Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)₄.

ABSTRACT: All-atom molecular dynamics (MD) computer simulations have been applied successfully to duplex DNA structures in solution for some years and found to give close accord with observed results. However, the MD force fields have generally not been parameterized against unusual DNA structures, and their use to obtain dynamical models for this class of systems needs to be independently validated. The four-way junction (4WJ), or Holliday junction, is a dynamic DNA structure involved in central cellular processes of homologous replication and double strand break repair. Two conformations are observed in solution: a planar open-X form (OPN) with a mobile center and four duplex arms, and an immobile stacked-X (STX) form with two continuous strands and two crossover strands, stabilized by high salt c

SUBMITTER: Wheatley EG 

PROVIDER: S-EPMC3274787 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature