title: Improved sensitivity for solid-support invasive cleavage reactions with flow cytometry analysis.
abstract: A new configuration of the solid-support invasive cleavage reaction provides a small reaction-volume format for high-sensitivity discrimination of nucleic acid targets with single nucleotide differences. With target concentrations as low as 2 amol/assay, the solid-support invasive cleavage reaction clearly distinguishes single base mutations. Two oligonucleotides tethered to the solid support hybridize to the target nucleic acid, forming a tripartite substrate that can be recognized and cleaved by Cleavase, a structure-specific 5'-nuclease. Each cleavage event yields fluorescence signal on the surface. When microspheres serve as the solid-support surface, analysis by fluorometer imparts real-time information about change in the reaction signal over time. Flow cytometry provides an alternative detection technology that collects endpoint information about the reaction signal on individual microspheres. A reaction volume of 10 microL with as few as 3000 microspheres is sufficient to distinguish single nucleotide differences at target concentrations less than 200 fM. This sensitivity level is within the range required for analysis of SNPs in genomic DNA. In addition, the flow cytometry format has multiplexing potential, making the microsphere-based invasive cleavage assay attractive for high-throughput genomic applications.
authors.affiliation: Department of Biomedical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3107, USA. pwilkins@northwestern.edu
authors.forename: P Wilkins
authors.initials: PW
authors.lastname: Stevens
authors.forename: K V N
authors.initials: KV
authors.lastname: Rao
authors.forename: J G
authors.initials: JG
authors.lastname: Hall
authors.forename: V
authors.initials: V
authors.lastname: Lyamichev
authors.forename: B P
authors.initials: BP
authors.lastname: Neri
authors.forename: D M
authors.initials: DM
authors.lastname: Kelso
mesh_terms: D001057:Apolipoproteins E / Q000235:genetics; D020137:Base Pair Mismatch / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000032:analysis / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D015342:DNA Probes / Q000138:chemical synthesis*; D005434:Flow Cytometry / Q000295:instrumentation / Q000379:methods*; D008863:Microspheres; D008969:Molecular Sequence Data; D017354:Point Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D001057:Apolipoproteins E; D015342:DNA Probes; D004247:DNA