title: High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation.
abstract: We describe a non-isotopic, semi-automated method for large-scale multiplex analysis of nucleic acid sequences, using the cystic fibrosis transmembrane regulator (CFTR) gene as an example. Products of a multiplex oligonucleotide ligation assay (OLA) are resolved electrophoretically from one another and from unligated probes under denaturing conditions with fluorescence detection. One ligation probe for each OLA target carries a fluorescent tag, while the other probe carries an oligomeric non-nucleotide mobility modifier. Each OLA product has a unique electrophoretic mobility determined by the ligated oligonucleotides and the mobility-modifier oligomer arbitrarily assigned (coded) to its target. The mobility range for practical mobility modifiers is much wider than the accessible range from unmodified ligated oligonucleotides of practical length. Each mobility modifier is built from phosphoramidite monomers in a stepwise manner on its associated oligonucleotide using an automated synthesizer. The resulting mobility modifiers lower the probe-target duplex Tm by less than 3 degrees C and retard probe-target annealing by less than 50%, with negligible effect on OLA yield and specificity. This method is especially useful for allelic discrimination in highly polymorphic genes such as CFTR.
authors.affiliation: Applied Biosystems Division, Perkin Elmer Corporation, Foster City, CA 94404.
authors.forename: P D
authors.initials: PD
authors.lastname: Grossman
authors.forename: W
authors.initials: W
authors.lastname: Bloch
authors.forename: E
authors.initials: E
authors.lastname: Brinson
authors.forename: C C
authors.initials: CC
authors.lastname: Chang
authors.forename: F A
authors.initials: FA
authors.lastname: Eggerding
authors.forename: S
authors.initials: S
authors.lastname: Fung
authors.forename: D M
authors.initials: DM
authors.lastname: Iovannisci
authors.forename: S
authors.initials: S
authors.lastname: Woo
authors.forename: E S
authors.initials: ES
authors.lastname: Winn-Deen
authors.forename: D A
authors.initials: DA
authors.lastname: Iovannisci
mesh_terms: D001322:Autoanalysis; D001483:Base Sequence; D002461:Cell Line, Transformed; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D004247:DNA / Q000737:chemistry; D004586:Electrophoresis; D005091:Exons; D005456:Fluorescent Dyes; D004854:Herpesvirus 4, Human; D008565:Membrane Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D009691:Nucleic Acid Denaturation; D015345:Oligonucleotide Probes; D009841:Oligonucleotides / Q000737:chemistry* / Q000302:isolation & purification; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature
chemical_list: D005456:Fluorescent Dyes; D008565:Membrane Proteins; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D004247:DNA