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Schroeder Lab Publications


Incorporating Global Features of RNA Motifs in Predictions for An Ensemble of Secondary Structures for Encapsidated MS2 Bacteriophage RNA.S. Bleckley, S. J. Schroeder. RNA Journal. 18, 1309-1318 (2012)

 Nucleotide Dynamics at the A-site Cleft in the Peptidyltransferase Center of H. marismortui 50 S Ribosomal SubunitsWang, Y., Shen, Jana K., Schroeder, S.J. J. Phys. Chem. Lett. 3, 1007-1010 (2012)

 Ensemble of Secondary Structures for Encapsidated Satellite Tobacco Mosaic Virus RNA Consistent with Constraints from Chemical Probing and Crystallography. S.J. Schroeder, J.W. Stone, S. Bleckley, T.R. Gibbons, D. Mathews, Biophys. J. 101, 167-175 (2011).

 Different Sequences Show Similar Quaternary Interaction Stabilities in Prohead Viral RNA Self Assembly. X. Gu, S.J. Schroeder, J. Biol. Chem., 286, 14419-14426 (2011).

 NMR Structure of a Prohead RNA E-loop Hairpin. S. Harris, S., S.J. Schroeder, Biochemistry, 49, 5989-5997 (2010).

 Consecutive Terminal GU Pairs Stabilize RNA Helices. M.-T. Nguyen, S. J. Schroeder, Biochemistry. 49, 10574-10581 (2010).

 Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships. S.J. Schroeder, J. Virol., 83, 6326-6334 (2009).

 Optical Melting Measurements of Nucleic Acid Thermodynamics,. in Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions, and Folding, Part A (D. Hershlag, ed.) S.J. Schroeder and D.H. Turner, Methods in Enzymology, 468, 371-387 (2009).

 3' Terminal Nucleotides Determine Thermodynamic Stabilities at the Ends of RNA Helices,. K. Clanton-Arrowood, J. McGurk, J., S.J. Schroeder, Biochemistry, 47, 13418-13427 (2008).

rRNA Mutations Outside the Anisomycin Binding Site can Make Ribosomes Drug-resistant,. G. Blaha, G. Gurel, S.J. Schroeder (co-first author), P.B. Moore, T.A. Steitz, J. Mol. Biol., 379, 505-519 (2008).

The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-deoxytedanolide and Girodazole. S.J. Schroeder, G. Blaha, J. Tirado-Rivas, T.A. Steitz, P.B. Moore, J. Mol. Biol., 367, 1471-1479 (2007).

Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit. S.J. Schroeder, G. Blaha, P.B. Moore. Antimicrobial Agents and Chemotherapeutics 51, 46662-4665 (2007).

The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the Structural Features that Shape the Thermodynamic Stability of Tandem GA Pairs,. B. Tolbert, S.D. Kennedy, S.J. Schroeder, T.R. Krugh, D.H.Turner, Biochemistry, 46, 1511-1522 (2007).

Predicting RNA Secondary Structure,. in The RNA World (ed. R.F. Gesteland, T.R. Cech, J.F. Atkins) D.H. Mathews, S.J. Schroeder, D.H. Turner, and M. Zuker, pp 631-657. Cold Spring Harbor Press (2005).

Incorporating Chemical Modification Restraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure,. D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, and D.H. Turner, Proc. Natl. Acad. Sci. USA, 101, 7287-7292 (2004).

Thermodynamic Stabilities and Structural Features of the J4/5 Loop in a Pneumocystis carinii Group I Intron,. S.J. Schroeder, M.A. Fountain, S.D. Kennedy, P.J. Lukavsky, J.D. Puglisi, T.R. Krugh, and D.H. Turner, Biochemistry, 42, 14184-14196 (2003).

Sheared Aanti . Aanti Base Pairs in a Destabilizing 2 X 2 Internal Loop: The NMR Structure of 5.(rGGCAAGCCU)2,. B.M. Znosko, M.E. Burkard, S.J. Schroeder, T.R. Krugh, and D.H. Turner, Biochemistry, 41, 14969-14977 (2002).

The Energetics of Small Internal Loops,. S.J. Schroeder, M.E. Burkard, and D.H. Turner, Biopolymers, 52, 157-167 (2001).

Thermodynamic Stabilities of Internal Loops with GU Closing Pairs in RNA,. S.J. Schroeder and D.H. Turner, Biochemistry, 40, 11509-11517 (2001).

Factors Affecting the Thermodynamic Stability of Small Asymmetric Internal Loops in RNA,. S.J. Schroeder and D.H. Turner, Biochemistry, 39, 9257-9274 (2000).

Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs, T. Xia, J. Santa Lucia, Jr., M.E. Burkard, R. Kierzek, S.J. Schroeder, X. Jiao, C. Cox, and D.H. Turner, Biochemistry, 37, 14719-14735 (1998).

GA and UU Mismatches Can Stabilize RNA Internal Loops of Three Nucleotides, S.J. Schroeder, J. Kim, and D.H. Turner, Biochemistry, 35, 16105-16109 (1996).