DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy

• Published in: Journal of molecular biology Vol. 294; no. 4; pp. 1015 - 1026
• Main Authors: Cherny, Dmitry I, Striker, George, Subramaniam, Vinod, Jett, Stephen D, Paleček, Emil, Jovin, Thomas M
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 10-12-1999
• Subjects: Base Sequence; Binding Sites; Consensus Sequence; DNA - chemistry; DNA - metabolism; DNA - ultrastructure; DNA bending; electron microscopy; Humans; In Vitro Techniques; Macromolecular Substances; Microscopy, Electron; Nucleic Acid Conformation; p53; Protein Binding; Protein Structure, Tertiary; Recombinant Proteins - chemistry; Recombinant Proteins - metabolism; Recombinant Proteins - ultrastructure; specific DNA/protein complex; Tumor Suppressor Protein p53 - chemistry; Tumor Suppressor Protein p53 - metabolism; Tumor Suppressor Protein p53 - ultrastructure; PNA; specific DNA/protein complex; p53CON; EM; s.d; electron microscopy; p53CD; p53; DNA bending; ds
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1999.3299

We have used transmission electron microscopy to analyze the specificity and the extent of DNA bending upon binding of full-length wild-type human tumor suppressor protein p53 (p53) and the p53 core domain (p53CD) encoding amino acid residues 94–312, to linear double-stranded DNA bearing the consensus sequence 5′-AGACATGCCTAGACATGCCT-3′ (p53CON). Both proteins interacted with high specificity and efficiency with the recognition sequence in the presence of 50 mM KCl at low temperature (∼4 °C) while the p53CD also exhibits a strong and specific interaction at physiological temperature. Specific complex formation did not result in an apparent reduction of the DNA contour length. The interaction of p53 and the p53CD with p53CON induced a noticeable salt-dependent bending of the DNA axis. According to quantitative analysis with folded Gaussian distributions, the bending induced by p53 varied from ∼40 ° to 48 ° upon decreasing of the KCl concentration from 50 mM to ∼1 mM in the mounting buffer used for adsorption of the complexes to the carbon film surface. The p53CD bent DNA by 35–37 ° for all salt concentrations used in the mounting buffer. The bending angle of the p53/DNA complex under low salt conditions showed a somewhat broader distribution (σ≈39 °) than at high salt concentration (σ≈31 °) or for p53CD (σ≈24–27 °). Together, these results demonstrate that the p53CD has a dominant role in complex formation and that the complexes formed both by p53 and p53CD under moderate salt conditions are similar. However, the dependence of the bending parameters on ambient conditions suggest that the segments flanking the p53CD contribute to complex formation as well. The problems associated with the analysis of bending angles in electron microscopy experiments are discussed.