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#DNA bending

3 public questions tagged with this topic.

Transcription in Eukaryotes

Which factor bends DNA by ~80° during initiation?

TBP saddle inserts into minor groove of eight base pair TATA box, using four phenylalanine side chains to intercalate between base steps, causing severe kinking of about eighty degrees toward major groove and slight unwinding. Such dramatic bending partially unwinds DNA, widens minor groove, and creates platform for TFIIA and TFIIB entry. Bending also brings upstream regulatory regions closer to initiation site and introduces strain facilitating promoter melting by TFIIH helicase. Crystallography of TBP-TATA shows twofold symmetric bending creating almost right angle conformation.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: TBP bends DNA ~80 degrees; PDB 1CDW TBP-TATA structure

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Nucleosome Packing

Main driving force for DNA bending around histones is:

Bending rigid DNA duplex around small histone octamer radius about 4.2 nanometers overcomes electrostatic repulsion and mechanical stiffness. Strong driving force arises from extensive attractive interactions between positively charged lysine and arginine side chains lining histone octamer superhelical ramp and negatively charged phosphate groups, plus multitude hydrogen bonds between histone main chain amides and DNA backbone phosphates and numerous water-mediated contacts. Charge neutralization lowers energetic barrier permitting sharp curvature. Hydrophobic interactions stabilize octamer core internal assembly, but DNA-histone attraction via electrostatics and hydrogen bonding governs bending energetics, not covalent bonds or dispersive forces alone.

Ref: Luger et al., Nature 1997 Structure; Lodish et al., Chapter 8: Driving Force DNA Bending Charge Neutralization

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DNA

What structural feature causes bends in DNA?

Presence of six consecutive adenines correctly identifies the characteristic feature or property described in this question. In DNA, specific characteristics define and distinguish biological molecules, organisms, or processes from one another. The feature described by Presence of six consecutive adenines is a defining property that arises from its unique molecular structure, evolutionary history, or physiological role. The other options (Alternating GC sequences, High AT content, and High GC content) describe characteristics of different entities, represent incorrect properties, or apply to the subject under different conditions.

Ref: Molecular Biology of the Gene, Watson et al., 7th Ed.

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