title: Periodic DNA nanotemplates synthesized by rolling circle amplification.
abstract: Rolling circle amplification (RCA) is an elegant biochemical method by which long single-stranded DNA molecules with a repeating sequence motif can be readily synthesized. In RCA, small circular single-stranded oligonucleotides serve as templates for the polymerization of the complementary strand. A DNA polymerase with an efficient strand displacement activity can copy the circular template without stopping. This results in a long DNA strand with periodic sequence. We here demonstrate that this method, using DNA recognition and biotin-streptavidin binding, provides a simple procedure for DNA-directed nanoscale organization of matter. As an example, a 74 nucleotide (nt) long circular DNA molecule is amplified into a sequence-periodic single strand with a length up to several micrometers. Hybridization of this long periodic DNA template to the biotinylated complement of the sequence motif results in a long DNA duplex with a periodic arrangement of biotin binding sites. On this duplex, streptavidin-coated particles can be organized into one-dimensional arrays. The resulting DNA constructs are characterized by gel electrophoresis and atomic force microscopy.
authors.affiliation: Department of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 München, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Beyer
authors.forename: Patrick
authors.initials: P
authors.lastname: Nickels
authors.forename: Friedrich C
authors.initials: FC
authors.lastname: Simmel
mesh_terms: D001710:Biotin / Q000737:chemistry; D019921:Biotinylation; D004261:DNA Replication; D004270:DNA, Circular / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000096:biosynthesis*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry; D049329:Nanostructures / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D019809:Streptavidin / Q000737:chemistry; D013698:Templates, Genetic
chemical_list: D004270:DNA, Circular; D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D001710:Biotin; D019809:Streptavidin; D004259:DNA-Directed DNA Polymerase