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Items: 1 to 50 of 159

1.

Correction to "Cellular Small Molecules Contribute to Twister Ribozyme Catalysis".

Messina KJ, Bevilacqua PC.

J Am Chem Soc. 2019 Jun 5. doi: 10.1021/jacs.9b05662. [Epub ahead of print] No abstract available.

PMID:
31184145
2.

Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates.

Poudyal RR, Keating CD, Bevilacqua PC.

ACS Chem Biol. 2019 Jun 7. doi: 10.1021/acschembio.9b00205. [Epub ahead of print]

PMID:
31181897
3.

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM.

ACS Chem Biol. 2019 Jun 7. doi: 10.1021/acschembio.9b00202. [Epub ahead of print]

PMID:
31095369
4.

In Vivo Genome-Wide RNA Structure Probing with Structure-seq.

Ritchey LE, Su Z, Assmann SM, Bevilacqua PC.

Methods Mol Biol. 2019;1933:305-341. doi: 10.1007/978-1-4939-9045-0_20.

PMID:
30945195
5.

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates.

Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC.

Nat Commun. 2019 Jan 30;10(1):490. doi: 10.1038/s41467-019-08353-4.

6.

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC.

Nucleic Acids Res. 2019 Jan 10;47(1):29-42. doi: 10.1093/nar/gky1118.

7.

Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance.

Su Z, Tang Y, Ritchey LE, Tack DC, Zhu M, Bevilacqua PC, Assmann SM.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12170-12175. doi: 10.1073/pnas.1807988115. Epub 2018 Nov 9.

8.

In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC).

Mitchell D 3rd, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2019 Jan;25(1):147-157. doi: 10.1261/rna.067868.118. Epub 2018 Oct 19.

PMID:
30341176
9.

Technique Development for Probing RNA Structure In Vivo and Genome-Wide.

Bevilacqua PC, Assmann SM.

Cold Spring Harb Perspect Biol. 2018 Oct 1;10(10). pii: a032250. doi: 10.1101/cshperspect.a032250. Review.

PMID:
30275275
10.

Cellular Small Molecules Contribute to Twister Ribozyme Catalysis.

Messina KJ, Bevilacqua PC.

J Am Chem Soc. 2018 Aug 22;140(33):10578-10582. doi: 10.1021/jacs.8b06065. Epub 2018 Aug 13. Erratum in: J Am Chem Soc. 2019 Jun 5;:.

PMID:
30102530
11.

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.

Yamagami R, Bingaman JL, Frankel EA, Bevilacqua PC.

Nat Commun. 2018 Jun 1;9(1):2149. doi: 10.1038/s41467-018-04415-1.

12.

Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms.

Leamy KA, Yennawar NH, Bevilacqua PC.

Biochemistry. 2018 May 22;57(20):2994-3002. doi: 10.1021/acs.biochem.8b00345. Epub 2018 May 7.

PMID:
29733204
13.

Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry.

Poudyal RR, Pir Cakmak F, Keating CD, Bevilacqua PC.

Biochemistry. 2018 May 1;57(17):2509-2519. doi: 10.1021/acs.biochem.8b00081. Epub 2018 Mar 21.

PMID:
29560725
14.

RNA structure: A LASER-focused view into cells.

Bevilacqua PC, Assmann SM.

Nat Chem Biol. 2018 Feb 14;14(3):200-201. doi: 10.1038/nchembio.2570. No abstract available.

PMID:
29443973
15.

StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.

Tack DC, Tang Y, Ritchey LE, Assmann SM, Bevilacqua PC.

Methods. 2018 Jul 1;143:12-15. doi: 10.1016/j.ymeth.2018.01.018. Epub 2018 Feb 2.

PMID:
29410279
16.

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

Frankel EA, Bevilacqua PC.

Biochemistry. 2018 Feb 6;57(5):483-488. doi: 10.1021/acs.biochem.7b00784. Epub 2017 Dec 22.

PMID:
29271644
17.

Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH.

Nucleic Acids Res. 2018 Jan 9;46(1):314-323. doi: 10.1093/nar/gkx1057.

18.

Glyoxals as in vivo RNA structural probes of guanine base-pairing.

Mitchell D 3rd, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2018 Jan;24(1):114-124. doi: 10.1261/rna.064014.117. Epub 2017 Oct 13.

19.

Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding.

Bingaman JL, Gonzalez IY, Wang B, Bevilacqua PC.

Biochemistry. 2017 Aug 22;56(33):4313-4317. doi: 10.1021/acs.biochem.7b00662. Epub 2017 Aug 8.

PMID:
28787138
20.

Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.

Leamy KA, Yennawar NH, Bevilacqua PC.

Biochemistry. 2017 Jul 11;56(27):3422-3433. doi: 10.1021/acs.biochem.7b00325. Epub 2017 Jun 28.

21.

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.

Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC.

Nucleic Acids Res. 2017 Aug 21;45(14):e135. doi: 10.1093/nar/gkx533.

22.

Cooperative Interactions in the Hammerhead Ribozyme Drive pKa Shifting of G12 and Its Stacked Base C17.

Frankel EA, Strulson CA, Keating CD, Bevilacqua PC.

Biochemistry. 2017 May 23;56(20):2537-2548. doi: 10.1021/acs.biochem.7b00174. Epub 2017 May 9.

PMID:
28485924
23.

Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics.

Bingaman JL, Messina KJ, Bevilacqua PC.

Methods. 2017 May 1;120:125-134. doi: 10.1016/j.ymeth.2017.03.011. Epub 2017 Mar 14.

24.

The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme.

Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC.

Nat Chem Biol. 2017 Apr;13(4):439-445. doi: 10.1038/nchembio.2300. Epub 2017 Feb 13.

25.

Eliminating blurry bands in gels with a simple cost-effective repair to the gel cassette.

Bingaman JL, Frankel EA, Hull CM, Leamy KA, Messina KJ, Mitchell D 3rd, Park H, Ritchey LE, Babitzke P, Bevilacqua PC.

RNA. 2016 Dec;22(12):1929-1930. Epub 2016 Oct 19.

26.

Assessing the Potential Effects of Active Site Mg2+ Ions in the glmS Ribozyme-Cofactor Complex.

Zhang S, Stevens DR, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S.

J Phys Chem Lett. 2016 Oct 6;7(19):3984-3988. Epub 2016 Sep 28.

27.

Bridging the gap between in vitro and in vivo RNA folding.

Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC.

Q Rev Biophys. 2016 Jan;49:e10. Epub 2016 Jun 24.

28.

Genome-Wide Analysis of RNA Secondary Structure.

Bevilacqua PC, Ritchey LE, Su Z, Assmann SM.

Annu Rev Genet. 2016 Nov 23;50:235-266. Epub 2016 Sep 14. Review.

PMID:
27648642
29.

Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.

Ucisik MN, Bevilacqua PC, Hammes-Schiffer S.

Biochemistry. 2016 Jul 12;55(27):3834-46. doi: 10.1021/acs.biochem.6b00203. Epub 2016 Jun 27.

30.

Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR.

Hull CM, Bevilacqua PC.

Acc Chem Res. 2016 Jun 21;49(6):1242-9. doi: 10.1021/acs.accounts.6b00151. Epub 2016 Jun 8. Review.

31.

Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes.

Sherlock ME, Rumble CA, Kwok CK, Breffke J, Maroncelli M, Bevilacqua PC.

J Phys Chem B. 2016 Jun 16;120(23):5146-58. doi: 10.1021/acs.jpcb.6b03790. Epub 2016 Jun 6.

PMID:
27267433
32.

Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR.

Hull CM, Anmangandla A, Bevilacqua PC.

ACS Chem Biol. 2016 Apr 15;11(4):1118-27. doi: 10.1021/acschembio.6b00081. Epub 2016 Mar 24.

33.

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg²⁺, Nucleotides, and RNA.

Frankel EA, Bevilacqua PC, Keating CD.

Langmuir. 2016 Mar 1;32(8):2041-9. doi: 10.1021/acs.langmuir.5b04462. Epub 2016 Feb 16.

PMID:
26844692
34.

A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility.

Yennawar NH, Fecko JA, Showalter SA, Bevilacqua PC.

Methods Enzymol. 2016;567:435-60. doi: 10.1016/bs.mie.2015.07.024. Epub 2015 Sep 5.

35.

Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex.

Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, Ansaloni S, Schweitzer-Stenner R, Akins MR, Bevilacqua PC, Saunders AJ.

PLoS One. 2015 Nov 30;10(11):e0143160. doi: 10.1371/journal.pone.0143160. eCollection 2015.

36.

Protein Structure Is Related to RNA Structural Reactivity In Vivo.

Tang Y, Assmann SM, Bevilacqua PC.

J Mol Biol. 2016 Feb 27;428(5 Pt A):758-766. doi: 10.1016/j.jmb.2015.11.012. Epub 2015 Nov 17.

PMID:
26598238
37.

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.

Ding Y, Kwok CK, Tang Y, Bevilacqua PC, Assmann SM.

Nat Protoc. 2015 Jul;10(7):1050-66. doi: 10.1038/nprot.2015.064. Epub 2015 Jun 18.

PMID:
26086407
38.

Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA.

Hull CM, Bevilacqua PC.

J Mol Biol. 2015 Nov 6;427(22):3501-3515. doi: 10.1016/j.jmb.2015.05.018. Epub 2015 May 27.

39.

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM.

Bioinformatics. 2015 Aug 15;31(16):2668-75. doi: 10.1093/bioinformatics/btv213. Epub 2015 Apr 16.

40.

Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density.

Thaplyal P, Ganguly A, Hammes-Schiffer S, Bevilacqua PC.

Biochemistry. 2015 Mar 31;54(12):2160-75. doi: 10.1021/acs.biochem.5b00190. Epub 2015 Mar 23.

41.

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

Kwok CK, Tang Y, Assmann SM, Bevilacqua PC.

Trends Biochem Sci. 2015 Apr;40(4):221-32. doi: 10.1016/j.tibs.2015.02.005. Epub 2015 Mar 18. Review.

PMID:
25797096
42.

A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation.

Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC.

Biochem J. 2015 Apr 1;467(1):91-102. doi: 10.1042/BJ20141063.

PMID:
25793418
43.

The wonder of RNA: a personal reflection of the last 20 years.

Bevilacqua PC.

RNA. 2015 Apr;21(4):515-6. doi: 10.1261/rna.050401.115. No abstract available.

44.

Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.

Zhang S, Ganguly A, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S.

J Am Chem Soc. 2015 Jan 21;137(2):784-98. doi: 10.1021/ja510387y. Epub 2015 Jan 12.

45.

Experimental approaches for measuring pKa's in RNA and DNA.

Thaplyal P, Bevilacqua PC.

Methods Enzymol. 2014;549:189-219. doi: 10.1016/B978-0-12-801122-5.00009-X.

46.

Bioreactor droplets from liposome-stabilized all-aqueous emulsions.

Dewey DC, Strulson CA, Cacace DN, Bevilacqua PC, Keating CD.

Nat Commun. 2014 Aug 20;5:4670. doi: 10.1038/ncomms5670.

PMID:
25140538
47.

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions.

Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC.

RNA. 2014 Mar;20(3):331-47. doi: 10.1261/rna.042747.113. Epub 2014 Jan 17.

48.

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.

Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S.

J Am Chem Soc. 2014 Jan 29;136(4):1483-96. doi: 10.1021/ja4104217. Epub 2014 Jan 15.

49.

Determination of in vivo RNA structure in low-abundance transcripts.

Kwok CK, Ding Y, Tang Y, Assmann SM, Bevilacqua PC.

Nat Commun. 2013;4:2971. doi: 10.1038/ncomms3971.

PMID:
24336128
50.

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM.

Nature. 2014 Jan 30;505(7485):696-700. doi: 10.1038/nature12756. Epub 2013 Nov 24.

PMID:
24270811

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