Periodic DNA nanotemplates synthesized by rolling circle amplification

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.