title: Measuring single-molecule DNA hybridization by active control of DNA in a nanopore.
abstract: We present a novel application of active voltage control of DNA captured in a nanopore to regulate the amount of time the DNA is available to molecules in the bulk phase that bind to the DNA. In this work, the control method is used to measure hybridization between a single molecule of DNA captured in a nanopore and complementary oligonucleotides in the bulk phase. We examine the effect of oligonucleotide length on hybridization, and the effect of DNA length heterogeneity on the measurements. Using a mathematical model, we are able to deduce the binding rate of complementary oligonucleotides, even when DNA samples in experiments are affected by heterogeneity in length. We analyze the lifetime distribution of DNA duplexes that are formed in the bulk phase and then pulled against the pore by reversing the voltage. The lifetime distribution reveals several dissociation modes. It remains to be resolved whether these dissociation modes are due to DNA heterogeneity or correspond to different states of duplex DNA. The control method is unique in its ability to detect single-molecule complex assembly in the bulk phase, free from external force and with a broad (millisecond-to-second) temporal range.
authors.affiliation: Department of Computer Engineering, University of California at Santa Cruz, Santa Cruz, California, USA.
authors.forename: Brett
authors.initials: B
authors.lastname: Gyarfas
authors.forename: Robin
authors.initials: R
authors.lastname: Abu-Shumays
authors.forename: Hongyun
authors.initials: H
authors.lastname: Wang
authors.forename: William B
authors.initials: WB
authors.lastname: Dunbar
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D004560:Electricity; D007700:Kinetics; D008958:Models, Molecular; D058608:Nanopores; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics; D013997:Time Factors
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA; D004259:DNA-Directed DNA Polymerase