Kirmizialtin, S, Hennelly, S.P, Schug, A, Onuchic, J.N, and Sanbonmatsu, K.Y. (2015) Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT. Methods in Enzymology 553, 215-234, published February 7, 2015. doi:10.1016/bs.mie.2014.10.061. View PDF »
Sanbonmatsu, K.Y. (2014) Dynamics of Riboswitches: Molecular Simulations. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1839 (10), 1046-1050. published October 2014. doi:10.1016/j.bbagrm.2014.06.010. View article »
Hayes, R.L, Noel, J.K, Whitford, P.C, Mohanty, U, Sanbonmatsu, K.Y, and Onuchic, J.N. (2014) Reduced Model Captures Mg(2+)-RNA Interaction Free Energy of Riboswitches. Biophysical journal 106 (7), 1508-1519, published April 1, 2014. doi:10.1016/j.bpj.2014.01.042.View PDF »
Hennelly, S.P, Novikova, I.V, and Sanbonmatsu, K.Y. (2012) The Expression Platform and the Aptamer: Cooperativity Between Mg2+ and Ligand in the SAM-I Riboswitch. Nucleic acids research 41 (3), 1922-1935, published December 20, 2012. doi:10.1093/nar/gks978. View PDF »
Hayes, R.L, Noel, J.K, Mohanty, U, Whitford, P.C, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2012) Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch. Journal of the American Chemical Society 134 (29), 12043-12053, published July 16, 2012. doi:10.1021/ja301454u. View PDF »
Hennelly, S.P, and Sanbonmatsu, K.Y. (2010) Tertiary Contacts Control Switching of the SAM-I Riboswitch. Nucleic Acids Research 39 (6), 2416-2431, published November 19, 2010. doi:10.1093/nar/gkq1096. View PDF »
Stoddard, C.D, Montange, R.K, Hennelly, S.P, Rambo, R.P, Sanbonmatsu, K.Y, and Batey, R.T. (2010) Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain. Structure 18 (7), 787-797, published July 14, 2010. doi:10.1016/j.str.2010.04.006. View PDF »
Whitford, P.C, Schug, A, Saunders, J, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2009) Nonlocal Helix Formation is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function. Biophysical journal 96 (2), L7-L9, published January 21, 2009. doi:10.1016/j.bpj.2008.10.033. View PDF »