Works matching AU Breaker, Ronald R.

Results: 66

Ancient, giant riboswitches at atomic resolution.

Published in:

Nature Structural & Molecular Biology, 2012, v. 19, n. 12, p. 1208, doi. 10.1038/nsmb.2453

By:

Breaker, Ronald R

Publication type:

Article

Structural basis of ligand binding by a c-di-GMP riboswitch.

Published in:

Nature Structural & Molecular Biology, 2009, v. 16, n. 12, p. 1218, doi. 10.1038/nsmb.1702

By:

Smith, Kathryn D.;
Lipchock, Sarah V.;
Ames, Tyler D.;
Jimin Wang;
Breaker, Ronald R.;
Strobel, Scott A.

Publication type:

Article

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.

Published in:

Nature Structural & Molecular Biology, 2009, v. 16, n. 5, p. 541, doi. 10.1038/nsmb.1588

By:

Hammond, Ming C.;
Wachter, Andreas;
Breaker, Ronald R.

Publication type:

Article

A riboswitch selective for the queuosine precursor preQ<sub>1</sub> contains an unusually small aptamer domain.

Published in:

Nature Structural & Molecular Biology, 2007, v. 14, n. 4, p. 308, doi. 10.1038/nsmb1224

By:

Roth, Adam;
Winkler, Wade C.;
Regulski, Elizabeth E.;
Lee, Bobby W. K.;
Lim, Jinsoo;
Jona, Inbal;
Barrick, Jeffrey E.;
Ritwik, Ankita;
Kim, Jane N.;
Welz, Rüdiger;
Iwata-Reuyl, Dirk;
Breaker, Ronald R.

Publication type:

Article

Characteristics of Ligand Recognition by a glmS Self-Cleaving RibozymeWe thank Dr. Gail Emilsson and other members of the Breaker group for helpful comments, and Inbal Jona for assisting with several assays. This work was supported by grants from the NIH, the NSF, and DARPA. B.C.G. was supported by a training grant (CMB) to Yale University from the NIH.

Published in:

Angewandte Chemie International Edition, 2006, v. 45, n. 40, p. 6689, doi. 10.1002/anie.200602534

By:

Jinsoo Lim;
Beth C. Grove;
Adam Roth;
Ronald R. Breaker

Publication type:

Article

Molecular-Recognition Characteristics of SAM-Binding RiboswitchesWe thank Prof. G. Michael Blackburn (University of Sheffield) for generous gifts of compounds 5 and 6 and Dr. Gail Emilsson and other members of the Breaker laboratory for helpful comments. This study was supported by the grants from the US National Institutes of Health, the US National Science Foundation, DARPA, and the David and Lucile Packard Foundation. SAM=S-adenosylmethionine.

Published in:

Angewandte Chemie International Edition, 2006, v. 45, n. 6, p. 964, doi. 10.1002/anie.200503198

By:

Jinsoo Lim;
Wade C. Winkler;
Shingo Nakamura;
Valerie Scott;
Ronald R. Breaker

Publication type:

Article

Identification of candidate structured RNAs in the marine organism'Candidatus Pelagibacter ubique'

Published in:

BMC Genomics, 2009, v. 10, p. 268, doi. 10.1186/1471-2164-10-268

By:

Meyer, Michelle M.;
Ames, Tyler D.;
Smith, Daniel P.;
Weinberg, Zasha;
Schwalbach, Michael S.;
Giovannoni, Stephen J.;
Breaker, Ronald R.

Publication type:

Article

Witnessing the structural evolution of an RNA enzyme.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.71557

By:

Portillo, Xavier;
Yu-Ting Huang;
Breaker, Ronald R.;
Horning, David P.;
Joyce, Gerald F.

Publication type:

Article

The lost language of the RNA World.

Published in:

Science Signaling, 2017, v. 10, n. 483, p. 1, doi. 10.1126/scisignal.aam8812

By:

Nelson, James W.;
Breaker, Ronald R.

Publication type:

Article

Adenine riboswitches and gene activation by disruption of a transcription terminator.

Published in:

Nature Structural & Molecular Biology, 2004, v. 11, n. 1, p. 29, doi. 10.1038/nsmb710

By:

Mandal, Maumita;
Breaker, Ronald R.

Publication type:

Article

Unique glycine-activated riboswitch linked to glycine–serine auxotrophy in SAR11.

Published in:

Environmental Microbiology, 2009, v. 11, n. 1, p. 230, doi. 10.1111/j.1462-2920.2008.01758.x

By:

Tripp, H. James;
Schwalbach, Michael S.;
Meyer, Michelle M.;
Kitner, Joshua B.;
Breaker, Ronald R.;
Giovannoni, Stephen J.

Publication type:

Article

Association of OLE RNA with bacterial membranes via an RNA-protein interaction.

Published in:

Molecular Microbiology, 2011, v. 79, n. 1, p. 21, doi. 10.1111/j.1365-2958.2010.07439.x

By:

Block, Kirsten F.;
Puerta-Fernandez, Elena;
Wallace, Jason G.;
Breaker, Ronald R.

Publication type:

Article

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.

Published in:

Molecular Microbiology, 2008, v. 68, n. 4, p. 918, doi. 10.1111/j.1365-2958.2008.06208.x

By:

Regulski, Elizabeth E.;
Moy, Ryan H.;
Weinberg, Zasha;
Barrick, Jeffrey E.;
Yao, Zizhen;
Ruzzo, Walter L.;
Breaker, Ronald R.

Publication type:

Article

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.

Published in:

Biochemistry & Cell Biology, 2008, v. 86, n. 2, p. 157, doi. 10.1139/O08-008

By:

Xin Wang, Joy;
Breaker, Ronald R.

Publication type:

Article

Riboswitches as antibacterial drug targets.

Published in:

Nature Biotechnology, 2006, v. 24, n. 12, p. 1558, doi. 10.1038/nbt1268

By:

Blount, Kenneth F.;
Breaker, Ronald R.

Publication type:

Article

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.

Published in:

Nature Biotechnology, 2005, v. 23, n. 11, p. 1424, doi. 10.1038/nbt1155

By:

Penchovsky, Robert;
Breaker, Ronald R.

Publication type:

Article

Immobilized RNA switches for the analysis of complex chemical and biological mixtures.

Published in:

Nature Biotechnology, 2001, v. 19, n. 4, p. 336, doi. 10.1038/86723

By:

Seetharaman, Sukeerthi;
Zivarts, Maris;
Sudarsan, Narasimhan;
Breaker, Ronald R.

Publication type:

Article

Catalytic DNA: in training and seeking employment.

Published in:

Nature Biotechnology, 1999, v. 17, n. 5, p. 422, doi. 10.1038/8588

By:

Breaker, Ronald R.

Publication type:

Article

Genetic Control by Metabolite-Binding Riboswitches.

Published in:

ChemBioChem, 2003, v. 4, n. 10, p. 1024, doi. 10.1002/cbic.200300685

By:

Wade C. Winkler;
Ronald R. Breaker

Publication type:

Article

Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria.

Published in:

Molecular Microbiology, 2023, v. 120, n. 3, p. 324, doi. 10.1111/mmi.15129

By:

Breaker, Ronald R.;
Harris, Kimberly A.;
Lyon, Seth E.;
Wencker, Freya D. R.;
Fernando, Chrishan M.

Publication type:

Article

Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans.

Published in:

Molecular Microbiology, 2019, v. 112, n. 5, p. 1552, doi. 10.1111/mmi.14379

By:

Harris, Kimberly A.;
Odzer, Nicole B.;
Breaker, Ronald R.

Publication type:

Article

Purine sensing by riboswitches.

Published in:

Biology of the Cell (Wiley-Blackwell), 2008, v. 100, n. 1, p. 1, doi. 10.1042/BC20070088

By:

Jane N. Kim;
Ronald R. Breaker

Publication type:

Article

An mRNA structure that controls gene expression by binding S-adenosylmethionine.

Published in:

Nature Structural Biology, 2003, v. 10, n. 9, p. 701, doi. 10.1038/nsb967

By:

Winkler, Wade C;
Nahvi, Ali;
Sudarsan, Narasimhan;
Barrick, Jeffrey E;
Breaker, Ronald R

Publication type:

Article

Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP.

Published in:

Nature Structural Biology, 1999, v. 6, n. 11, p. 1062

By:

Koizumi, Makoto;
Soukup, Garrett A.;
Kerr, Jo Nita Q.;
Breaker, Ronald R.

Publication type:

Article

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 5, p. 1, doi. 10.1371/journal.pcbi.1002031

By:

Perreault, Jonathan;
Weinberg, Zasha;
Roth, Adam;
Popescu, Olivia;
Chartrand, Pascal;
Ferbeyre, Gerardo;
Breaker, Ronald R.

Publication type:

Article

Control of gene expression by a natural metabolite-responsive ribozyme.

Published in:

Nature, 2004, v. 428, n. 6980, p. 281, doi. 10.1038/nature02362

By:

Winkler, Wade C.;
Nahvi, Ali;
Roth, Adam;
Collins, Jennifer A.;
Breaker, Ronald R.

Publication type:

Article

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Published in:

Nature, 2002, v. 419, n. 6910, p. 952, doi. 10.1038/nature01145

By:

Winkler, Wade;
Nahvi, Ali;
Breaker, Ronald R.

Publication type:

Article

The discovery of novel noncoding RNAs in 50 bacterial genomes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 9, p. 5152, doi. 10.1093/nar/gkae248

By:

Narunsky, Aya;
Higgs, Gadareth A;
Torres, Blake M;
Yu, Diane;
de Andrade, Gabriel Belem;
Kavita, Kumari;
Breaker, Ronald R

Publication type:

Article

Exploiting natural riboswitches for aptamer engineering and validation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 2, p. 966, doi. 10.1093/nar/gkac1218

By:

Mohsen, Michael G;
Midy, Matthew K;
Balaji, Aparaajita;
Breaker, Ronald R

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. 19, p. 10082, doi. 10.1093/nar/gky709

By:

Klähn, Stephan;
Bolay, Paul;
Wright, Patrick R;
Atilho, Ruben M;
Brewer, Kenneth I;
Hagemann, Martin;
Breaker, Ronald R;
Hess, Wolfgang R

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2017, v. 45, n. 18, p. 10811, doi. 10.1093/nar/gkx699

By:

Weinberg, Zasha;
Lünse, Christina E.;
Corbino, Keith A.;
Ames, Tyler D.;
Nelson, James W.;
Roth, Adam;
Perkins, Kevin R.;
Sherlock, Madeline E.;
Breaker, Ronald R.

Publication type:

Article

Architectures and complex functions of tandem riboswitches.

Published in:

RNA Biology, 2022, v. 19, n. 1, p. 1059, doi. 10.1080/15476286.2022.2119017

By:

Sherlock, Madeline E.;
Higgs, Gadareth;
Yu, Diane;
Widner, Danielle L.;
White, Neil A.;
Sudarsan, Narasimhan;
Sadeeshkumar, Harini;
Perkins, Kevin R.;
Arachchilage, Gayan Mirihana;
Malkowski, Sarah N.;
King, Christopher G.;
Harris, Kimberly A.;
Gaffield, Glenn;
Atilho, Ruben M.;
Breaker, Ronald R.

Publication type:

Article

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.

Published in:

RNA Biology, 2021, v. 18, n. 12, p. 2417, doi. 10.1080/15476286.2021.1917891

By:

Brewer, Kenneth I.;
Greenlee, Etienne B.;
Higgs, Gadareth;
Yu, Diane;
Mirihana Arachchilage, Gayan;
Chen, Xi;
King, Nicholas;
White, Neil;
Breaker, Ronald R.

Publication type:

Article

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

Published in:

RNA Biology, 2018, v. 15, n. 3, p. 377, doi. 10.1080/15476286.2017.1403002

By:

Greenlee, Etienne B.;
Stav, Shira;
Atilho, Ruben M.;
Brewer, Kenneth I.;
Harris, Kimberly A.;
Malkowski, Sarah N.;
Mirihana Arachchilage, Gayan;
Perkins, Kevin R.;
Sherlock, Madeline E.;
Breaker, Ronald R.

Publication type:

Article

SAM-VI RNAs selectively bind <italic>S</italic>-adenosylmethionine and exhibit similarities to SAM-III riboswitches.

Published in:

RNA Biology, 2018, v. 15, n. 3, p. 371, doi. 10.1080/15476286.2017.1399232

By:

Mirihana Arachchilage, Gayan;
Sherlock, Madeline E.;
Weinberg, Zasha;
Breaker, Ronald R.

Publication type:

Article

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

Published in:

RNA Biology, 2017, v. 14, n. 11, p. 1499, doi. 10.1080/15476286.2016.1251002

By:

Lünse, Christina E.;
Weinberg, Zasha;
Breaker, Ronald R.

Publication type:

Article

RNA Science and its Applications—a look toward the future: Albany, NY USA, November 3–4, 2011.

Published in:

RNA Biology, 2012, v. 9, n. 8, p. 1050, doi. 10.4161/rna.21209

By:

Breaker, Ronald R.;
Conklin, Douglas S.;
Gold, Larry;
Söll, Dieter;
Montimurro, Jennifer S.;
Agris, Paul F.

Publication type:

Article

Bacterial aptamers that selectively bind glutamine.

Published in:

RNA Biology, 2011, v. 8, n. 1, p. 82, doi. 10.4161/rna.8.1.13864

By:

Ames, Tyler D.;
Breaker, Ronald R.

Publication type:

Article

Challenges of ligand identification for riboswitch candidates.

Published in:

RNA Biology, 2011, v. 8, n. 1, p. 5, doi. 10.4161/rna.8.1.13865

By:

Meyer, Michelle M.;
Hammond, Ming C.;
Salinas, Yasmmyn;
Roth, Adam;
Sudarsan, Narasimhan;
Breaker, Ronald R.

Publication type:

Article

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

Published in:

Nature Chemical Biology, 2015, v. 11, n. 8, p. 606, doi. 10.1038/nchembio.1846

By:

Weinberg, Zasha;
Kim, Peter B;
Chen, Tony H;
Li, Sanshu;
Harris, Kimberly A;
Lünse, Christina E;
Breaker, Ronald R

Publication type:

Article

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

Published in:

Nature Chemical Biology, 2014, v. 10, n. 1, p. 56, doi. 10.1038/nchembio.1386

By:

Roth, Adam;
Weinberg, Zasha;
Chen, Andy G Y;
Kim, Peter B;
Ames, Tyler D;
Breaker, Ronald R

Publication type:

Article

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

Published in:

Nature Chemical Biology, 2013, v. 9, n. 12, p. 834, doi. 10.1038/nchembio.1363

By:

Nelson, James W;
Sudarsan, Narasimhan;
Furukawa, Kazuhiro;
Weinberg, Zasha;
Wang, Joy X;
Breaker, Ronald R

Publication type:

Article

Antibacterial lysine analogs that target lysine riboswitches.

Published in:

Nature Chemical Biology, 2007, v. 3, n. 1, p. 44, doi. 10.1038/nchembio842

By:

Blount, Kenneth F.;
Joy Xin Wang;
Jinsoo Lim;
Sudarsan, Narasimhan;
Breaker, Ronald R.

Publication type:

Article

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.

Published in:

Nature, 2009, v. 462, n. 7273, p. 656, doi. 10.1038/nature08586

By:

Weinberg, Zasha;
Perreault, Jonathan;
Meyer, Michelle M.;
Breaker, Ronald R.

Publication type:

Article

Control of alternative RNA splicing and gene expression by eukaryotic riboswitches.

Published in:

Nature, 2007, v. 447, n. 7143, p. 497, doi. 10.1038/nature05769

By:

Cheah, Ming T.;
Wachter, Andreas;
Sudarsan, Narasimhan;
Breaker, Ronald R.

Publication type:

Article

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.

Published in:

2006

By:

Serganov, Alexander;
Polonskaia, Anna;
Anh Tuân Phan;
Breaker, Ronald R.;
Patel, Dinshaw J.

Publication type:

Letter

Natural and engineered nucleic acids as tools to explore biology.

Published in:

Nature, 2004, v. 432, n. 7019, p. 838, doi. 10.1038/nature03195

By:

Breaker, Ronald R.

Publication type:

Article

Gene regulation by riboswitches.

Published in:

Nature Reviews Molecular Cell Biology, 2004, v. 5, n. 6, p. 451, doi. 10.1038/nrm1403

By:

Mandal, Maumita;
Breaker, Ronald R.

Publication type:

Article

Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans.

Published in:

Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1465811

By:

Wencker, Freya D. R.;
Lyon, Seth E.;
Breaker, Ronald R.

Publication type:

Article

Engineered allosteric ribozymes that respond to specific divalent metal ions.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 2, p. 622, doi. 10.1093/nar/gki182

By:

Zivarts, Maris;
Liu, Yong;
Breaker, Ronald R.

Publication type:

Article