(Undergraduate authors denoted in Penn State blue)
30. McKinley, L. N., Meyer, M. O., Sebastian, A., Chang, B. K., Messina, K. J., Albert, I., Bevilacqua, P. C. Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections. bioRxiv (2024). [PubMed]
29. Forstmeier, P. C., Meyer, M. O., Bevilacqua, P. C. The Functional RNA IDentification (FRID) pipeline: Identification of potential pseudoknot-containing RNA elements as therapeutic targets for SARS-CoV-2. bioRxiv (2023). [PubMed].
28. Sieg, J. P., McKinley, L. N., Huot, M. J., Yennawar, N. H., Bevilacqua, P. C. The metabolome weakens RNA thermodynamic stability and strengthens RNA chemical stability. Biochemistry 61, 2579-2591 (2022). [PubMed].
27. Jolley, E. A., Bormes, K. M., Bevilacqua, P. C. Upstream flanking sequence assists folding of an RNA thermometer. J. Mol. Biol. 434, 167786 (2022). [PubMed].
26. Williams, A. M., Dickson, T. M., Lagoa-Miguel, C. A., Bevilacqua, P. C. Biological solution conditions and flanking sequence modulate LLPS of RNA G-quadruplex structures. RNA 28, 1197-1209 (2022). [PubMed].
25. Ferrero-Serrano, Á., Sylvia, M. M., Forstmeier, P. C., Olson, A. J., Ware, D., Bevilacqua, P. C., Assmann, S. M.* Experimental demonstration and pan-structurome prediction of climate associated riboSNitches in Arabidopsis. to Genome Biol. 23, 1-28 (2022). [PubMed].
24. Renda, A., Poly, S., Lai, Y. J., Pannuri, A., Yakhnin, H., Potts, A. H., Bevilacqua, P. C., Romeo, T. & Babitzke, P. CsrA-Mediated Translational Activation of ymdA Expression in Escherichia coli. mBio 11 (2020). [PubMed].
23. Yamagami, R., Huang, R. & Bevilacqua, P. C. Cellular concentrations of nucleotide diphosphate-chelated magnesium ions accelerate catalysis by RNA and DNA enzymes. Biochemistry 58, 3971-3979 (2019). [PubMed]
22. Messina, K. J., Kierzek, R., Tracey, M. A., Bevilacqua, P. C. Small molecule rescue and glycosidic conformational analysis of the twister ribozyme. Biochemistry 58, 4857-4868 (2019). [PubMed].
21. Poudyal, R.R., Guth, R.M., Veenis, A.J., Frankel, E.A., Keating, C.D., Bevilacqua, P.C. RNA functions inside membraneless compartments: Non-enzymatic RNA polymerization, small-molecule binding, and enhanced ribozyme catalysis. Nat. Commun. 10, 1-13 (2019) [PubMed] (open access).
20. Bevilacqua, PC, Bingaman, JL, Frankel, E A, Messina, K J, Seith, D D. Key catalytic strategies in ribozymes, Chapter in “Catalysis in Chemistry and Biology”, Proceedings of the 24th International Solvay Conference in Chemistry: Catalysis in Chemistry and Biology. (2018) [Google Books].
19. Seith, D., Bingaman, J. L., Veenis, A.J., Button, A.C., & Bevilacqua, P. C. “Elucidation of catalytic strategies of small nucleolytic ribozymes from comparative analysis of active sites.” ACS Catalysis 8, 314-327 (2018) [link] (link to 50 free e-prints).
18. Sherlock, M. E., Rumble, C. A., Kwok, C. K., Breffke, J., Maroncelli, M., Bevilacqua, P. C. “Steady-state and time-resolved studies into the origin of the intrinsic fluorescence of G-quadruplexes.” J. Phys. Chem. B 120, 5146-5158 (2016). [PubMed]
17. Hull, C. M., Anmangandla, A., Bevilacqua, P. C. “Bacterial riboswitches and ribozymes potently activate the human innate immune sensor PKR” ACS Chem. Biol. 11, 1118-1127 (2016). [PubMed]
16. Crenshaw, E., Leung, B. P., Kwok, C. K., Olson, K., Sebastian, N. P., Ansaloni, S., Schweitzer-Stenner, R., Akins, M. R., Bevilacqua, P. C., Saunders, A. J. “Amyloid Precursor Protein Translation is Regulated by a 3’UTR Guanine Quadruplex” PLoS One 10, e0143160, 1-18 (2015). [PubMed]
15. Kwok, C. K., Sherlock, M. E., and Bevilacqua, P. C. “Effect of Loop Sequence and Loop Length on the Intrinsic Fluorescence of G-Quadruplexes.” Biochemistry 52, 3019-3021 (2013). [PubMed]
14. Kwok, C.K., Ding, Y., Sherlock, M.E., Assmann, S.M., Bevilacqua, P.C. “A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation.” Anal. Biochem. 435, 181-186 (2013). [PubMed].
13. Tubbs, J.D., Condon, D.E., Kennedy, S.D., Hauser, M., Bevilacqua, P.C., Turner, D.H. “The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics.” Biochemistry 52, 996-1010 (2013). [PubMed].
12. Kwok, C.K., Sherlock, M.E., Bevilacqua, P.C. “Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes” Angew. Chem. Int. Ed. Engl. 52, 683-686 (2013). [PubMed]
11. Bevilacqua, P. C., Breen, P. C., Thaplyal, P. “Prospecting for aptamers in the human genome” Chem. Biol., 19, 1218-1220 (2012). [Pubmed]
10. Sokoloski, J. E., Dombrowski, S. E., Bevilacqua, P. C. “Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer.” Biochemistry 51, 565-572 (2012). [Pubmed]
9. Wilcox, J. L., Ahluwalia, A. K., Bevilacqua, P. C. “Charged nucleobases and their potential for RNA catalysis.” Accounts Chem. Res. 44, 1270-1279 (2011). [Pubmed]
8. Sokoloski, J. E., Godfrey, S. A., Dombrowski, S. E., Bevilacqua, P. C. “Prevalence of syn nucleobases in the active sites of functional RNAs.” RNA 17, 1775-1787 (2011). [Pubmed]
7. Mullen, M. A., Olson, K. J., Dallaire, P., Major, F., Assmann, S. M., Bevilacqua, P. C. “RNA G-quadruplexes in the model plant species Arabidopsis thaliana: Prevalence and possible functional roles.” Nucleic Acids Res. 38 8149-8163 (2010). [Pubmed]
6. Chadalavada, D. M., Gratton, E., and Bevilacqua, P. C. “The human HDV-like CPEB3 ribozyme is intrinsically fast reacting” Biochemistry 49, 5321-5330 (2010). [Pubmed]
5. Blose, J. M., Lloyd, K. P., and Bevilacqua, P. C. “Portability of the GN(R)A hairpin loop motif between RNA and DNA.” Biochemistry 48, 8787-8794 (2009). [Pubmed]
4. Siegfried, N.A., Metzger, S.L., Bevilacqua, P.C. “Folding cooperativity in RNA and DNA is dependent on position in the helix.” Biochemistry 46, 172-181 (2007). [Pubmed]
3. Moody, E. M., Feerrar, J. C., and Bevilacqua, P. C. “Evidence that folding of RNA tetraloop hairpin is less cooperative than its DNA counterpart.” Biochemistry, 43, 7992-7998 (2004). [Pubmed]
2. Nakano, M., Moody, E. M., Liang, J., and Bevilacqua, P. C. “Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc).” Biochemistry, 41, 14281-14292 (2002). [Pubmed]
1. Chadalavada, D. M., Knudsen, S. K., Nakano, S., and Bevilacqua, P. C. “A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme.” J. Mol. Biol. 301, 349-368 (2000). [Pubmed]