Mapping nucleic acid structure by hydroxyl radical cleavage.

Hydroxyl radical footprinting is a widely used method for following the folding of RNA molecules in solution. This method has the unique ability to provide experimental information on the solvent accessibility of each nucleotide in an RNA molecule, so that the folding of all domains of the RNA species can be followed simultaneously at single-nucleotide resolution. In recent work, hydroxyl radical footprinting has been used, often in combination with other global measures of structure, to work out detailed folding pathways and three-dimensional structures for increasingly large and complicated RNA molecules. These include synthetic ribozymes, and group I and group II ribozymes, from yeast, the Azoarcus cyanobacterium and Tetrahymena thermophila. Advances have been made in methods for analysis of hydroxyl radical data, so that the large datasets that result from kinetic folding experiments can be analyzed in a semi-automated and quantitative manner.

[1]  N C Seeman,et al.  Assembly and characterization of five-arm and six-arm DNA branched junctions. , 1991, Biochemistry.

[2]  M. Chance,et al.  Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. , 2004, Journal of molecular biology.

[3]  T. Tullius,et al.  DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[4]  S. Woodson,et al.  Structural requirement for Mg2+ binding in the group I intron core. , 2003, Journal of molecular biology.

[5]  D. K. Treiber,et al.  Beyond kinetic traps in RNA folding. , 2001, Current opinion in structural biology.

[6]  Scott A Strobel,et al.  Crystal structure of a group I intron splicing intermediate. , 2004, RNA.

[7]  M. Chance,et al.  Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme , 2002, Nature Structural Biology.

[8]  Scott A. Strobel,et al.  Crystal structure of a self-splicing group I intron with both exons , 2004, Nature.

[9]  Elizabeth C. Theil,et al.  Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy. , 1998, Biochemistry.

[10]  T. Tullius,et al.  Quantitative analysis of electrophoresis data: novel curve fitting methodology and its application to the determination of a protein-DNA binding constant. , 1997, Nucleic acids research.

[11]  T. Cech,et al.  Defining the inside and outside of a catalytic RNA molecule. , 1989, Science.

[12]  C. Merryman,et al.  Nucleotides in 23S rRNA protected by the association of 30S and 50S ribosomal subunits. , 1999, Journal of molecular biology.

[13]  Thomas D. Tullius,et al.  Structural details of an adenine tract that does not cause DNA to bend , 1988, Nature.

[14]  S. Levene,et al.  Analysis of chemical and enzymatic cleavage frequencies in supercoiled DNA. , 2004, Journal of molecular biology.

[15]  M. Chance,et al.  Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. , 1997, Journal of molecular biology.

[16]  T. Earnest,et al.  X-ray crystal structures of 70S ribosome functional complexes. , 1999, Science.

[17]  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.

[18]  Keiji Takamoto,et al.  Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions. , 2004, Nucleic acids research.

[19]  L. J. Su,et al.  An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme. , 2003, Journal of molecular biology.

[20]  T. Tullius,et al.  What Species Is Responsible for Strand Scission in the Reaction of [FeIIEDTA]2- and H2O2 with DNA? , 1995 .

[21]  T. Tullius,et al.  Gapped DNA is anisotropically bent , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  B. Dombroski,et al.  Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[23]  N. Seeman,et al.  Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. , 2004, Journal of the American Chemical Society.

[24]  M. Brenowitz,et al.  'Footprinting' proteins on DNA with peroxonitrous acid. , 1993, Nucleic acids research.

[25]  N C Seeman,et al.  A Holliday recombination intermediate is twofold symmetric. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[26]  T. Cech,et al.  In vitro splicing of the ribosomal RNA precursor of tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence , 1981, Cell.

[27]  C. Merryman,et al.  Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. , 1999, Journal of molecular biology.

[28]  Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA. , 2004, Journal of molecular biology.

[29]  L. J. Su,et al.  Visualizing the solvent‐inaccessible core of a group II intron ribozyme , 2001, The EMBO journal.

[30]  B. Dombroski,et al.  Iron(II) EDTA used to measure the helical twist along any DNA molecule. , 1985, Science.

[31]  M R Chance,et al.  RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. , 1998, Science.

[32]  T. Brown,et al.  Cleavage of fragments containing DNA mismatches by enzymic and chemical probes. , 2003, The Biochemical journal.

[33]  N. Bergman,et al.  The three-dimensional architecture of the class I ligase ribozyme. , 2004, RNA.

[34]  T. Tullius,et al.  The unusual conformation adopted by the adenine tracts in kinetoplast DNA , 1987, Cell.

[35]  Elizabeth C. Theil,et al.  Ferritin mRNA: interactions of iron regulatory element with translational regulator protein P-90 and the effect on base-paired flanking regions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.