title: Improved artificial origins for phage Φ29 terminal protein-primed replication. Insights into early replication events.
abstract: The replication machinery of bacteriophage Φ29 is a paradigm for protein-primed replication and it holds great potential for applied purposes. To better understand the early replication events and to find improved origins for DNA amplification based on the Φ29 system, we have studied the end-structure of a double-stranded DNA replication origin. We have observed that the strength of the origin is determined by a combination of factors. The strongest origin (30-fold respect to wt) has the sequence CCC at the 3' end of the template strand, AAA at the 5' end of the non-template strand and 6 nucleotides as optimal unpairing at the end of the origin. We also show that the presence of a correctly positioned displaced strand is important because origins with 5' or 3' ssDNA regions have very low activity. Most of the effect of the improved origins takes place at the passage between the terminal protein-primed and the DNA-primed modes of replication by the DNA polymerase suggesting the existence of a thermodynamic barrier at that point. We suggest that the template and non-template strands of the origin and the TP/DNA polymerase complex form series of interactions that control the critical start of terminal protein-primed replication.
authors: Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
authors: Pablo
authors: P
authors: Gella
authors: Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain msalas@cbm.csic.es.
authors: Margarita
authors: M
authors: Salas
authors: Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain msalas@cbm.csic.es.
authors: Mario
authors: M
authors: Mencía
mesh_terms: D017103:Bacillus Phages / Q000235:genetics / Q000502:physiology; D004247:DNA / Q000737:chemistry; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D009711:Nucleotides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D018741:Replication Origin; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism*; D014779:Virus Replication
chemical_list: D004268:DNA-Binding Proteins; D009711:Nucleotides; D014764:Viral Proteins; C040784:terminal protein, Bacillus phage phi29; D004247:DNA; D004259:DNA-Directed DNA Polymerase