Footprinting hydroxyl radical

Rothmel, RK, DL Shinbarger, MR Parsek, TL Aldrich, AM Chakrabarty (1991) Functional analysis of the Pseudomonas putida regulatory protein CatR transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J Bacterial 173 4717-4724. 

Tullius, T.D., and Dombroski, B.A. (1986) Hydroxyl radical footprinting high-resolution information about DNA-protein contacts and application to repressor and Cro protein. PNAS 83, 5469-5473. 

In one of the earlier reports hydroxyl radical footprinting was employed to analyze the interaction of distamycin and actinomycin with the 5s ribosomal RNA genes of Xenopus (Churchill et al, 1990). The two drugs showed different hydroxyl radical footprints. Distamycin gives a conventional (albeit high-resolution) footprint, while actinomycin does not protect DNA from hydroxyl radical attack, but instead induces... 

The second major area of interaction is near the dyad axis. Hydroxyl radical footprinting revealed protection at 65 and 75 bp from the DNA ends [40]. On the... 

Figure 12-28 (A) A hairpin ribozyme formed from the minus strand of a satellite RNA associated with tobacco ringspot virus. On the basis of hydroxyl radical footprinting (see Fig. 5-50), to identify protected areas a folding pattern that brings domains A and B together to form a compact catalytic core has been proposed.798 (B) A "leadzyme," a ribozyme dependent upon Pb2+ for cleavage of RNA.802 803 (C) An RNA-cleaving DNA enzyme.804...

As the present book is concerned with the free-radical chemistry of DNA, it is worth mentioning that hydroxyl radical footprinting, based on the forma-... 

As shown in Fig. 10.3C, comparison with hydroxyl radical footprinting data on the same RNA, under identical experimental condition, revealed that while both native and nonnative tertiary contacts are formed during the first compaction phase, only native tertiary contact formation drives the ribozyme to its folded structure in the second phase. The slightly larger global dimension observed in 1.5 M Na+ as compared to that in 10 mM Mg2+ indicates the inability of monovalent ions, even at sufficiently high concentrations, to fully compact this RNA to its native shape. 

Sclavi, B., Sullivan, M., et al. (1998). RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279(5358), 1940-1943. 

K., Probing the stractural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical footprinting, Curr. Opin. Struct. Biol. 12, 648-653, 2002 Knight, J.C., Functional implications of genetic variation in noncoding DNA for disease susceptibility and gene regulation, Clin. Sci. 104, 493-501, 2003. 

Adilakshmi T, Lease RA, Woodson SA. (2006) Hydroxyl radical footprinting in vivo Mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res 34 e64. 

Hydroxyl Radical Footprinting of Proteins Using Metal Ion Complexes... 

Schlatterer JC, Brenowitz M. Complementing global measures of RNA folding with local reports of backbone solvent accessibibty by time resolved hydroxyl radical footprinting. Methods. 2009 49 142-147. 

Kiselar, J.G., Chance, M.R. (2010) Future Directions of Structural Mass Spectrometry Using Hydroxyl Radical Footprinting. J. Mass. Spectrom. 45 1373-1382. 

AbrB is a repressor that binds to DNA in the regulatory region of genes under its control (115). In the case of tycA, DNAase and hydroxyl-radical footprinting studies... 

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