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OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences
1Cold Spring Harbor Laboratory, New York 11724.
Genes & Development
|November 1, 1988
Summary
The HeLa cell octamer-binding protein OBP100 demonstrates flexible DNA sequence recognition, binding to both conserved and degenerate motifs. This flexibility arises from multiple independent interactions rather than obligatory contact sites.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Octamer-binding protein 100 (OBP100) from HeLa cells is a model for studying protein-DNA interactions.
- OBP100 recognizes the octamer motif ATGCAAAT in various promoters.
- It also binds degenerate octamer motifs in the SV40 enhancer.
Purpose of the Study:
- To investigate the flexible DNA sequence recognition capabilities of OBP100.
- To explore how OBP100 recognizes diverse DNA sequences, including those with low similarity.
- To understand the molecular basis of flexible promoter-binding protein recognition.
Main Methods:
- Utilized OBP100 as a model system.
- Analyzed binding to conserved and degenerate octamer motifs.
- Employed mutational analysis and chemical modification interference assays on SV40 site II.
Main Results:
- OBP100 recognizes the herpes simplex virus immediate early promoter motif TAATGARAT, distinct from its known binding sites.
- A continuum of OBP100 binding sites links seemingly unrelated sequences through incremental changes.
- Flanking sequences can compensate for degeneracy in the core octamer motif, demonstrating interdependent sequence divergence.
Conclusions:
- Flexible DNA sequence recognition by OBP100 is characterized by numerous weak, independent interactions.
- Specific binding is determined by the sum of these interactions, not by a few essential contact sites.
- This mechanism allows OBP100 to bind a range of DNA sequences with varying degrees of similarity.