Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA.
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[1] Thomas A. Steitz,et al. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[2] D. Crothers,et al. Conformational changes of transfer RNA. The role of magnesium(II). , 1976, Biochemistry.
[3] R. Micura,et al. Ligand‐Induced Folding of the Adenosine Deaminase A‐Riboswitch and Implications on Riboswitch Translational Control , 2007, Chembiochem : a European journal of chemical biology.
[4] F. Michel,et al. Frequent use of the same tertiary motif by self‐folding RNAs. , 1995, The EMBO journal.
[5] David E Draper,et al. Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. , 2007, Biochemistry.
[6] R. Altman,et al. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. , 2005, RNA.
[7] D. Draper,et al. Mg2+–RNA interaction free energies and their relationship to the folding of RNA tertiary structures , 2006, Proceedings of the National Academy of Sciences.
[8] R. Römer,et al. tRNA Conformation and Magnesium Binding , 1975 .
[9] T. Ha,et al. Multivector Fluorescence Analysis of the xpt Guanine Riboswitch Aptamer Domain and the Conformational Role of Guanine† , 2010, Biochemistry.
[10] Eric Westhof,et al. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[11] N. Pace,et al. Crystal structure of a bacterial ribonuclease P RNA. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[12] D. Lafontaine,et al. Core requirements of the adenine riboswitch aptamer for ligand binding. , 2007, RNA.
[13] Jeffrey E. Barrick,et al. Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.
[14] D. Draper,et al. Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye. , 2009, Methods in enzymology.
[15] T. Pan,et al. Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. , 2010, Journal of molecular biology.
[16] Sebastian Doniach,et al. Rapid compaction during RNA folding , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[17] R. Breaker,et al. Adenine riboswitches and gene activation by disruption of a transcription terminator , 2004, Nature Structural &Molecular Biology.
[18] T. Alatossava,et al. Manipulation of intracellular magnesium content in polymyxin B nonapeptide-sensitized Escherichia coli by ionophore A23187 , 1985, Journal of bacteriology.
[19] D. Thirumalai,et al. RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. , 2005, Journal of molecular biology.
[20] Peter V. Konarev,et al. ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis , 2007 .
[21] R. Batey,et al. Ligand-dependent folding of the three-way junction in the purine riboswitch. , 2008, RNA.
[22] P. Dehaseth,et al. Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. , 1977, Biochemistry.
[23] D. Draper,et al. The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration. , 2010, Journal of molecular biology.
[24] Scott A. Strobel,et al. Crystal structure of a self-splicing group I intron with both exons , 2004, Nature.
[25] D. Herschlag,et al. Small angle X-ray scattering reveals a compact intermediate in RNA folding , 2000, Nature Structural Biology.
[26] T. Cech,et al. Defining the inside and outside of a catalytic RNA molecule. , 1989, Science.
[27] R. Batey,et al. Mutational analysis of the purine riboswitch aptamer domain. , 2007, Biochemistry.
[28] J. Doudna,et al. A magnesium ion core at the heart of a ribozyme domain , 1997, Nature Structural Biology.
[29] Dmitri I. Svergun,et al. Automated matching of high- and low-resolution structural models , 2001 .
[30] Karen L. Buchmueller,et al. Near native structure in an RNA collapsed state. , 2003, Biochemistry.
[31] R. London,et al. Methods for measurement of intracellular magnesium: NMR and fluorescence. , 1991, Annual review of physiology.
[32] P. Nygaard,et al. The Purine Efflux Pump PbuE in Bacillus subtilis Modulates Expression of the PurR and G-Box (XptR) Regulons by Adjusting the Purine Base Pool Size , 2005, Journal of bacteriology.
[33] D. Draper,et al. Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model. , 2000, Journal of molecular biology.
[34] A. Serganov,et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.
[35] Frank Dieterich,et al. Fluorescence measurements of free [Mg2+] by use of mag-fura 2 in Salmonella enterica. , 2004, FEMS microbiology letters.
[36] Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. , 2004, Biochemistry.
[37] David E Draper,et al. Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. , 2009, Methods in enzymology.
[38] M. Record,et al. Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. , 1991, Journal of molecular biology.
[39] D. Thirumalai,et al. Metal ion dependence of cooperative collapse transitions in RNA. , 2009, Journal of molecular biology.
[40] P. Schimmel,et al. Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe. , 1974, Biochemistry.
[41] Karen L. Buchmueller,et al. A collapsed non-native RNA folding state , 2000, Nature Structural Biology.
[42] K. Burton. Adenine transport in Escherichia coli , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[43] D. Draper,et al. Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient. , 2010, Biochemistry.
[44] D. Draper,et al. A thermodynamic framework for Mg2+ binding to RNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[45] John A Tainer,et al. Improving small-angle X-ray scattering data for structural analyses of the RNA world. , 2010, RNA.
[46] T. Pan,et al. Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. , 2000, Biochemistry.
[47] David E Draper,et al. Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. , 2007, Journal of Molecular Biology.
[48] M. Guéron,et al. Role of divalent ions in folding of tRNA. , 1977, European journal of biochemistry.
[49] Rhiju Das,et al. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. , 2003, Journal of molecular biology.
[50] Harald Schwalbe,et al. Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain , 2007, Nucleic acids research.
[51] D. Draper,et al. The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory. , 1999, Journal of molecular biology.
[52] D. Lilley,et al. Folding of the adenine riboswitch. , 2006, Chemistry & biology.