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DNA exhibits slow conformational exchanges between Watson-Crick and Hoogsteen base-pairing, particularly in TAA segments. These dynamics, observed using NMR, reveal transient Hoogsteen pairs that influence DNA structure and protein interactions.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Free B-DNA exhibits dynamic motions beyond standard base-pairing.
  • Slow conformational exchanges (microsecond-to-millisecond) can mediate DNA-protein assemblies.
  • Watson-Crick (WC) and Hoogsteen (HG) base-pairing represent distinct DNA conformations.

Purpose of the Study:

  • To investigate slow conformational dynamics in a DNA dodecamer with a TTAAA element using NMR.
  • To identify transient base-pairing conformations and their role in DNA structure.
  • To understand how DNA sequence modulates dynamics on the micro- to millisecond timescale.

Main Methods:

  • Utilized R1ρ relaxation dispersion NMR spectroscopy.
  • Employed 13C/15N labeled DNA for enhanced signal detection.
  • Analyzed NMR data to infer exchange parameters and conformational populations.

Main Results:

  • Identified transient Hoogsteen (HG) base pairs within the TAA·TTA segment of the DNA dodecamer.
  • Observed HG base pairs as minor conformers with an abundance up to 1.2%.
  • Demonstrated non-simultaneous motions of adenine bases, optimizing HG pair formation.

Conclusions:

  • The TAA·TTA sequence facilitates transient HG base-pairing in DNA.
  • DNA sequence plays a crucial role in modulating dynamics across various timescales.
  • These findings enhance understanding of DNA functional elements and their dynamic repertoire for protein binding.