The stacked-X DNA Holliday junction and protein recognition.
The crystal structure of the four-stranded DNA Holliday junction has now been determined in the presence and absence of junction binding proteins, with the extended open-X form of the junction seen in all protein complexes, but the more compact stacked-X structure observed in free DNA. The structures of the stacked-X junction were crystallized because of an unexpected sequence dependence on the stability of this structure. Inverted repeat sequences that contain the general motif NCC or ANC favor formation of stacked-X junctions, with the junction cross-over occurring between the first two positions of the trinucleotides. This review focuses on the sequence dependent structure of the stacked-X junction and how it may play a role in structural recognition by a class of dimeric junction resolving enzymes that themselves show no direct sequence recognition.
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA.
Patricia A
PA
Khuu
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA.
Andrea Regier
AR
Voth
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA.
Franklin A
FA
Hays
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA.
P Shing
PS
Ho
D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D045566:DNA, Cruciform / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011995:Recombination, Genetic / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
D045566:DNA, Cruciform; D004247:DNA