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Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

Reinharz V, Ponty Y, Waldispühl J.

Nucleic Acids Res. 2016 Jun 20;44(11):e104. doi: 10.1093/nar/gkw217. Epub 2016 Apr 19.


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.


The RNA Domain Vc1 Regulates Downstream Gene Expression in Response to Cyclic Diguanylate in Vibrio cholerae.

Kariisa AT, Weeks K, Tamayo R.

PLoS One. 2016 Feb 5;11(2):e0148478. doi: 10.1371/journal.pone.0148478. eCollection 2016.


Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.

Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ.

Cell Rep. 2015 Dec 1;13(9):1800-13. doi: 10.1016/j.celrep.2015.10.062. Epub 2015 Nov 19.


Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes.

Baird NJ, Inglese J, Ferré-D'Amaré AR.

Nat Commun. 2015 Dec 7;6:8898. doi: 10.1038/ncomms9898.


Two nucleotide second messengers regulate the production of the Vibrio cholerae colonization factor GbpA.

Kariisa AT, Grube A, Tamayo R.

BMC Microbiol. 2015 Aug 19;15:166. doi: 10.1186/s12866-015-0506-5.


Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains.

Jones CP, Ferré-D'Amaré AR.

Nat Struct Mol Biol. 2015 Sep;22(9):679-85. doi: 10.1038/nsmb.3073. Epub 2015 Aug 17.


Cooperativity, allostery and synergism in ligand binding to riboswitches.

Peselis A, Gao A, Serganov A.

Biochimie. 2015 Oct;117:100-9. doi: 10.1016/j.biochi.2015.06.028. Epub 2015 Jul 2. Review.


Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.

Ren A, Rajashankar KR, Patel DJ.

Structure. 2015 Aug 4;23(8):1375-81. doi: 10.1016/j.str.2015.05.016. Epub 2015 Jun 25.


A minimalist biosensor: Quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer.

Kellenberger CA, Sales-Lee J, Pan Y, Gassaway MM, Herr AE, Hammond MC.

RNA Biol. 2015;12(11):1189-97. doi: 10.1080/15476286.2015.1062970. Epub 2015 Jun 26.


Bacterial Signal Transduction by Cyclic Di-GMP and Other Nucleotide Second Messengers.

Hengge R, Gründling A, Jenal U, Ryan R, Yildiz F.

J Bacteriol. 2016 Jan;198(1):15-26. Review.


Consistent global structures of complex RNA states through multidimensional chemical mapping.

Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R.

Elife. 2015 Jun 2;4:e07600. doi: 10.7554/eLife.07600. Erratum in: Elife. 2015;4:e10095.


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.


GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP.

Kellenberger CA, Wilson SC, Hickey SF, Gonzalez TL, Su Y, Hallberg ZF, Brewer TF, Iavarone AT, Carlson HK, Hsieh YF, Hammond MC.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5383-8. doi: 10.1073/pnas.1419328112. Epub 2015 Apr 6.


Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch.

Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ.

Cell Rep. 2015 Apr 7;11(1):1-12. doi: 10.1016/j.celrep.2015.03.004. Epub 2015 Mar 26. Erratum in: Cell Rep. 2015 Apr 28;11(4):671.


The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element.

Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G.

Mol Cell. 2015 Mar 19;57(6):1099-109. doi: 10.1016/j.molcel.2015.01.035.


RNA quaternary structure and global symmetry.

Jones CP, Ferré-D'Amaré AR.

Trends Biochem Sci. 2015 Apr;40(4):211-20. doi: 10.1016/j.tibs.2015.02.004. Epub 2015 Mar 13. Review.


Riboswitch structure and dynamics by smFRET microscopy.

Suddala KC, Walter NG.

Methods Enzymol. 2014;549:343-73. doi: 10.1016/B978-0-12-801122-5.00015-5.


Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.

Jones CP, Ferré-D'Amaré AR.

EMBO J. 2014 Nov 18;33(22):2692-703. doi: 10.15252/embj.201489209. Epub 2014 Sep 30.


High-throughput electrophoretic mobility shift assays for quantitative analysis of molecular binding reactions.

Pan Y, Duncombe TA, Kellenberger CA, Hammond MC, Herr AE.

Anal Chem. 2014 Oct 21;86(20):10357-64. doi: 10.1021/ac502700b. Epub 2014 Oct 7.

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