(Undergraduate authors denoted in Penn State blue)
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:2023.04.03.535424 (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]