Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.

[1]  P. Auffinger,et al.  A short guide for molecular dynamics simulations of RNA systems. , 2009, Methods.

[2]  Eric B Brauns,et al.  Rearrangement of partially ordered stacked conformations contributes to the rugged energy landscape of a small RNA hairpin. , 2008, Biochemistry.

[3]  Milo M. Lin,et al.  Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes. , 2008, Physical chemistry chemical physics : PCCP.

[4]  Zaida Luthey-Schulten,et al.  Dynamics of Recognition between tRNA and elongation factor Tu. , 2008, Journal of molecular biology.

[5]  F. Noé,et al.  Transition networks for modeling the kinetics of conformational change in macromolecules. , 2008, Current opinion in structural biology.

[6]  A. Garcia,et al.  Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. , 2008, Journal of the American Chemical Society.

[7]  G. Stock,et al.  Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg. , 2008, The journal of physical chemistry. B.

[8]  S. Woodson,et al.  Loop dependence of the stability and dynamics of nucleic acid hairpins , 2007, Nucleic acids research.

[9]  G. M. Wilson,et al.  Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence. , 2007, Biochemistry.

[10]  K. Dill,et al.  Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. , 2007, The Journal of chemical physics.

[11]  A. Zewail,et al.  DNA folding and melting observed in real time redefine the energy landscape , 2007, Proceedings of the National Academy of Sciences.

[12]  K. Thompson,et al.  Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. , 2006, Biochemistry.

[13]  Martin Gruebele,et al.  Exploring the energy landscape of a small RNA hairpin. , 2006, Journal of the American Chemical Society.

[14]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[15]  Harald Schwalbe,et al.  Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study. , 2005, Structure.

[16]  B. Schuler Single-molecule fluorescence spectroscopy of protein folding. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[17]  A. Ansari,et al.  Is hairpin formation in single-stranded polynucleotide diffusion-controlled? , 2005, The journal of physical chemistry. B.

[18]  Martin Gruebele,et al.  Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. , 2004, Biochemistry.

[19]  D. Dlott,et al.  Vibrational energy dynamics of water studied with ultrafast Stokes and anti-Stokes Raman spectroscopy , 2004 .

[20]  K. Hall,et al.  Stacking-unstacking dynamics of oligodeoxynucleotide trimers. , 2004, Biochemistry.

[21]  M. Gruebele,et al.  Detection-dependent kinetics as a probe of folding landscape microstructure. , 2004, Journal of the American Chemical Society.

[22]  M. Gruebele,et al.  Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. , 2004, Journal of molecular biology.

[23]  W. Nau,et al.  Kinetics of end-to-end collision in short single-stranded nucleic acids. , 2004, Journal of the American Chemical Society.

[24]  R. Kierzek,et al.  Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. , 2003, Journal of the American Chemical Society.

[25]  Alexander D. MacKerell,et al.  CHARMM: The Energy Function and Its Parameterization , 2002 .

[26]  Yiqing Shen,et al.  Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[27]  R. Osman,et al.  Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. , 2001, Biochemistry.

[28]  K. Hall,et al.  2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A. Serganov,et al.  The crystal structure of UUCG tetraloop. , 2000, Journal of molecular biology.

[30]  F. Eckstein,et al.  Dynamics of the RNA hairpin GNRA tetraloop. , 2000, Biochemistry.

[31]  Martin Gruebele,et al.  Observation of distinct nanosecond and microsecond protein folding events , 1996, Nature Structural Biology.

[32]  M. Gruebele,et al.  A single‐sweep, nanosecond time resolution laser temperature‐jump apparatus , 1996 .

[33]  M. Kataoka,et al.  Cold denaturation of the molten globule states of apomyoglobin and a profile for protein folding. , 1994, Biochemistry.

[34]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[35]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[36]  C. E. Longfellow,et al.  Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. , 1989, Biochemistry.

[37]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[38]  H. Kramers Brownian motion in a field of force and the diffusion model of chemical reactions , 1940 .

[39]  Martin Gruebele,et al.  Engineering a beta-sheet protein toward the folding speed limit. , 2005, The journal of physical chemistry. B.

[40]  K. Hall,et al.  Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. , 2004, RNA.

[41]  T. Kulinski,et al.  Parametrization of 2 - aminopurine and purine in charmm all - atom empirical force field , 2003 .

[42]  Alexander D. MacKerell,et al.  All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000, J. Comput. Chem..

[43]  P. Schleyer Encyclopedia of computational chemistry , 1998 .

[44]  W. M. Haynes CRC Handbook of Chemistry and Physics , 1990 .