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The cytoplasm of adjacent animal cells can exchange small molecules, ions, and secondary messengers via the communication channels which form the gap junctions. These junctions comprise a few hundred to thousands of molecular channels, each made of two halves, called the connexon hemichannel. A connexon is a hexamer of six transmembrane connexin proteins, which assemble radially, thus forming a pore or channel in the center. One connexon hemichannel docks with a corresponding connexon on the...
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Computer models of DNA four-way junctions

A R Srinivasan1, W K Olson

  • 1Department of Chemistry, Wright-Rieman Laboratories, Rutgers, State University of New Jersey, New Brunswick 08903.

Biochemistry
|August 16, 1994
PubMed
Summary
This summary is machine-generated.

This study models four-stranded DNA Holliday junctions using computational methods. The models reveal flexible structures with preserved base pairing, suggesting mechanisms for DNA branch migration.

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Molecular modeling

Background:

  • Holliday junctions are crucial four-way DNA structures involved in genetic recombination.
  • Understanding their conformational flexibility and dynamics is essential for elucidating DNA repair and replication mechanisms.

Purpose of the Study:

  • To develop a computational model for constructing and analyzing four-stranded DNA Holliday junction structures.
  • To investigate the conformational diversity and flexibility of Holliday junctions.

Main Methods:

  • A constrained backbone generating algorithm combined with hard-sphere packing calculations.
  • Systematic rotation and translation of DNA duplexes to find contact-free states.
  • Identification of low-energy sugar-phosphate linkages for strand exchange using a backbone torsion algorithm.
  • Analysis of long-range electrostatic energies with varying dielectric constant treatments.

Main Results:

  • Sterically acceptable four-arm Holliday junctions were formed over a wide range of angles.
  • Models preserved base stacking and Watson-Crick pairing, with deformation only at the backbone exchange site.
  • Calculations revealed multiple conformational solutions, indicating significant junctional mobility.
  • Electrostatic energy analysis provided insights into conformational preferences and flexibility.

Conclusions:

  • The developed modeling scheme can generate diverse Holliday junction structures with variable arm conformations and lengths.
  • The models suggest a possible mechanism for branch migration and link solution and crystal structure observations.
  • Holliday junction structures exhibit considerable conformational variability and flexibility, influenced by electrostatic interactions.