Chemical nucleases as probes for studying DNA-protein interactions.

@article{Papavassiliou1995ChemicalNA,
  title={Chemical nucleases as probes for studying DNA-protein interactions.},
  author={Athanasios G. Papavassiliou},
  journal={The Biochemical journal},
  year={1995},
  volume={305 ( Pt 2)},
  pages={
          345-57
        }
}
  • A. Papavassiliou
  • Published 15 January 1995
  • Biology, Chemistry
  • The Biochemical journal
Over the past fifteen years much research has been devoted to the mode(s) by which the linear DNA macromolecule communicates with cellular proteins in the course of genetic programming, thus determining the patterns of growth and development in living organisms. A plethora of proteins have been shown to interact non-covalently with DNA either as structural elements, exemplified by the histones of eukaryotic chromatin, or as components of the complex cellular machineries operating in the… 

Figures from this paper

Footprinting DNA-protein interactions in native polyacrylamide gels by chemical nucleolytic activity of 1,10-phenanthroline-copper.
TLDR
These limitations can be circumvented by combining the advantages of EMSA, with the subsequent exposure of the resolved DNA-protein complex(es) to the chemical nuclease 1,10-phenanthroline-copper ion (OP-Cu) while they are still embedded in the polyacrylamide matrix (in-gel assay).
Site-specific Interactions of JBP with Base and Sugar Moieties in Duplex J-DNA
TLDR
Examination of molecular interactions that contribute to recognition of the glycosylated base in synthetic DNA substrates using modification interference, modification protection, DNA footprinting, and photocross-linking techniques finds that the two primary requirements for J-DNA recognition include contacts at base J and a base immediately 5′ of J (J-1).
Footprinting and missing nucleoside analysis of transcription factor-DNA complexes.
TLDR
Methods and protocols to analyze the interaction of proteins with DNA using footprinting and related techniques based on the modification of DNA with either hydroxyl radicals or methylating agents are described.
Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases.
TLDR
Theoretical alignment of the region of best contacts between the protein and DNA showed that in the case of a palindromic interaction site, a zone covering the 5'-symmetric residues is located in the major groove versus a zone of contact covering the 3'-symetric residues in the minor groove, fitting a simple rule of thumb that the most important contacts are aligned around the methylation target base.
Interaction of the bacteriophage Mu transcriptional activator protein, C, with its target site in the mom promoter.
TLDR
The bacteriophage Mu C gene encodes a 16.5 kDa site-specific DNA binding protein that is a transcriptional activator of the four "late" promoters, Pmom, Plys, PI and PP, and it is shown that C binding induces a deformation, possibly a bend, in Pmom DNA.
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.
TLDR
Results of extensive cross-linking and affinity cleavage experiments using single-cysteine P protein variants derivatized with either azidophenacyl bromide or 5-iodoacetamido-1,10-o-phenanthroline to determine distance constraints and to model the Bacillus subtilis holoenzyme-substrate complex indicate that P protein is positioned close to the RNase P active site and may play a role in organizing the RN enzyme.
...
...

References

SHOWING 1-4 OF 4 REFERENCES
DNA-protein interactions : principles and protocols
TLDR
This work presents a meta-modification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli using the Cassette Method, and some of the results show marked improvements over the previous work on this topic.
Protein function : a practical approach
Minizing protein in activation ligand-protein binding affinities ligand blotting affinity labelling cross-linking of protein subunits and ligands by the introduction of disulphide bonds determining
Gel electrophoresis of nucleic acids : a practical approach
TLDR
Two-dimensional gel electrophoresis of nucleic acids, R de Wachter et al gel retardation of nucletic acid-protein interactions, and the analysis of sequence-specific DNA-binding proteins in cell extracts are reported.
EMBO J . 7 , 1871 - 1879 48
  • 1988