[STROBEL, Scott, Allen, BREAKER, Ronald, R., SMITH, Kathryn, D.] Two Whitney Avenue New Haven, CT 06511;1180 Main Street Hamden, CT 06514;131 Sugar Loaf Road Guiford, CT 06437;94 Livingston Street, Apartment 25 New Haven, CT 06511 Disclosed is the crystal structure of a GEMM riboswitch from V. cholerae bound to c- di-GMP. The crystal structures show that the RNA binds the ligand within a three helix junction that involves base pairing and extensive base stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to the both the bases and the backbone. Also disclosed are methods of identifying and using compounds and compositions that modulate GEMM riboswitches.

[Ronald R. Breaker, Jinsoo Lim, Kenneth F. Blount, Joy Wang, Narasimhan Sudarsan] US CT New Haven The lysine riboswitch is a target for antibiotics and other small molecule therapies. Compounds can be used to stimulate, active, inhibit and/or inactivate the lysine riboswitch.

[JOYCE GERALD F, BREAKER RONALD R] US

[Ronald R. Breaker, Sanshu Li] US CT New Haven Disclosed are compositions and methods for antimicrobial use. The compositions contain a small antimicrobial agent and a permeabilizing agent. The antimicrobial compositions can be antifungal or antibacterial compositions.

[Ronald R. Breaker, Jeffrey E. Barrick, Adam Roth, Wade Winkler] US CT New Haven The preQ1 riboswitch is a target for antibiotics and other small molecule therapies. The preQ1 riboswitch and portions thereof can be used to regulate the expression or function of RNA molecules and other elements and molecules. The preQ1 riboswitch and portions thereof can be used in a variety of other methods to, for example, identify or detect compounds. Compounds can be used to stimulate, active, inhibit and/or inactivate the preQ1 riboswitch. The preQ1 riboswitch and portions thereof, both alone and in combination with other nucleic acids, can be used in a variety of constructs and RNA molecules and can be encoded by nucleic acids.

[Ronald R. Breaker, Kenneth F. Blount, Izabela J. Puskarz, John K. Wickiser] US CT New Haven Disclosed herein are methods and compositions related to the detection of conformational changes and interactions with trigger molecules in riboswitches.

[Ronald R. Breaker, Jenny Baker, Elaine Lee, Narasimhan Sudarsan, Zasha Weinberg] US CT Guilford Disclosed are compositions and methods involving cyclic di-GMP—responsive Riboswitches and cyclic di-GMP-II motifs.

[BREAKER RONALD R, JOYCE GERALD F] US

[BREAKER, Ronald, R.] Office of Cooperative Research, 155 Whitney Avenue P.O. Box 208336, New Haven, CT 06520-8336, US

[BREAKER, Ronald, R., SOUKUP, Garrett A.] Office of Cooperative Research,Room 210,155 Whitney Avenue, New Haven, CT 06520-8336, US