title: Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules.
abstract: Nanoscale alpha-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson-Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5' versus 3' orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson-Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore.
authors.affiliation: Center for Biomolecular Science and Engineering, Department of Chemistry and Biochemistry, and. Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Wenonah A
authors.initials: WA
authors.lastname: Vercoutere
authors.forename: Stephen
authors.initials: S
authors.lastname: Winters-Hilt
authors.forename: Veronica S
authors.initials: VS
authors.lastname: DeGuzman
authors.forename: David
authors.initials: D
authors.lastname: Deamer
authors.forename: Sam E
authors.initials: SE
authors.lastname: Ridino
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Rodgers
authors.forename: Hugh E
authors.initials: HE
authors.lastname: Olsen
authors.forename: Andre
authors.initials: A
authors.lastname: Marziali
authors.forename: Mark
authors.initials: M
authors.lastname: Akeson
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006460:Hemolysin Proteins / Q000737:chemistry; D007700:Kinetics; D036103:Nanotechnology / Q000379:methods; D009690:Nucleic Acid Conformation / Q000187:drug effects; D014050:Toluene / Q000031:analogs & derivatives* / Q000494:pharmacology
chemical_list: D006460:Hemolysin Proteins; D014050:Toluene; C110527:difluorotoluene; D004247:DNA