DNA bending in protein-DNA complexes.
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Base Composition↗
Biomedical subjects
M R Gartenberg
Publications and source records attributed to M R Gartenberg.
Molecular characterization of the GCN4-DNA complex.
We report studies of the DNA complex formed by GCN4, a transcriptional activator of eukaryotic amino acid biosynthetic operons. The DNA thermodynamic binding domain, defined by primer extension analysis, spans at least 18 base pairs, a site much larger than the 9-base-pair consensus defined by homology with naturally occurring binding sites. Chemical modification experiments reveal multiple sites of protein-DNA contact: methylation of any guanine N-7 or adenine N-3, ethylation of any phosphate oxygen, or elimination of any nucleoside within a region spanning nearly one and a half turns of the double helix reduces the binding affinity of the complex measurably. Nevertheless, the protein yields no detectable hydroxyl radical footprint, implying that the minor groove is reagent-accessible in the protein-DNA complex. These chemical modification patterns indicate that GCN4 does not utilize any of the DNA-recognition motifs of paradigm DNA-binding proteins. Assays to detect DNA bending induced by truncated or intact GCN4 indicate that protein conformation and not a protein-induced bend is responsible for the anomalous electrophoretic behavior of GCN4-DNA complexes.
Base Sequence↗
DNA sequence determinants of CAP-induced bending and protein binding affinity.
The sites of DNA bending induced by binding catabolite activator protein are identified and shown to coincide with positions where DNA grooves face the protein. The bendability of DNA with different sequences at these bend centres parallels the bending preference of the sequences in nucleosomal DNA. Anisotropic DNA bendability significantly affects the structure and strength of regulatory protein-DNA complexes.
Bacterial Proteins↗
The DNA binding domain and bending angle of E. coli CAP protein.
We use a new gel electrophoretic analysis to map the thermodynamically defined DNA binding domain of Escherichia coli CAP protein in the lac promoter. Strong binding interactions span a 28-30 bp duplex DNA region, substantially larger than that found for typical repressors. Sequence changes outside the central 28 bp of the binding site are found to affect the electrophoretically observed extent of bending. We also report a study of the DNA bending induced at a symmetrized CAP binding site, compared with the wild-type site; binding and bending are stronger at the upstream than at the downstream half of the wild-type site. Bends of the estimated 90 degrees - 180 degrees magnitude could play a vital regulatory role by producing tertiary structure in a local DNA domain, and by storing elastic energy for subsequent use in transcription or replication.
Bacterial Proteins↗