title: Single molecule fluorescence spectroscopy of pH sensitive oligonucleotide switches.
abstract: Several authors demonstrated that an oligonucleotide based pH-sensitive construct can act as a switch between an open and a closed state by changing the pH. To validate this process, specially designed fluorescence dye-quencher substituted oligonucleotide constructs were developed to probe the switching between these two states. This paper reports on bulk and single molecule fluorescence investigations of a duplex-triplex pH sensitive oligonucleotide switch. On the bulk level, only a partial quenching of the fluorescence is observed, similarly to what is observed for other published switches and is supposed to be due to intermolecular interactions between oligonucleotide strands. On the single molecule level, each DNA-based nanometric construct shows a complete switching. These observations suggest the tendency of the DNA construct to associate at high concentration.
authors.affiliation: Katholieke Universiteit Leuven, Department Chemistry and Institute for Nanoscale Physics and Chemistry (INPAC), Celestijnenlaan 200F, Heverlee, B-3001, Belgium.
authors.forename: Branko
authors.initials: B
authors.lastname: Kolaric
authors.forename: Michel
authors.initials: M
authors.lastname: Sliwa
authors.forename: Marco
authors.initials: M
authors.lastname: Brucale
authors.forename: Renaud A L
authors.initials: RA
authors.lastname: Vallée
authors.forename: Giampaolo
authors.initials: G
authors.lastname: Zuccheri
authors.forename: Bruno
authors.initials: B
authors.lastname: Samori
authors.forename: Johan
authors.initials: J
authors.lastname: Hofkens
authors.forename: Frans C
authors.initials: FC
authors.lastname: De Schryver
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D004247:DNA