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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Research Keywords
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Recent Publications
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
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
In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans
Williams, A. M., Jolley, E. A., Santiago-Martínez, M. G., Chan, C. X. I. N., Gutell, R. R., Ferry, J. G. & Bevilacqua, P. C., Oct 2023, In: RNA. 29, 10, p. 1610-1620 11 p.Research output: Contribution to journal › Article › peer-review
Regulatory Mechanisms through RNA Conformational Switching and Dynamics
Bevilacqua, P. C. & Tolbert, B. S., Sep 30 2022, In: Journal of Molecular Biology. 434, 18, 167794.Research output: Contribution to journal › Editorial › peer-review
RNA multimerization as an organizing force for liquid–liquid phase separation
Bevilacqua, P. C., Williams, A. M., Chou, H. L. & Assmann, S. M., Jan 2022, In: RNA. 28, 1, p. 16-26 11 p.Research output: Contribution to journal › Article › peer-review
Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles
Choi, S., Meyer, M. C. O., Bevilacqua, P. C. & Keating, C. D., Oct 2022, In: Nature Chemistry. 14, 10, p. 1110-1117 8 p.Research output: Contribution to journal › Article › peer-review
Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis
Ferrero-Serrano, Á., Sylvia, M. M., Forstmeier, P. C., Olson, A. J., Ware, D., Bevilacqua, P. C. & Assmann, S. M., Dec 2022, In: Genome biology. 23, 1, 101.Research output: Contribution to journal › Article › peer-review