title: Single-stranded structures are present within plasmids containing the Epstein-Barr virus latent origin of replication.
abstract: The Epstein-Barr virus (EBV) latent origin of plasmid replication (oriP) contains two essential regions, a family of repeats with 20 imperfect copies of a 30-bp sequence and a dyad symmetry element with four similar 30-bp repeats. Each of the repeats has an internal palindromic sequence and can bind EBNA 1, a protein that together with oriP constitutes the only viral element necessary for EBV maintenance and replication. Using single-strand-specific nucleases, we have probed plasmids containing oriP-derived sequences for the presence of secondary structural elements. Multiple single-stranded structures were detected within the oriP region. Of the two essential elements of oriP, the family of repeats seemed to extrude these structures at a much higher frequency than did sequences within the dyad symmetry region. Though negative supercoiling was found to stabilize the single-stranded structures, they showed significant stability even after linearization of the oriP plasmids. Two major single-stranded structures detected involved approximately 12 bp of DNA. These loci could be transiently unwound regions that form because of negative supercoiling and the high A + T content of this region of DNA, or they could be cruciform structures extruded within the palindromic sequences of oriP that may be important sites for protein-DNA interactions in the EBV oriP.
authors.affiliation: Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510-8064.
authors.forename: R
authors.initials: R
authors.lastname: Orlowski
authors.forename: G
authors.initials: G
authors.lastname: Miller
mesh_terms: D000956:Antigens, Viral / Q000378:metabolism; D001483:Base Sequence; D004261:DNA Replication; D004277:DNA, Single-Stranded / Q000235:genetics*; D004278:DNA, Superhelical / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics*; D019309:Epstein-Barr Virus Nuclear Antigens; D004854:Herpesvirus 4, Human / Q000235:genetics* / Q000276:immunology / Q000502:physiology; D006801:Humans; D008969:Molecular Sequence Data; D010957:Plasmids; D012091:Repetitive Sequences, Nucleic Acid; D015183:Restriction Mapping; D014779:Virus Replication
chemical_list: D000956:Antigens, Viral; D004277:DNA, Single-Stranded; D004278:DNA, Superhelical; D004279:DNA, Viral; D019309:Epstein-Barr Virus Nuclear Antigens