207. McKinley, L. N., Bevilacqua, P. C. CHiTA: A scarless high-throughput pipeline for characterization of ribozymes. Methods (2024) in press. [PubMed]
206. 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. Nucleic Acids Res. (2024). [PubMed]
205. Douds, C. A.; Babitzke, P.; Bevilacqua, P. C. A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS. RNA (2024). [PubMed]
202. Sieg, J. P., Jolley, E. A., Huot, M. J., Babitzke, P., Bevilacqua, P. C. In vivo-like nearest neighbor parameters accurately predict fractional base-pairing in cells. Nucleic Acids Res. (in press). [PubMed]
201. Meyer M.O., Yamagami R., Choi S., Keating C.D., Bevilacqua P.C. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life. Sci. Adv. 22, 9(38):eadh5152 (2023). [PubMed].
200. Williams, A. M., Jolley, E. A., Santiago-Martínez, M. G., Chan, C. X., Gutell, R. R., Ferry, J. G., Bevilacqua, P. C. In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans. RNA 29, 1610-1620 (2023). [PubMed]
199. Meyer, M. O., Choi, S., Keating, C. D., Bevilacqua, P. C. & Yamagami, R. Structure-seq of tRNAs and other short RNAs in droplets and in vivo. Methods Enzymol. 681, 81-126 (2023). [PubMed].
198. Jolley, E. A., Yakhnin, H., Tack, D. C., Babitzke, P. & Bevilacqua, P. C. Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis. RNA 29, 1368-1378 (2023) (2023).
197. Sieg J.P., Arteaga S.J., Znosko B.M., Bevilacqua PC. Meltr software provides facile determination of nucleic acid thermodynamics. Biophys Rep 3, 100101 (2023). [PubMed].
196. Assmann S.M., Chou H.L., Bevilacqua P.C. Rock, scissors, paper: How RNA structure informs function. Plant Cell. (in press). [PubMed].
194. 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].
193. Bevilacqua, P. C., Tolbert, B. S. Regulatory mechanisms through RNA conformational switching and dynamics, Mol. Biol. 434, 167794 (2022). [PubMed].
192. Jolley, E. A., Bormes, K. M., Bevilacqua, P. C. Upstream flanking sequence assists folding of an RNA thermometer. Mol. Biol. 434, 167786 (2022). [PubMed].
191. 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].
190. Yamagami, R., Sieg, J., Assmann, S. A., Bevilacqua, P. C. Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress. Proc. Natl. Acad. Sci. 119, e2201237119 (2022). [PubMed].
188. Choi, S., Bevilacqua, P. C., Keating, C. D. Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles. Nature Chem. 14, 1110-1117 (2022).
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). [PubMed]. Article (link).
186. Poudyal, R. R., Sieg, J. P., Portz, B., Keating, C. D., Bevilacqua, P. C. RNA sequence and structure assembly and function of RNA condensates. RNA 12, 1589-1601 (2021). [PubMed]. Article (link). 50 free downloads (link).
184. Williams, A. M., Poudyal, R., Bevilacqua, P. C. Long tracts of guanines drive aggregation of RNA G-quadruplexes in the presence of spermine. Biochemistry 60, 2715-2726 (2021). [PubMed]. 50 Free Downloads (link).
183. Yamagami, R., Sieg, J. P., Bevilacqua, P. C. Functional Roles of Chelated Magnesium Ions in RNA Folding and Function. Biochemistry 60, 2374-2386 (2021). [PubMed] 50 Free Downloads (link).
178. Kayedkhordeh, M., Yamagami, R., Bevilacqua, P. C., Mathews, D. H. Inverse RNA folding workflow to design and test ribozymes including pseudoknots. Mol. Biol. (in press).
177. Ritchey, L. E., Tack, D. C., Yakhnin, H., Jolley, E. A., Assmann, S. M., Bevilacqua, P. C., Babitzke, P. Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis. RNA (in press). [PubMed].
176. Tack, D. C.; Su, Z.; Yu, Y.; Bevilacqua, P. C.; Assmann, S. M. Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. RNA (2020). [PubMed].
173. Leamy, K. A., Yamagami, R., Yennawar, N., Bevilacqua, P. C. Single nucleotide control of tRNA folding cooperativity. Proc Natl. Acad. Sci. 116, 23075-23082 (2019).[PubMed].
172. 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]
171. Mitchell, D., Assmann, S. M., Bevilacqua, P. C. Probing RNA structure in vivo. Curr. Opin. Struct. Biol. 59, 151-158 (2019). [PubMed].
168. Ritchey, L.E., Su, Z., Assmann, S.M., Bevilacqua, P.C. In vivo genome-wide RNA structure probing with Structure-seq2. Methods Mol. Biol. 1933, 305-341 (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).
165. Mitchell III, D., Renda, A.J., Douds, C.A, Babitzke, P., Assmann, S.M., Bevilacqua, P.C. In vivo structural probing of uracil and guanine base pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) RNA 25, 147-157 (2019) [PubMed].
164. Su, Z., Tang, Y., Ritchey, L.E., Tack, D.C., Zhu, M., Bevilacqua, P. C., Assmann, S. M. Genome-wide RNA structurome reprogramming reveals temperature-dependent regulation. Proc. Natl. Acad. Sci. 115, 12170-12175 (2018) [PubMed] (open access).
163. Bevilacqua, P.C. & Assmann, S.M. Technique development for probing RNA structure in vivo and genome-wide. Book Chapter in RNA World 5th Editors: J. Atkins, T.R. Cech, J. A. Steitz. (2018). [PubMed] (link to 50 free e-prints).
160. Yamagami R, Bingaman JL, Frankel EA, Bevilacqua PC. Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis. Nature Communications 9, 2149 (2018) [PubMed] (open access).
156. Tack, D. C., Tang, Y., Ritchey, L. E., Assmann, S. M., Bevilacqua, P. C. “StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.” Methods 143, 12-15 (2018) [PubMed].
153. Spasic, A., Assmann, S. M., Bevilacqua, P. C., & Mathews, D. H. “Modeling RNA secondary structure folding ensembles using SHAPE mapping data.” Nucleic Acids Res. 46. 314-323 (2018) [PubMed].
152. Mitchell, D. III, Ritchey, L. E., Park, H., Babitzke, P., Assmann, S. A., & Bevilacqua, P. C. “Glyoxals as in vivo RNA structural probes of guanine base pairing.” RNA 24, 114-124 (2018). [PubMed]
150. Leamy, K. A., Yennawar, N. H. & Bevilacqua, P. C. “Cooperative RNA folding under cellular conditions arises from both tertiary structure stabilization and secondary structure destabilization.” Biochemistry 56, 3422-3433 (2017). [PubMed] (link for 50 free e-prints)
149. Ritchey, L. E., Su, Z., Tang, Y., Tack, D. C., Assmann, S. M. & Bevilacqua, P. C. “Structure-seq2: Sensitive and accurate genome-wide profiling of RNA structure in vivo.” Nucleic Acids Res. 45, e135 (2017). [PubMed]
143. Bevilacqua, P. C., Ritchey, L. E., Su, Z., Assmann, S. M. “Genome-wide analysis of RNA secondary structure”. Annu. Rev. Genet. 50, 235-266 (2016). [PubMed]
142. Leamy, K. A., Assmann, S. M., Mathews, D. H., Bevilacqua, P. C.. “Bridging the gap between in vitro and in vivo RNA folding.” Q. Rev. Biophys. 49, e10 (2016). [PubMed]
139. 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]
136. Yennawar, N. H., Fecko, J. A., Showalter, S. A., Bevilacqua, P. C. “A high-throughput biological calorimetry core—Steps to startup, run, and maintain a multi-user facility” Methods Enzymol. 567, 2016, 435-460 (2016). [PubMed]
135. Tang, Y., Assmann, S. M., Bevilacqua, P. C. “Protein structure is related to RNA structural reactivity in vivo” Accepted November 2015. Awaiting publication in 2016 in special issue “Challenges in RNA Structural Modeling and Design”. J. Mol. Biol. 428, 758-766 (2016). [PubMed]
134. 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]
132. Tang, Y., Bouvier, E., Ding, Y., Nekrutenko, A., Bevilacqua, P.C. Assmann, S. M. “StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo” Bioinformatics 31, 2668-2675. [PubMed]
131. Ding. Y., Kwok, C. K., Tang, Y., Bevilacqua, P. C., Assmann, S. M. “Structure-Seq: Genome-wide profiling of in vivo RNA structure at single nucleotide resolution” Nat. Protoc. 10, 1050-1066 (2015). [PubMed]
129. Kwok, C.K., Tang, Y., Assmann, S. M., Bevilacqua, P. C. “The RNA Structurome: Transcriptome-Wide Structure Probing with Next-Gen Sequencing” for Trends Biochem. Sci. 40, 221-232 (2015). [TiBS]
127. Kwok, C. K., Ding, Y., Shahid, S. Assmann, S. M., and Bevilacqua, P. C. “A stable RNA G-quadruplex within the 5’UTR of Arabidopsis thaliana ATR mRNA downregulates translation” for Biochem. J. 467, 91-102 (2015). [Biochem. J.]
122. Ding, Y., Tang, Y., Kwok, C.K., Zhang, Y., Bevilacqua, P.C. & Assmann, S.M. “In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.” Nature 505, 696-700 (2014).[Pubmed]
121. Strulson, C. A., Boyer, J. A., Whitman, E. E. & Bevilacqua, P. C. “Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions.” RNA 20, 331-347 (2014). [PubMed]
120. Kwok, C. K., Ding, Y., Tang, Y., Assmann, S. M. & Bevilacqua, P. C. “Determination of in vivo RNA structure in low-abundance transcripts.” Nature Commun. 4, 2971 (2013). [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]
116. 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]
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]
112. 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].
111. 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].
109. 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]
103. Sokoloski, J. E., Bevilacqua, P. C. “Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry.” Methods Mol. Biol. 905, 145-74 (2012). [Pubmed]
101. Mullen, M. A., Assmann, S. M., Bevilacqua, P. C. “Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity.” J. Am. Chem. Soc. 134, 812-815 (2012). [Pubmed]
92. 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]
86. Siegfried, N. A., Kierzek, R., and Bevilacqua, P. C. “Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity.” J. Am. Chem. Soc. 132, 5342-5344 (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]
84. Chadalavada, D. M., and Bevilacqua, P. C. “Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with applications to in vitro selections.” Methods Enzymol. 468, 389-408 (2009). [Pubmed]
80. 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]
77. Blose, J. M., Proctor, D. J., Misra, V. K., and Bevilacqua, P. C. “Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors.” J. Am. Chem. Soc. 131, 8474-8484 (2009). [Pubmed]
76. Siegfried, N. A., & Bevilacqua, P. C. “Thinking inside the box: Designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding.” Methods Enzymol. 455, 365-393 (2009). [Pubmed]
67. Bevilacqua, P.C., Blose, J.M. “Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.” Annu. Rev. Phys. Chem. 59, 79-103 (2008). [Pubmed]
59. Blose, J.M., Silverman, SK, Bevilacqua, P.C. “A simple molecular model for thermophilic adaptation of functional nucleic acids.” Biochemistry 46, 4232-4240 (2007). [Pubmed]
56. 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]
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]
48. Proctor, D. J., Ma, H., Kierzek, E., Kierzek, R., Gruebele, M., and Bevilacqua, P. C. “Folding thermodynamics and kinetics of YNMG RNA hairpins: Specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate.” Biochemistry 43, 14004-14014 (2004). [Pubmed]
46. Moody, E. M., Brown, T. S., and Bevilacqua, P. C. “Simple method for determining nucleobase pKa values by indirect labeling and demonstration of a pKa of neutrality in dsDNA.” J. Am. Chem. Soc. 126, 10200-10201 (2004). [Pubmed]
44. Moody, E. M., and Bevilacqua, P. C. “Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop.” J. Am. Chem. Soc. 126, 9570-9577 (2004). [Pubmed]
43. 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]
40. Moody, E. M., and Bevilacqua, P. C. “Folding of a stable DNA motif involves a highly cooperative network of interactions.” J. Am. Chem. Soc.. 125, 16285-16293 (2003). [Pubmed]
39. Schaak, J. E., Babitzke, P., and Bevilacqua, P. C. “Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus.” RNA 9, 1502-1515 (2003). [Pubmed]
38. Schaak, J. E., Yakhnin, H., Bevilacqua, P. C., and Babitzke, P. “A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding.” J. Mol. Biol., 332, 555-574 (2003). [Pubmed]
37. Babitzke, P., Schaak, J., Yakhnin, A. V., and Bevilacqua, P. C. “Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system.” Methods Enzymol., 371, 392-404 (2003). [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]
33. Proctor, D. J., Kierzek, E., Kierzek, R., and Bevilacqua, P. C. “Restricting the conformational heterogeneity of RNA by specific incorporation of 8-Bromoguanosine.” J. Am. Chem. Soc., 125, 2390-2391 (2003). [Pubmed]
32. Moody, E. M., and Bevilacqua, P. C. “Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs.” J. Am. Chem. Soc., 125, 2032-2033 (2003). [Pubmed]
31. 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]
29. Proctor, D. J., Schaak, J. E., Bevilacqua, J. M., Falzone, C. J. and Bevilacqua, P. C. “Isolation and characterization of a family of stable tetraloops with the motif YNMG that participate in tertiary interactions.” Biochemistry, 41, 12062-12075 (2002). [Pubmed]
28. Bevilacqua, P. C. “Battle for the bulge: Directing natural products to DNA defects.” Chem. Biol., 9, 854-855 (2002). [Pubmed]
27. Bevilacqua, P.C. and Turner, D.H. “Use of fluorescence spectroscopy to elucidate RNA folding pathways.” In Current Protocols in Nucleic Acid Chemistry (S. Beaucage et al., eds.). John Wiley & Sons, New York. 11.8.1-11.8.6 (2002). [Pubmed]
17. Shu, Z., and Bevilacqua, P. C. “Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library.” Biochemistry, 38, 15369-15379 (1999). [Pubmed]
15. Bevilacqua, J. M. and Bevilacqua, P. C. “Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin.” Biochemistry, 37, 15877-15884 (1998). [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]