Direct evidence for spontaneous branch migration in antiparallel DNA Holliday junctions.
The Holliday junction is a central intermediate in genetic recombination. It contains four strands of DNA that are paired into four double helical arms flanking a branch point. In naturally occurring Holliday junctions, the sequence flanking the branch point contains 2-fold (homologous) symmetry. As a consequence of this symmetry, the junction can undergo a conformational isomerization known as branch migration, which relocates the site of branching. In the absence of proteins and in the presence of Mg(2+), the four arms are known to stack in pairs, forming two helical domains whose orientations are antiparallel. Nevertheless, the mechanistic models proposed for branch migration are all predicated on a parallel alignment of helical domains. Here, we have used antiparallel DNA double crossover molecules to demonstrate that branch migration can occur in antiparallel Holliday junctions. We have constructed a DNA double crossover molecule with three crossover points. Two adjacent branch points in this molecule are flanked by symmetric sequences. The symmetric crossover points are held immobile by the third crossover point, which is flanked by asymmetric sequences. Restriction of the helices that connect the immobile junction to the symmetric junctions releases this constraint. The restricted molecule undergoes branch migration, even though it is constrained to an antiparallel conformation.
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Department of Chemistry, New York University, New York, New York 10003, USA.
Liu
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Seeman
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D001483:Base Sequence; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics; D018983:DNA Footprinting; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry; D017665:Hydroxyl Radical / Q000737:chemistry; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D013816:Thermodynamics
D009692:Nucleic Acid Heteroduplexes; D017665:Hydroxyl Radical; D004247:DNA; C025630:CAGCTG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; C024403:GGCC-specific type II deoxyribonucleases