187. Bevilacqua, P. C., Williams, A. M., Chou, H. L., Assmann, S. M.* RNA multimerization as an organizing force for liquid-liquid phase separation. RNA (in press).
185. Veenis, A. J., Li, P., Soudackov, A. V., Hammes-Schiffer, S., Bevilacqua, P. C. Investigation of the pKa of the nucleophilic O2′ of the hairpin ribozyme. J. Phys. Chem. B. 43, 11869-11883 (2021). [PubMed]. 50 Free Downloads (link). CLICK HERE TO SEE DREW’S COVER ART!!
174. 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).
172. Yamagami, R., Huang, R. & Bevilacqua, P. C. Cellular concentrations of nucleotide diphosphate-chelated magnesium ions accelerate catalysis by RNA and DNA enzymes. Biochemistry (in press). [PubMed]
170. Poudyal, R., Keating, C. D., Bevilacqua, P. C. Polyanion-assisted catalysis inside complex coacervates. ACS Chem. Biol. 14, 1243-1248.
169. Bevilacqua, P. C., Harris, M. E., Piccirilli, J. A., Gaines, C., Ganguly, A., Kostenbader, K., Ekesan, S., York D. M. An ontology for facilitating discussion of catalytic strategies of RNA-cleaving enzymes. ACS Chem. Biol. 14, 1068-1076 (2019) [PubMed]
166. Yamagami, R., Kayedkhordeh, M., Mathews, D.H., Bevilacqua, P.C. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study. Nucleic Acids Res. 47, 29-42 (2019) [PubMed] (open access).
162. Messina, KJ & Bevilacqua, PC. Cellular small molecules contribute to twister ribozyme catalysis. J. Am. Chem. Soc. 140, 10578-10582 (2018) [PubMed] (link to 50 free e-prints).
161. 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].
155. Frankel, E.A. & Bevilacqua, P.C. “Complexity in pH-dependent ribozyme kinetics: Dark pKa shifts and wavy rate-pH profiles.” Biochemistry 57, 483-488 (2018). [PubMed]
154. 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] [Minor comments and additions].
151. Bingaman, J. L., Gonzalez, I. Y., Wang, B. & Bevilacqua, P. C. “Activation of the glmS ribozyme nucleophile via overdetermined hydrogen bonding.” Biochemistry 56, 4313-4317 (2017). [PubMed] (link to 50 free e-prints)
148. Frankel, E. A., Strulson, C., Keating, C. D. & Bevilacqua, P. C. “Cooperative interactions in the hammerhead ribozyme drive pKa shifting of G12 and its stacked base C17. Biochemistry 56, 2537-2548 (2017). [PubMed]
147. Bingaman, J. L., Messina, K. J., Bevilacqua, P. C. “Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics” Methods 120, 125-134 (2017). [PubMed]
146. Bingaman, J. L., Zhang, S., Stevens, D. R., Yennawar, N. H., Hammes-Schiffer, S., Bevilacqua, P. C. “GlcN6P Cofactor serves multiple catalytic roles in the glmS ribozyme” Nat. Chem. Biol. 13, 439-445 (2017). [PubMed]
144. Zhang, S., Stevens, D. R., Goyal, P., Bingaman, J., Bevilacqua, P.C. , Hammes-Schiffer, S. “Assessing the potential effects of active site Mg2+ ions in the glmS ribozyme-cofactor complex” J. Phys. Chem. Letters 7 , 3984-3988 (2016). [PubMed]
141. Ucisik, M. N., Bevilacqua, P. C., Hammes-Schiffer, S. “Molecular dynamics study of env22 twister ribozyme: Role of Mg2+ ions and hydrogen-bonding network in active site”. Biochemistry 55, 3834-3846. [PubMed]
130. Thaplyal, P., Ganguly, A., Hammes-Schiffer, S., Bevilacqua, P. C. “Inverse thio effects in the HDV ribozyme reveal that the reaction pathway is controlled by metal ion charge density” for Biochemistry 54, 2160–2175 (2015).
126. Zhang, S., Ganguly, A., Goyal, P., Bingaman, J. L., Bevilacqua, P. C., Hammes-Schiffer, S. “Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations” for J. Am. Chem. Soc. 137, 784-798 (2015). JACS Featured in JACS Spotlight
125. Thaplyal, P. and Bevilacqua, P.C. “Experimental approaches for measuring pKa’s in RNA and DNA” Methods Enzmol. 549, 188-219 (2014). [PubMed]
123. Ganguly, A., Thaplyal, P., Rosta, E., Bevilacqua, P. C., and Hammes-Schiffer, S. “Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.” J. Am. Chem. Soc. 136, 1483-1496 (2014). [PubMed]
119. Strulson, C.A., Yennawar, N.H., Rambo, R.P., and Bevilacqua, P.C. “Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions.” Biochemistry, 52, 8187-8197 (2013). [Pubmed]
118.Wilcox, J.L. and Bevilacqua, P.C. “pKa Shifting in double-stranded RNA (dsRNA) is highly dependent upon nearest neighbors and bulge positioning.” Biochemistry, 52, 7470-7476 (2013). [Pubmed]
117.Thaplyal, P., Ganguly, A., Golden, B.L., Hammes-Schiffer, S. and Bevilacqua, P.C. “Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme.” Biochemistry 52, 6499-6514 (2013). [Pubmed]
115. Wilcox, J.L and Bevilacqua, P.C. “A simple fluorescence method for pKa determination in RNA and DNA reveals highly shifted pKa’s” J. Am. Chem. Soc. 135, 7390-7393 (2013). [Pubmed]
114. Golden B.L., Hammes-Schiffer S., Carey P.R., Bevilacqua PC. “An integrated picture of HDV ribozyme catalysis.” Springer 2013. Rick Russell editor. pp 135-168. [Springer]
110. Chen, J., Ganguly, A., Miswan, Z., Hammes-Schiffer, S., Bevilacqua, P.C., Golden, B.L. “Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme” Biochemistry 52, 557-567 (2013). [Pubmed]
105. Strulson, C. A., Molden, R. C., Keating, C. D., Bevilacqua, P. C. “RNA catalysis through compartmentalization” Nature Chemistry 4, 941-946 (2012). [Pubmed]
102. Chadalavada, D. M., Cerrone-Szakal, A. L., Wilcox, J. L., Siegfried, N. A., Bevilacqua, P. C. “Mechanistic analysis of the Hepatitis Delta Virus (HDV) ribozyme: Methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage.” Methods Mol. Biol. 848, 21-40 (2012). [Pubmed]
99. 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]
98. Ganguly, A., Bevilacqua, P. C., Hammes-Schiffer, S. “Quantum Mechanical/Molecular Mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism.” J. Phys. Chem. Lett. 2, 2906-2911 (2011). [Pubmed]
97. 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]
96. Veeraraghavan, N., Ganguly, A., Golden, B. L., Bevilacqua, P. C., and Hammes-Schiffer, S. “Mechanistic strategies in the HDV ribozyme: Chelated and Diffuse Metal ion Interactions and Active Site Protonation.” J. Phys. Chem. B. 115, 8346-8357 (2011). [Pubmed]
94. Veeraraghavan, N., Ganguly, A., Chen, J. H., Bevilacqua, P. C., Hammes-Schiffer, S., and Golden, B. L. “A metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.” Biochemistry 50, 2672-2682 (2011). [Pubmed]
91. Veeraraghavan, N., Bevilacqua, P. C., Hammes-Schiffer, S. “Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments.” J. Mol. Biol. 402, 278-291 (2010). [Pubmed]
90. Chen, J.-H., Yajima, R., Chadalavada, D. M., Chase, E., Bevilacqua, P. C., Golden, B. L. “A 1.9 Å crystal structure of the HDV ribozyme pre-cleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage.” Biochemistry 49, 6508-6518 (2010). [Pubmed]
89. 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]
85. Siegfried, N. A., O’Hare, B., Bevilacqua, P. C. “Driving forces for nucleic acid pKa shifting: Effects of helix position, temperature, and ionic strength.” Biochemistry 49, 3225-3236 (2010). [Pubmed]
83. Gong, B., Chen, J.-H., Bevilacqua, P. C., Golden, B. L., and Carey, P. R. “Competition between Co(NH3)63+ and inner sphere Mg2+ ions in the HDV ribozyme.” Biochemistry 48, 11961-11970 (2009). [Pubmed]
81. Gong, B., Chen, J.-H., Yajima, R., Chen, Y., Chase, E., Chadalavada, D. M., Golden, B. L., Carey, P. R., and Bevilacqua, P. C. “Raman crystallography of RNA.” Methods 49, 101-111 (2009). [Pubmed]
75. Chen, J.-H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. “A catalytic metal ion interacts with the cleavage site GU wobble in the HDV ribozyme.” Biochemistry 48, 1498-1507 (2009). [Pubmed]
73. Bevilacqua, P. C., & Russell, R. “Editorial overview: Exploring the vast dynamics of RNA dynamics.” Curr. Opin. Chem. Biol. 12, 601-603 (2008). [Pubmed]
71. Cerrone-Szakal, A.L., Siegfried, N.A., Bevilacqua, P.C. “Mechanistic characterization of the HDV genomic ribozyme: Solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid.” J. Am. Chem. Soc. 130, 14504-14520 (2008). [Pubmed]
70. Cerrone-Szakal, A.L., Chadalavada, D.M., Golden, B.L., Bevilacqua, P.C. “Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis.” RNA 14, 1746-1760 (2008). [Pubmed]
69. Gong, B., Chen, Y., Christian, E.L., Chen, J.H., Chase, E., Chadalavada, D.M., Yajima, R., Golden, B.L., Bevilacqua, P.C., Carey, P.R. “Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography.” J. Am. Chem. Soc. 130, 9670-9672 (2008). [Pubmed]
65. Nallagatla, S.R., Hwang, J., Toroney, R., Zheng, X., Cameron, C.E., Bevilacqua. P.C. “5′-triphosphate-dependent activation of PKR by RNAs with short stem-loops.” Science 318, 1455-1458 (2007). [Pubmed]
64. Gong, B, Chen, J.H., Chase, E., Chadalavada, D.M., Yajima, R., Golden, B.L., Bevilacqua, P.C., Carey, P.R. “Direct measurement of a pKa near neutrality for the catalytic cytosine in the genomic HDV ribozyme by Raman crystallography.” J. Am. Chem. Soc. 129, 13335-13342 (2007). [Pubmed]
63. McGraw, A.P., Bevilacqua, P.C., Babitzke, P. “TRAP-5′ Stem-Loop interaction increases the effect the efficiency of transcription termination in the Bacillus subtillis trpEDCFBA operon leader region by increasing the rate of TRAP binding to the nascent transcript.” RNA 13, 2020-2033 (2007). [Pubmed]
62. Chadalavada, D.M., Cerrone-Szakal, A.L., Bevilacqua, P.C. “Wild-type is the optimal sequence of the HDV ribozyme under co-transcriptional conditions.” RNA 13, 2189-2201 (2007). [Pubmed]
58. Nakano, S., Bevilacqua, P.C. “Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons.” Biochemistry 46, 3001-3012 (2007). [Pubmed]
57. Yajima, R., Proctor, D.J., Kierzek, R., Kierzek, E., Bevilacqua, P.C. “A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme.” Chem. Biol. 14, 23-30 (2007). [Pubmed]
55. Bevilacqua, P.C., Yajima, R. “Nucleobase catalysis in ribozyme mechanism.” Curr. Opin. Chem. Biol. 10, 455-464 (2006). [Pubmed]
53. Bevilacqua, P. C., Brown, T. S., Chadalavada, D., Lecomte, J., Moody, E., and Nakano, S.-i. “Linkage between proton binding and folding in RNA: Implications for RNA catalysis.” Biochem. Soc. Trans. 33, 466-470 (2005). [Pubmed]
51. Moody, E. M., Lecomte, J. T. J., and Bevilacqua, P. C. “Linkage between proton binding and RNA folding: A thermodynamic framework and its experimental application for investigating pKa shifting.” RNA 11, 157-172 (2005). [Pubmed]
47. Paxon, T. L., Brown, T. S. Hsiao-yu, N. L. Brancato, S. J., Roddy, E. S., Bevilacqua, P. C., and Ewing, A. G. “Continuous monitoring of enzyme reactions on a microchip: Application to catalytic RNA self-cleavage.” Anal. Chem. 76, 6921-6927 (2004). (A 1 page overview of the article appears in the front of this issue.) [Pubmed]
45. Brown, T. S., Chadalavada, D. M., and Bevilacqua, P. C. “Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.” J. Mol. Biol. 341, 695-712 (2004). [Pubmed]
42. Bevilacqua, P. C. “Mechanism of catalytic RNA.” Biopolymers 73, 69-70 (2004). [Pubmed]
41. Bevilacqua, P. C., Brown, T. S., Nakano, S., and Yajima, R. “Catalytic roles for proton transfer and protonation in ribozymes.” Biopolymers 73, 90-109 (2004). [Pubmed]
36. Bevilacqua, P. C., Brown, T. S., Chadalavada, D. M., Parente, A. D. and Yajima, R. “Kinetic analysis of ribozyme cleavage.” In Kinetic Analysis of Macromolecules: A Practical Approach (K. Johnson, ed.) Oxford University Press. Chpt 3, 49-74 (2003). [pdf]
35. Nakano, S., Cerrone, A. L., and Bevilacqua, P. C. “Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.” Biochemistry, 42, 2982-2994 (2003). [Pubmed]
34. Bevilacqua, P. C. “Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of thehairpin ribozyme.” Biochemistry, 42, 2259-2265 (2003). [Pubmed]
26. Chadalavada, D. M., Senchak, S. E., and Bevilacqua, P. C. “The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots.” J. Mol. Biol., 317, 559-575 (2002).
25. Nakano, S. and Bevilacqua, P. C. “Proton inventory of the genomic HDV ribozyme in Mg2+-containing solutions.” J. Am. Chem. Soc., 123, 11333-11334 (2001). [Pubmed]
24. Nakano, S., Proctor, D. J., and Bevilacqua, P. C. “Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multi-channel reaction mechanism.” Biochemistry, 40, 12022-12038 (2001). [Pubmed]
20. 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]
19. Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. “General acid-base catalysis in the mechanism of an HDV ribozyme.” Science, 287, 1493-1497 (2000). [Pubmed]
14. Szewczak, A. A., Podell, E., Bevilacqua, P. C., and Cech, T. R. “Thermodynamic stability of the P4-P6 domain RNA tertiary structure measure by temperature gradient gel electrophoresis.” Biochemistry 37, 11162-11170 (1998). [Pubmed]
11. Turner, D. H., Li, Y., Fountain, M., Profenno, L. and Bevilacqua, P. C. “Dynamics of a group I ribozyme detected by spectroscopic methods.” In Nucleic Acids & Molecular Biology, eds Fritz Eckstein & David M. J. Lilley, 10, 19-32 (1996). (pdf)
10. Bevilacqua, P. C., Sugimoto, N. and Turner, D. H. “A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme.” Biochemistry 35, 648-658 (1996). [Pubmed] (pdf)
9. Li, Y., Bevilacqua, P. C., Mathews, D. and Turner, D. H. “Thermodynamic and activation parameters for binding of a pyrene labelled substrate by the Tetrahymena ribozyme: Docking is not diffusion controlled and is driven by a favorable entropy change.” Biochemistry 34, 14394-14399 (1995). [Pubmed] (pdf)
8. Bevilacqua, P. C., Li, Y. and Turner, D. H. “Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5′ cleavage site into a high free energy binding mode in the Tetrahymena ribozyme.” Biochemistry 33, 11340-11348 (1994). [Pubmed] (pdf)
7. Cech, T. R., Bevilacqua, P. C., Doudna, J. A., McConnell, T. S., Strobel, S. A., Weinstein, L. B. “Mechanism and structure of a catalytic RNA molecule.” In Proceedings of the Robert A. Welch Foundation, 91-110 (1993). [pdf]
6. Turner, D. H. and Bevilacqua, P. C. “Thermodynamic considerations for evolution by RNA.” Invited Chapter in RNA World, Cold Spring Harbor Press, eds Ray Gesteland and John Atkins, 447-464 (1993). (pdf)
5. Bevilacqua, P. C., Johnson, K. A. and Turner, D. H. “Cooperative and anticooperative binding to a ribozyme.” Proc. Natl. Acad. Sci. USA 90, 8357-8361 (1993). [Pubmed] (pdf)
4. Kierzek, R., Li, Y., Turner, D. H. and Bevilacqua, P. C. “5′-Amino pyrene provides a sensitive, non-perturbing fluorescent probe of RNA secondary and tertiary structure formation.” J. Am. Chem. Soc. 115, 4985-4992 (1993). [ACS Link] (pdf)
3. Bevilacqua, P. C., Kierzek, R., Johnson, K. A. and Turner, D. H. “Dynamics of ribozyme binding of substrate revealed by fluorescence detected stopped-flow.” Science 258, 1355-1358 (1992). [Pubmed] (pdf)
2.Bevilacqua, P. C. and Turner, D. H. “Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: Evidence for ribozyme specific interactions with 2′ OH groups.” Biochemistry 30, 10632-10640 (1991). [Pubmed] (pdf)
1.Sugimoto, N., Tomka, M., Kierzek, R., Bevilacqua, P. C. and Turner, D. H. “Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: Evidence for substrate and Mg2+ binding interactions.” Nucleic Acids Res. 17, 355-371 (1989). [Pubmed] (pdf)