title: Structure-specific DNA cleavage on surfaces.
abstract: The structure-specific invasive cleavage reaction is a useful means for sensitive and specific detection of single nucleotide polymorphisms, or SNPs, directly from genomic DNA without a need for prior target amplification. A new approach integrating this invasive cleavage assay and surface DNA array technology has been developed for potentially large-scale SNP scoring in a parallel format. Two surface invasive cleavage reaction strategies were designed and implemented for a model SNP system in codon 158 of the human ApoE gene. The upstream oligonucleotide, which is required for the invasive cleavage reaction, is either co-immobilized on the surface along with the probe oligonucleotide or alternatively added in solution. The ability of this approach to unambiguously discriminate a single base difference was demonstrated using PCR-amplified human genomic DNA. A theoretical model relating the surface fluorescence intensity to the progress of the invasive cleavage reaction was developed and agreed well with experimental results.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396, USA.
authors.forename: Manchun
authors.initials: M
authors.lastname: Lu
authors.forename: Jeff G
authors.initials: JG
authors.lastname: Hall
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.forename: Liman
authors.initials: L
authors.lastname: Wang
authors.forename: W Travis
authors.initials: WT
authors.lastname: Berggren
authors.forename: Priscilla Wilkins
authors.initials: PW
authors.lastname: Stevens
authors.forename: David M
authors.initials: DM
authors.lastname: Kelso
authors.forename: Victor
authors.initials: V
authors.lastname: Lyamichev
authors.forename: Bruce
authors.initials: B
authors.lastname: Neri
authors.forename: James L
authors.initials: JL
authors.lastname: Skinner
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D013379:Substrate Specificity; D013499:Surface Properties; D013696:Temperature
chemical_list: D004247:DNA