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Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity.

Atilho RM, Perkins KR, Breaker RR.

RNA. 2019 Jan;25(1):23-34. doi: 10.1261/rna.067975.118. Epub 2018 Oct 4.


A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria.

Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR.

Nucleic Acids Res. 2018 Nov 2;46(19):10082-10094. doi: 10.1093/nar/gky709.


Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates.

Sherlock ME, Sadeeshkumar H, Breaker RR.

Biochemistry. 2019 Feb 5;58(5):401-410. doi: 10.1021/acs.biochem.8b00617. Epub 2018 Aug 24.


Large Noncoding RNAs in Bacteria.

Harris KA, Breaker RR.

Microbiol Spectr. 2018 Jul;6(4). doi: 10.1128/microbiolspec.RWR-0005-2017. Review.


A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex.

Harris KA, Zhou Z, Peters ML, Wilkins SG, Breaker RR.

Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6319-E6328. doi: 10.1073/pnas.1803191115. Epub 2018 Jun 18.


Riboswitches and Translation Control.

Breaker RR.

Cold Spring Harb Perspect Biol. 2018 Nov 1;10(11). pii: a032797. doi: 10.1101/cshperspect.a032797. Review.


Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems.

Sherlock ME, Sudarsan N, Breaker RR.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6052-6057. doi: 10.1073/pnas.1720406115. Epub 2018 May 21.


Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria.

Sherlock ME, Sudarsan N, Stav S, Breaker RR.

Elife. 2018 Mar 5;7. pii: e33908. doi: 10.7554/eLife.33908.


Challenges of ligand identification for the second wave of orphan riboswitch candidates.

Greenlee EB, Stav S, Atilho RM, Brewer KI, Harris KA, Malkowski SN, Mirihana Arachchilage G, Perkins KR, Sherlock ME, Breaker RR.

RNA Biol. 2018 Mar 4;15(3):377-390. doi: 10.1080/15476286.2017.1403002. Epub 2018 Feb 1.


SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches.

Mirihana Arachchilage G, Sherlock ME, Weinberg Z, Breaker RR.

RNA Biol. 2018 Mar 4;15(3):371-378. doi: 10.1080/15476286.2017.1399232. Epub 2018 Feb 12.


Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.

Li S, Breaker RR.

BMC Genomics. 2017 Oct 13;18(1):785. doi: 10.1186/s12864-017-4171-y.


Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions.

Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR.

Nucleic Acids Res. 2017 Oct 13;45(18):10811-10823. doi: 10.1093/nar/gkx699.


The lost language of the RNA World.

Nelson JW, Breaker RR.

Sci Signal. 2017 Jun 13;10(483). pii: eaam8812. doi: 10.1126/scisignal.aam8812. Review.


Riboswitch diversity and distribution.

McCown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR.

RNA. 2017 Jul;23(7):995-1011. doi: 10.1261/rna.061234.117. Epub 2017 Apr 10.


Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

Naghdi MR, Smail K, Wang JX, Wade F, Breaker RR, Perreault J.

Methods. 2017 Mar 15;117:3-13. doi: 10.1016/j.ymeth.2017.02.009. Epub 2017 Mar 6.


Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity.

Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):E2077-E2085. doi: 10.1073/pnas.1619581114. Epub 2017 Mar 6. Erratum in: Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8326.


Mechanistic Debris Generated by Twister Ribozymes.

Breaker RR.

ACS Chem Biol. 2017 Apr 21;12(4):886-891. doi: 10.1021/acschembio.7b00010. Epub 2017 Feb 21. Review.


The Biology of Free Guanidine As Revealed by Riboswitches.

Breaker RR, Atilho RM, Malkowski SN, Nelson JW, Sherlock ME.

Biochemistry. 2017 Jan 17;56(2):345-347. doi: 10.1021/acs.biochem.6b01269. Epub 2017 Jan 6. No abstract available.


Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria.

Sherlock ME, Breaker RR.

Biochemistry. 2017 Jan 17;56(2):359-363. doi: 10.1021/acs.biochem.6b01271. Epub 2017 Jan 6.


Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria.

Sherlock ME, Malkowski SN, Breaker RR.

Biochemistry. 2017 Jan 17;56(2):352-358. doi: 10.1021/acs.biochem.6b01270. Epub 2017 Jan 6.


Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class.

Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR.

Mol Cell. 2017 Jan 19;65(2):220-230. doi: 10.1016/j.molcel.2016.11.019. Epub 2016 Dec 15.


Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.

Lünse CE, Weinberg Z, Breaker RR.

RNA Biol. 2017 Nov 2;14(11):1499-1507. doi: 10.1080/15476286.2016.1251002. Epub 2017 Nov 3.


Singlet glycine riboswitches bind ligand as well as tandem riboswitches.

Ruff KM, Muhammad A, McCown PJ, Breaker RR, Strobel SA.

RNA. 2016 Nov;22(11):1728-1738. Epub 2016 Sep 22.


The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds.

Li S, Hwang XY, Stav S, Breaker RR.

RNA. 2016 Apr;22(4):530-41. doi: 10.1261/rna.054890.115. Epub 2016 Feb 3.


Biochemical analysis of hatchet self-cleaving ribozymes.

Li S, Lünse CE, Harris KA, Breaker RR.

RNA. 2015 Nov;21(11):1845-51. doi: 10.1261/rna.052522.115. Epub 2015 Sep 18.


Biochemical analysis of pistol self-cleaving ribozymes.

Harris KA, Lünse CE, Li S, Brewer KI, Breaker RR.

RNA. 2015 Nov;21(11):1852-8. doi: 10.1261/rna.052514.115. Epub 2015 Sep 18.


Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora.

Blount KF, Megyola C, Plummer M, Osterman D, O'Connell T, Aristoff P, Quinn C, Chrusciel RA, Poel TJ, Schostarez HJ, Stewart CA, Walker DP, Wuts PG, Breaker RR.

Antimicrob Agents Chemother. 2015 Sep;59(9):5736-46. doi: 10.1128/AAC.01282-15. Epub 2015 Jul 13.


New classes of self-cleaving ribozymes revealed by comparative genomics analysis.

Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lünse CE, Breaker RR.

Nat Chem Biol. 2015 Aug;11(8):606-10. doi: 10.1038/nchembio.1846. Epub 2015 Jul 13.


Small molecule fluoride toxicity agonists.

Nelson JW, Plummer MS, Blount KF, Ames TD, Breaker RR.

Chem Biol. 2015 Apr 23;22(4):527-534. doi: 10.1016/j.chembiol.2015.03.016.


Control of bacterial exoelectrogenesis by c-AMP-GMP.

Nelson JW, Sudarsan N, Phillips GE, Stav S, Lünse CE, McCown PJ, Breaker RR.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5389-94. doi: 10.1073/pnas.1419264112. Epub 2015 Apr 6.


Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.

Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR.

Mol Cell. 2015 Mar 19;57(6):1088-1098. doi: 10.1016/j.molcel.2015.02.009.


An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.

Kim PB, Nelson JW, Breaker RR.

Mol Cell. 2015 Jan 22;57(2):317-28. doi: 10.1016/j.molcel.2015.01.001.


The expanding view of RNA and DNA function.

Breaker RR, Joyce GF.

Chem Biol. 2014 Sep 18;21(9):1059-65. doi: 10.1016/j.chembiol.2014.07.008.


Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes.

McCown PJ, Liang JJ, Weinberg Z, Breaker RR.

Chem Biol. 2014 Jul 17;21(7):880-889. doi: 10.1016/j.chembiol.2014.05.015.


Gramicidin D enhances the antibacterial activity of fluoride.

Nelson JW, Zhou Z, Breaker RR.

Bioorg Med Chem Lett. 2014 Jul 1;24(13):2969-2971. doi: 10.1016/j.bmcl.2014.03.061. Epub 2014 Mar 28.


In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP.

Furukawa K, Gu H, Breaker RR.

Methods Mol Biol. 2014;1111:209-20. doi: 10.1007/978-1-62703-755-6_15.


A widespread self-cleaving ribozyme class is revealed by bioinformatics.

Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR.

Nat Chem Biol. 2014 Jan;10(1):56-60. doi: 10.1038/nchembio.1386. Epub 2013 Nov 17.


Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins.

Li S, Smith KD, Davis JH, Gordon PB, Breaker RR, Strobel SA.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19018-23. doi: 10.1073/pnas.1310439110. Epub 2013 Oct 30.


Riboswitches in eubacteria sense the second messenger c-di-AMP.

Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR.

Nat Chem Biol. 2013 Dec;9(12):834-9. doi: 10.1038/nchembio.1363. Epub 2013 Oct 20.


Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes.

Roth A, Breaker RR.

Cell. 2013 Jun 20;153(7):1417-8. doi: 10.1016/j.cell.2013.05.043. No abstract available.


Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products.

Gu H, Breaker RR.

Biotechniques. 2013 Jun;54(6):337-43. doi: 10.2144/000114009.


Small, highly active DNAs that hydrolyze DNA.

Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR.

J Am Chem Soc. 2013 Jun 19;135(24):9121-9. doi: 10.1021/ja403585e. Epub 2013 Jun 6.


Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing.

Li S, Breaker RR.

Nucleic Acids Res. 2013 Mar 1;41(5):3022-31. doi: 10.1093/nar/gkt057. Epub 2013 Feb 1.


Ancient, giant riboswitches at atomic resolution.

Breaker RR.

Nat Struct Mol Biol. 2012 Dec;19(12):1208-9. doi: 10.1038/nsmb.2453. Epub 2012 Nov 11. No abstract available.


RNA science and its applications-a look toward the future: Albany, NY USA, November 3-4, 2011.

Breaker RR, Conklin DS, Gold L, Söll D, Montimurro JS, Agris PF.

RNA Biol. 2012 Aug;9(8):1050-3. doi: 10.4161/rna.21209. Epub 2012 Aug 1.


Identification of ligand analogues that control c-di-GMP riboswitches.

Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker RR.

ACS Chem Biol. 2012 Aug 17;7(8):1436-43. doi: 10.1021/cb300138n. Epub 2012 Jun 19.


OLE RNA protects extremophilic bacteria from alcohol toxicity.

Wallace JG, Zhou Z, Breaker RR.

Nucleic Acids Res. 2012 Aug;40(14):6898-907. doi: 10.1093/nar/gks352. Epub 2012 May 4.


Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5'-monophosphate.

Gu H, Furukawa K, Breaker RR.

Anal Chem. 2012 Jun 5;84(11):4935-41. doi: 10.1021/ac300415k. Epub 2012 May 21.


Fluoride enhances the activity of fungicides that destabilize cell membranes.

Li S, Breaker RR.

Bioorg Med Chem Lett. 2012 May 1;22(9):3317-22. doi: 10.1016/j.bmcl.2012.03.006. Epub 2012 Mar 8.


New insight on the response of bacteria to fluoride.

Breaker RR.

Caries Res. 2012;46(1):78-81. doi: 10.1159/000336397. Epub 2012 Feb 10.

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