title: Effects of external transport on discrimination between perfect and mismatch duplexes on gel-based oligonucleotide microchips.
abstract: Using hydrogel-based oligonucleotide microchips developed previously for the choice of drugs during leukemia treatment and the other diseases, it is shown that the acceleration of external transport by mixing buffer solution with peristaltic pump not only enhances the observable fluorescence signals, but also improves significantly the discrimination between perfect and mismatch duplexes at the intermediate stage of hybridization on the oligonucleotide microchips. The discrimination efficiency for a given hybridization time grows monotonously with the frequency of flow pulsations. The mixing with frequency 10 Hz accelerates the hybridization rate approximately thrice and improves the discrimination efficiency 1.5-2.5 times higher for overnight hybridization. To study these effects, we have developed the special peristaltic pump mixing solution in a hybridization chamber of 35 mul in volume (area approximately 1 x 1 cm(2) and height 0.3 mm). We present also the brief theoretical summary for the interpretation and assessment of the observed experimental features.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, Russia 119991.
authors.forename: N V
authors.initials: NV
authors.lastname: Sorokin
authors.forename: D Y
authors.initials: DY
authors.lastname: Yurasov
authors.forename: A I
authors.initials: AI
authors.lastname: Cherepanov
authors.forename: J M
authors.initials: JM
authors.lastname: Kozhekbaeva
authors.forename: V R
authors.initials: VR
authors.lastname: Chechetkin
authors.forename: O A
authors.initials: OA
authors.lastname: Gra
authors.forename: M A
authors.initials: MA
authors.lastname: Livshits
authors.forename: T V
authors.initials: TV
authors.lastname: Nasedkina
authors.forename: A S
authors.initials: AS
authors.lastname: Zasedatelev
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence
chemical_list: D009838:Oligodeoxyribonucleotides; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate; D004247:DNA