A 96-well DNase I footprinting screen for drug–DNA interactions

@article{Ellis2007A9D,
  title={A 96-well DNase I footprinting screen for drug–DNA interactions},
  author={Tom Ellis and Davidr . Evans and Christopher R. H. Martin and John A. Hartley},
  journal={Nucleic Acids Research},
  year={2007},
  volume={35},
  pages={e89 - e89}
}
The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect of the traditional method and making appropriate modifications it has been possible to considerably reduce the time, risk of sample loss and complexity of footprinting, whilst dramatically increasing the yield of data (30-fold). A semi-automated analysis system has also been developed to present footprinting… 

Figures from this paper

An extended pyrrolobenzodiazepine-polyamide conjugate with selectivity for a DNA sequence containing the ICB2 transcription factor binding site.
TLDR
Molecular modeling and computational studies have provided details of the covalent attachment process that leads to formation of the PBD-DNA adduct, and have allowed the preference of 3a for ICB2 to be rationalized.
The Use of Automated Sequencing Techniques to Investigate the Sequence Selectivity of DNA‐Damaging Agents
TLDR
The interaction of the antitumour drug, bleomycin, with DNA is utilized to illustrate the recent technological advances.
Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli
TLDR
A library of Escherichia coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation is presented.
Tunable Transcription Factor Library for Robust Quantification of Gene Expression Dynamics in E. coli
TLDR
A library of E. coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation is presented.
Transcriptional Profiling Analysis of the Global Regulator NorG, a GntR-Like Protein of Staphylococcus aureus
TLDR
Transcriptional-profiling assays indicate that NorG has broad regulatory function in S. aureus and positively affected the transcription of global regulators mgrA, arlS, and sarZ.

References

SHOWING 1-10 OF 42 REFERENCES
High-resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes.
Footprinting with an automated capillary DNA sequencer.
TLDR
An easy four-step footprinting method that uses long-lived, safe and easy-to-make fluorescently labeled target fragments, uses sensitive, robust and highly reproducible fragment analysis using an automated DNA sequencer, instead of gel electrophoresis and autoradiography; and is cost effective.
Solid phase DNase I footprinting: quick and versatile.
TLDR
An adaptation of the standard procedure 10 solid phase technology with many unique advantages over conventional footprinl ing assays is described, minimizing the exposure of the researcher 10 radiation.
Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes.
Nonradiochemical DNase I footprinting by capillary electrophoresis.
TLDR
The CE protocol was found to be effective for footprint analysis of the immediate upstream region of the rat glutathione peroxidase (GPX) and it permitted identification of a previously unknown binding site in the upstream sequence of the GPX gene.
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity.
TLDR
Estimates indicate that 10-fold sequence-specificity (differential binding constant) could be studied easily using this technique, and the binding of lac repressor to lac operator is visualized by "footprinting" as an example.
DNase I footprinting of small molecule binding sites on DNA.
TLDR
The method is described and technical details are given for performing deoxyribonuclease (DNase) I footprinting with DNA-binding drugs for probing sequence-selective binding of small molecules to DNA.
Long-range and highly sensitive DNase I footprinting by an automated infrared DNA sequencer.
TLDR
It is shown that an automated DNA sequencer is applicable to fluorescence-based detection of fragments in DNase I footprinting and developed techniques in data collection and subsequent image processing for highly sensitive detection.
Ligation-mediated PCR for quantitative in vivo footprinting
TLDR
It is shown that the LM-PCR technique could be used for sensitive and reproducible in vivo photofootprinting of the human phosphoglycerate kinase 1 (PGK1) promoter, as well as providing good Maxam–Gilbert sequence information.
...
...