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Quantifying length-dependent DNA end-binding by nucleoproteins.

Tam Vo1, Amanda V Albrecht1, W David Wilson2

  • 1Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States of America.

Biophysical Chemistry
|May 19, 2019
PubMed
Summary
This summary is machine-generated.

DNA end-binding is a poorly understood phenomenon. This study reveals that end-binding to DNA is negligible for longer fragments but significant for short oligomers, impacting binding statistics.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • End effects in nucleic acid oligomers influence ligand binding statistics.
  • The physical nature and impact of DNA end-binding remain largely unknown.
  • Understanding end-binding is crucial for various studies involving nucleic acid oligomers.

Purpose of the Study:

  • To investigate and characterize DNA end-binding using a model system.
  • To determine the dependence of end-binding on DNA sequence length.
  • To elucidate the mechanism and implications of end-binding in DNA-protein interactions.

Main Methods:

  • Utilized spectral analysis of intrinsic tryptophan fluorescence from the ETV6 DNA-binding domain.
  • Employed singular value decomposition for data analysis.
  • Assessed end-binding as a function of DNA fragment length.

Main Results:

  • DNA end-binding was found to be negligible for fragments longer than 0.2 kilobase pairs (kbp).
  • End-binding accounted for up to 8% of total binding to 23-base pair (bp) oligomers.
  • End-binding affinity was salt-insensitive and correlated with interior binding affinity, suggesting a translocation mechanism.
  • Cognate site presence suppressed end-binding on short DNA fragments.

Conclusions:

  • End-binding to DNA is significant for short oligomers but minimal for longer fragments.
  • Neglecting end-binding introduces minimal error for short DNA with cognate sites.
  • For nonspecific short DNA, end-binding must be considered unless fragments exceed 0.2 kbp.