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Turner, D.H.1
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RNA folding: Models and perspectives
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A very good review that describes experimental in vitro folding studies of large ribozymes and presents several widely accepted folding models.
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Sosnick T.R., Pan T. RNA folding: models and perspectives. Curr Opin Struct Biol. 13:2003;309-316 A very good review that describes experimental in vitro folding studies of large ribozymes and presents several widely accepted folding models.
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Sosnick, T.R.1
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Single-molecule folding
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An excellent summary of the latest details of RNA and protein folding revealed by two single-molecule techniques: FRET and force spectroscopy.
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Zhuang X., Rief M. Single-molecule folding. Curr Opin Struct Biol. 13:2003;88-97 An excellent summary of the latest details of RNA and protein folding revealed by two single-molecule techniques: FRET and force spectroscopy.
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Yeast RNA helicases of the DEAD-box family involved in translation initiation
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The NS3 RNA helicase/protease, present during RNA replication of hepatitis C virus, was studied using standard biochemical techniques to dissect the unwinding mechanism into individual isolated steps.
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Pang P.S., Jankowsky E., Planet P.J., Pyle A.M. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. EMBO J. 21:2002;1168-1176 The NS3 RNA helicase/protease, present during RNA replication of hepatitis C virus, was studied using standard biochemical techniques to dissect the unwinding mechanism into individual isolated steps.
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DExD/H-box proteins and their partners: Helping RNA helicases unwind
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Reversible unfolding of single RNA molecules by mechanical force
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Estimating the persistence length of a worm-like chain molecule from force-extension measurements
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Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
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Pulling geometry defines the mechanical resistance of a beta-sheet protein
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Brockwell D.J., Paci E., Zinober R.C., Beddard G.S., Olmsted P.D., Smith D.A., Perham R.N., Radford S.E. Pulling geometry defines the mechanical resistance of a beta-sheet protein. Nat Struct Biol. 10:2003;731-737
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The mechanical stability of ubiquitin is linkage dependent
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Carrion-Vazquez M., Li H., Lu H., Marszalek P.E., Oberhauser A.F., Fernandez J.M. The mechanical stability of ubiquitin is linkage dependent. Nat Struct Biol. 10:2003;738-743
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Mechanically probing the folding pathway of single RNA molecules
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Gerland U., Bundschuh R., Hwa T. Mechanically probing the folding pathway of single RNA molecules. Biophys J. 84:2003;2831-2840
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Force as a useful variable in reactions: Unfolding RNA
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Tinoco I Jr: Force as a useful variable in reactions: unfolding RNA. Annu Rev Biophys Biomol Struct 2004, in press.
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A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
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A four-way RNA junction holds the catalytic loops of the hairpin ribozyme close together; this greatly increases their rate of docking and thus the catalytic activity. The minimal form of the ribozyme is active, but much slower.
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Tan E., Wilson T.J., Nahas M.K., Clegg R.M., Lilley D.M., Ha T. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc Natl Acad Sci USA. 100:2003;9308-9313 A four-way RNA junction holds the catalytic loops of the hairpin ribozyme close together; this greatly increases their rate of docking and thus the catalytic activity. The minimal form of the ribozyme is active, but much slower.
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Ansari A., Shen Y., Kuznetsov S.V. Misfolded loops decrease the effective rate of DNA hairpin formation. Phys Rev Lett. 88:2002;069801
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Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?
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Hyeon C., Thirumalai D. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci USA. 100:2003;10249-10259
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RNABase: An annotated database of RNA structures
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Murthy V.L., Rose G.D. RNABase: an annotated database of RNA structures. Nucleic Acids Res. 31:2003;502-504
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A thermodynamic framework for the magnesium-dependent folding of RNA
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2+ ions is coupled to the tertiary structure of several well-characterized RNAs.
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2+ ions is coupled to the tertiary structure of several well-characterized RNAs.
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