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Related Experiment Videos

The structure of DAPI bound to DNA.

T A Larsen1, D S Goodsell, D Cascio

  • 1Molecular Biology Institute, University of California, Los Angeles 90024-1570.

Journal of Biomolecular Structure & Dynamics
|December 1, 1989
PubMed
Summary

The DNA stain 4

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • The DNA stain 4'-6-diamidine-2-phenyl indole (DAPI) is widely used in molecular biology.
  • Understanding DAPI's binding mechanism to DNA is crucial for its applications.

Purpose of the Study:

  • To determine the precise structural arrangement of DAPI bound to a synthetic B-DNA oligonucleotide.
  • To elucidate the molecular interactions driving DAPI's sequence specificity.

Main Methods:

  • Single crystal X-ray diffraction at 2.4 A resolution.
  • Crystallographic structure determination of DAPI complexed with a C-G-C-G-A-A-T-T-C-G-C-G DNA sequence.

Main Results:

  • DAPI binds within the minor groove of B-DNA, displacing water molecules.
  • A single DAPI molecule and a water molecule interact with four AT base pairs.
  • The binding involves hydrogen bonding between DAPI's indole nitrogen and thymine O2 atoms.

Conclusions:

  • DAPI exhibits sequence specificity for AT-rich regions due to groove width, electrostatic potential, and steric factors.
  • These factors collectively contribute to DAPI's preferential binding and fine-tune its interaction with specific DNA sequences.

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