: Journal of Biological Chemistry. 301, 11, 110686.Research output: Contribution to journal › Article › peer-review
VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction
Kirven, K. J., Bevilacqua, P. C. & Assmann, S. M., Jun 1 2025, In: NAR Genomics and Bioinformatics. 7, 2, lqaf066.Research output: Contribution to journal › Article › peer-review
CHiTA: A scarless high-throughput pipeline for characterization of ribozymes
McKinley, L. N. & Bevilacqua, P. C., Feb 2025, In: Methods. 234, p. 120-130 11 p.Research output: Contribution to journal › Article › peer-review
Identification and characterization of shifted G•U wobble pairs resulting from alternative protonation of RNA
Saon, M. S., Douds, C. A., Veenis, A. J., Pearson, A. N., Yennawar, N. H. & Bevilacqua, P. C., Aug 12 2025, In: Nucleic acids research. 53, 14, gkaf575.Research output: Contribution to journal › Article › peer-review
Erratum: Correction to "The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability" (Biochemistry (2022) 61 22 DOI: 10.1021/acs.biochem.2c00488.)
Sieg, J. P., McKinley, L. N., Huot, M. J., Yennawar, N. H. & Bevilacqua, P. C., Aug 5 2025, In: Biochemistry. 64, 15, p. 3486 1 p.Research output: Contribution to journal › Comment/debate › peer-review
A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS
Douds, C. A., Babitzke, P. & Bevilacqua, P. C., Jul 2024, In: RNA. 30, 7, p. 901-919 19 p.Research output: Contribution to journal › Article › peer-review
Single-cell probing of RNA structure
Jolley, E. A. & Bevilacqua, P. C., Mar 2024, In: Nature methods. 21, 3, p. 377-378 2 p.Research output: Contribution to journal › Comment/debate › peer-review
Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections
McKinley, L. N., Meyer, M. O., Sebastian, A., Chang, B. K., Messina, K. J., Albert, I. & Bevilacqua, P. C., Dec 11 2024, In: Nucleic acids research. 52, 22, p. 14133-14153 21 p.Research output: Contribution to journal › Article › peer-review
Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity
McKinley, L. N., Kern, R. G., Assmann, S. M. & Bevilacqua, P. C., Jan 2 2024, In: Biochemistry. 63, 1, p. 53-68 16 p.Research output: Contribution to journal › Article › peer-review
Rock, scissors, paper: How RNA structure informs function
Assmann, S. M., Chou, H. L. & Bevilacqua, P. C., Jun 2023, In: Plant Cell. 35, 6, p. 1671-1707 37 p.Research output: Contribution to journal › Review article › peer-review
Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis
Jolley, E. A., Yakhnin, H., Tack, D. C., Babitzke, P. & Bevilacqua, P. C., Sep 2023, In: RNA. 29, 9, p. 1365-1378 14 p.Research output: Contribution to journal › Article › peer-review
RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life
Meyer, M. O., Yamagami, R., Choi, S., Keating, C. D. & Bevilacqua, P. C., 2023, In: Science Advances. 9, 38, eadh5152.Research output: Contribution to journal › Article › peer-review
In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells
Sieg, J. P., Jolley, E. A., Huot, M. J., Babitzke, P. & Bevilacqua, P. C., Nov 10 2023, In: Nucleic acids research. 51, 20, p. 11298-11317 20 p.Research output: Contribution to journal › Article › peer-review
MeltR software provides facile determination of nucleic acid thermodynamics
Sieg, J. P., Arteaga, S. J., Znosko, B. M. & Bevilacqua, P. C., Jun 14 2023, In: Biophysical Reports. 3, 2, 100101.Research output: Contribution to journal › Article › peer-review