title: Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure.
abstract: Nature has evolved replicable biological molecules, such as DNA, as genetic information carriers. The replication process is tightly controlled by complicated cellular machinery. It is interesting to ask if artificial DNA nano-objects with a complex secondary structure can be replicated in the same way as simple DNA double helices. Here we demonstrate that paranemic crossover DNA, a structurally complicated multi-crossover DNA molecule, can be replicated successfully using Rolling Circle Amplification (RCA). The amplification efficiency is moderate with high fidelity, confirmed by native PAGE, thermal transition study, and Ferguson analysis. The structural details of the DNA structure after the full replication circle are verified by hydroxyl radical autofootprinting. We conclude that RCA can serve as a reliable method to replicate complex DNA structures. We also discuss the possibility of using viruses and bacteria to clone artificial DNA nano-objects. The findings that single stranded paranemic crossover DNA molecules can be replicated by DNA polymerase will not only be useful in nanotechnology but also may have implications for the possible existence of such complicated DNA structures in nature.
authors.affiliation: Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Chenxiang
authors.initials: C
authors.lastname: Lin
authors.forename: Xing
authors.initials: X
authors.lastname: Wang
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.forename: Nadrian C
authors.initials: NC
authors.lastname: Seeman
authors.forename: Hao
authors.initials: H
authors.lastname: Yan
mesh_terms: D001483:Base Sequence; D003434:Crossing Over, Genetic; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D018983:DNA Footprinting; D004261:DNA Replication / Q000235:genetics*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D021141:Nucleic Acid Amplification Techniques; D009690:Nucleic Acid Conformation; D013696:Temperature
chemical_list: D004247:DNA; D004259:DNA-Directed DNA Polymerase