RNA Groups and Selected Publications

RNA Folding and Structure Groups

Ken Dill,

http://www.dillgroup.ucsf.edu
Secondary structure graphs, partition functions, and folding energetics.

Publications

Chen, Shi-Jie and Dill, Ken A. 2000. RNA folding energy landscapes. Proceedings of the National Academy of Sciences of the United States of America. 97 :646-651. [PNAS site]

Tostesen, Eivind and Chen, Shi-Jie and , Ken A. Dill. 2001. RNA Folding Transitions and Cooperativity. J. Phys. Chem. B. 105 :1618-1630. [DOI]

Shi-Jie Chen,

http://www.biochem.missouri.edu/schen.php
Research description taken from Dr. Chen's website: "We are studying the statistical thermodynamics and kinetics and computer modeling of biomolecules and polymers, particularly RNA & protein folding."

Publications

Tan, Zhijie and ShiJie Chen 2007 RNA helix stability in mixed Na+/Mg2+ solution Biophysical Journal. 92 :3615-3632. [DOI]

Tan, Zhijie and ShiJie Chen 2006 Electrostatic free energy landscapes for nucleic acid helix assembly Nucleic Acids Research. 34 :6629-6639. [DOI]

Jennifer Doudna,

http://rna.berkeley.edu/
Experimental research on ribozymes and folding using structural and biochemical techniques. P4-P6 Ribozyme, Hepatitis Delta Virus Ribozyme and Dicer.

Publications

Ian J. MacRae and Kaihong Zhou and Fei Li and Adrian Repic and Angela N. Brooks and Zacheus Cande and Paul D. Adams and Jennifer A. Doudna. 2006. Structural Basis for Double-Stranded RNA Processing by Dicer Science. 311 :195-198. [DOI]

Stephen Harvey, http://rumour.biology.gatech.edu
Simulations of nucleic acids using coarse-grained (reduced atom) modeling.

Publications

Mariana Tihova, Kelly A. Dryden, Thuc-vy L. Le, Stephen C. Harvey, John E. Johnson, Mark Yeager and Anette Schneemann 2004. Nodavirus Coat Protein Imposes Dodecahedral RNA Structure Independent of Nucleotide Sequence and Length. Journal of Virology. 78 :2897-2905. [DOI]

Stagg, Scott M. and Mears, Jason A. and Harvey, Stephen C. 2003. A Structural Model for the Assembly of the 30 S Subunit of the Ribosome. Journal of Molecular Biology. 328 :49-61. [DOI]

Malhotra A., Tan R.K.Z., Harvey S.C. 1994. Modeling Large RNA's and Ribonucleoprotein-Particles Using Molecular Mechanics Techniques. Biophysical Journal. 66 :1777-1795. [Abstract]

Steven Brenner, http://compbio.berkeley.edu/people/brenner/
Makes the SCOP and SCOR databases. Also worked or works with Gavin E. Crooks (Crooks fluctuation theorem) which is used by Tinoco, Bustamante and coworkers for recovery of RNA folding free energies. That is, they are working in getting the thermodynamics from single molecule unfolding and pretty much already solved the problem.

Publications

Peter S. Klosterman, Donna K. Hendrix, Makio Tamura, Stephen R. Holbrook, and Steven E. Brenner. 2004. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns Nucleic Acids Research. 32 :2342-2352 [DOI]

Tamura M, Hendrix DK, Klosterman PS, Schimmelman NRB, Brenner SE, Holbrook SR. 2004. SCOR: Structural Classification of RNA, version 2.0 Nucleic Acids Research. 32 :182-184 [DOI]

Sung-Hou Kim, http://www-kimgrp.lbl.gov/
Publications

Holbrook SR, Kim SH. 1997. RNA crystallography. Biopolymers. 44 :3-21 [Biopolymers]

S. H. Kim; G. J. Quigley; F. L. Suddath; A. McPherson; D. Sneden; J. J. Kim; J. Weinzierl; Alexander Rich 1973. Three-dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain. Science. 179 :285-288 [JSTOR]

Ana Marie Pyle, http://www.pylelab.org/
Also experimental like Doudna, interested in discovery and understanding of RNA motifs. Has a paper reviewing RNA conformations in the ribosome using the virtual bond model of Olson, Macromolecules 1975 (8), 272.

Publications

Pyle A.M., Green J.B. 1995. RNA Folding. Current Opinion in Structural Biology. 5 :303-310. [DOI]

Su LHJ, Brenowitz M, Pyle AM 2003. An alternative route for the folding of large RNAs: Apparent two-state folding by a group II intron ribozyme. Journal of Molecular Biology. 334 :639-652. [DOI]

Duarte CM, Wadley LM, Pyle AM 2003. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Research. 31 :4755-4761. [DOI]

Abramovitz DL, Pyle AM 1997. Remarkable morphological variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction. Journal of Molecular Biology. 266 :493-506. [DOI]

Harry F. Noller, http://rna.ucsc.edu/rnacenter/noller_lab_rht.html
Amazing crystallographic studies. Responsable for many of the ribosome structures available at the PDB.

Publications

Harry F. Noller 2005. RNA Structure: Reading the Ribosome Science. 309 :1508-1514 [DOI]

Ignacio Tinoco Jr., http://ww.cchem.berkeley.edu/intgrp/tinoco.shtml
RNA Folding and RNA Thermodynamics pioneer. Currently, single molecule spectroscopy of RNA main expert along with Bustamante.
Publications

Tinoco I., Bustamante C. 1999. How RNA folds. Journal of Molecular Biology. 293 :271-281 [DOI]

Tinoco, Ignacio 2004. Force as a Useful Variable in Reactions: Unfolding RNA. Annual Review of Biophysics & Biomolecular Structure. 33 :363-385 [EBSCO]

Onoa, Bibiana and Tinoco, Ignacio 2004. RNA folding and unfolding. Current Opinion in Structural Biology. 17 :374-379 [DOI]

D. Thirumalai, http://www.chem.umd.edu/faculty/thirumalai/index.html
RNA Folding. Proposes common model for RNA and protein folding. Kinetic Partitioning Mechanism.
Publications

Thirumalai, D. and , Changbong Hyeon 2005 RNA and Protein Folding: Common Themes and Variations Biochemistry. 44 :4957-4970 [DOI]

Thirumalai, D. and Lee, Namkyung and Woodson, Sarah A. and Klimov, D.K. 2001 Early Events in RNA Folding Annu. Rev. Phys. Chem. 52 :751-761 [EBSCO]

Hyeon Changbong and Thirumalai D. 2005 Mechanical Unfolding of RNA hairpins PNAS :6789-6794 [DOI]

E. Westhof http://www-ibmc.u-strasbg.fr/upr9002/westhof/
Along with Leontis and Lescoute they propose the isostere (Isostericity "Matrices") way of looking at base-pairs as a classification paradigm.
Publications

Eric Westhof, and Vale﹔ie Fritsch 2000. RNA folding: beyond Watson-Crick pairs Structure. 8 :R55-R65 [DOI]

RNA Motifs

Thomas Hermann and Dinshaw J Patel 2000. RNA bulges as architectural and recognition motifs Structure. 8 :R47-R54 [DOI]

P. B. Moore 1999. Structural Motifs in RNA. Annual Reviews in Biochemistry. 68 :287-300 [EBSCO]

RNA X-Ray Structures

Thomas A. Steitz http://www.csb.yale.edu/people/steitz/steitz_people.html
Publications

Klein, D.J. and Schmeing, T.M. and Moore, P.B. and Steitz, T.A 2001. The kink-turn: a new RNA secondary structure motif. EMBO Journal. 20 :4214-4221. [DOI]

/b> http://www.csb.yale.edu/people/steitz/steitz_people.html
Publications

Klein, D.J. and Schmeing, T.M. and Moore, P.B. and Steitz, T.A 2001. The kink-turn: a new RNA secondary structure motif. EMBO Journal. 20 :4214-4221. [DOI]

Other RNA Interesting Papers & Links

Liphardt, J. and Onoa, B. and Smith, S.B. and Tinoco Jr., I. and Bustamante, C. 2001. Reversible unfolding of single RNA molecules by mechanical force. Science. 292 :733-737. [DOI]

Robert W. Holley - Nobel Lecture. 1968. Alanine Transfer RNA. [Nobel]
Holley proposed the cloverleaf structure of tRNA

Online article from NOVA on Nucleic Acid History.
Friedrich Miescher discovered DNA. [NOVA]

Sean R. Eddy. How do RNA folding algorithms work? 2004. Nature Biotechnology. 22 :1457-1458. [DOI]

Graph Theory Related

Milan Randic, Chemometrics Lab. National Institute of Chemistry of Slovenia
Publications

Milan Randic and Goran Krilov 1999. On a characterization of the folding of proteins International Journal of Quantum Chemistry. 75 :1017-1026. [DOI]