title: Homogeneous detection of single rolling circle replication products.
abstract: We describe a simple and straightforward approach for homogeneous and isothermal detection of individual rolling circle replication (RCR) products, which represent individual padlock probe circularization events. The RCR products constitute tens of kilobases long single-stranded tandem repeated copies of the probe sequence, and in solution, they fold into micrometer-sized random coils. The method is based on the local enrichment of fluorescence-labeled probes that hybridize to the coiled RCR products compared to the concentration of free probes in solution. We present a detailed characterization of the fluorescence-labeled products using a highly sensitive and fast microscopy setup. At a 10(4)-fold excess of free label, we were able to detect and follow individual RCR products at a signal-to-background noise ratio of 27. This high signal-to-background noise ratio leaves room for analysis in a simple detection device at higher speeds or at lower labeling ratios.
authors.affiliation: Department of Biophysics, Huygens Laboratory, Leiden University, Leiden, The Netherlands.
authors.forename: Gerhard A
authors.initials: GA
authors.lastname: Blab
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
mesh_terms: D000818:Animals; D002232:Carbocyanines / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004261:DNA Replication; D004270:DNA, Circular / Q000737:chemistry* / Q000235:genetics; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D005456:Fluorescent Dyes / Q000737:chemistry; D007834:Lasers; D008297:Male; D044085:Microfluidics; D008856:Microscopy, Fluorescence; D015336:Molecular Probe Techniques; D021141:Nucleic Acid Amplification Techniques; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry / Q000235:genetics; D012235:Rhodamines / Q000737:chemistry; D020080:Tandem Repeat Sequences
chemical_list: D002232:Carbocyanines; D004270:DNA, Circular; D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D012235:Rhodamines; C085321:cyanine dye 5; D004247:DNA