ArticleNucleic acids research2002
Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor.Journal of microbiology (Seoul, Korea) · 2023Review
- DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures.Nucleic acids research · 2013Article
- The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein.Journal of molecular biology · 2011Article
- Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids.Nucleic acids research · 2008Article
- Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.Biochemistry · 2006Article
- Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.Nucleic acids research · 2006Article
- The contribution of phosphate-phosphate repulsions to the free energy of DNA bending.Nucleic acids research · 2005Article
- Axis curvature and ligand induced bending in the CAP-DNA oligomers.Biophysical journal · 2005Article
- Catabolite activator protein: DNA binding and transcription activation.Current opinion in structural biology · 2004Review
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We are interested in the role of asymmetric phosphate neutralization in DNA bending induced by proteins. We describe an experimental estimate of the actual electrostatic contribution of asymmetric phosphate neutralization to the bending of DNA by the Escherichia coli catabolite activator protein (CAP), a prototypical DNA-bending protein. Following assignment of putative electrostatic interactions between CAP and DNA phosphates based on X-ray crystal structures, appropriate phosphates in the CAP half-site DNA were chemically neutralized by methylphosphonate substitution. DNA shape was then evaluated using a semi-synthetic DNA electrophoretic phasing assay. Our results confirm that the unmodified CAP DNA half-site sequence is intrinsically curved by 26 degrees in the direction enhanced in the complex with protein. In the absence of protein, neutralization of five appropriate phosphates increases DNA curvature to 32 degrees (approximately 23% increase), in the predicted direction. Shifting the placement of the neutralized phosphates changes the DNA shape, suggesting that sequence-directed DNA curvature can be modified by the asymmetry of phosphate neutralization. We suggest that asymmetric phosphate neutralization contributes favorably to DNA bending by CAP, but cannot account for the full DNA deformation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.