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#DNA-protein binding

2 public questions tagged with this topic.

Regulation of chromatin structure

What happens if two DNA-binding proteins bind closer than 147 bp?

Nucleosome formation requires approximately 147 base pairs of DNA wrapping 1.65 turns around histone octamer plus accessible linker. When sequence-specific DNA binding proteins occupy sites less than this distance apart, steric hindrance prevents octamer deposition because binding proteins block wrapping path and compete for major groove contacts. In vitro reconstitution shows that tight clustering of transcription factors, insulators or polymerases creates nucleosome-depleted regions, while cooperative positioning can generate phased arrays adjacent to barriers. This principle underlies promo

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Nucleosome Positioning and Barrier Models

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Transcript analysis

In EMSA, slower mobility of DNA indicates:

In EMSA, labeled DNA probe is subjected to non-denaturing gel electrophoresis maintaining native complexes. Free unbound DNA, being small and highly negatively charged, migrates rapidly toward positive electrode, appearing near bottom of autoradiogram. When sequence-specific DNA-binding protein present, DNA engages in stable nucleoprotein complex with substantially larger hydrodynamic radius and altered charge-to-mass ratio. Consequently, electrophoretic mobility is retarded, complex migrates slower and appears as higher band. Intensity and position of retarded band reflect affinity, stoichiom

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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