title: Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection.
abstract: Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately, different short probes (< 30 bases) selected using widely accepted criteria do not perform consistently in this type of assay. Here we present a systematic study on the effect of secondary structure on the ability of oligonucleotide probes to detect an SNP, using real-time array monitoring of a porous microarray substrate that incorporates a novel intra-array mixing system. These results demonstrate that, although positioning of an SNP in the middle of the probe is highly destabilizing, the effect of stable secondary structure on the signal obtained is so dramatic that such probes may be very insensitive. Therefore, if the SNP flanking sequence contains significant secondary structure, then more sensitive probes with good specificity may be obtained by positioning the mutation towards one end of the probe.
authors.affiliation: KIT Biomedical Research, Amsterdam, The Netherlands. r.anthony@kit.nl
authors.forename: R M
authors.initials: RM
authors.lastname: Anthony
authors.forename: A R J
authors.initials: AR
authors.lastname: Schuitema
authors.forename: A B
authors.initials: AB
authors.lastname: Chan
authors.forename: P J
authors.initials: PJ
authors.lastname: Boender
authors.forename: P R
authors.initials: PR
authors.lastname: Klatser
authors.forename: L
authors.initials: L
authors.lastname: Oskam
mesh_terms: D016477:Artifacts; D015342:DNA Probes / Q000737:chemistry* / Q000145:classification; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D008567:Membranes, Artificial; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016062:Porosity; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D015342:DNA Probes; D008567:Membranes, Artificial; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit