Thu, 21 Aug 2008 17:22:23 BST CiteULike: penka Oskam http://www.citeulike.org/user/penka/author/Oskam CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/penka/article/1857692 <i>Biotechniques, Vol. 34, No. 5. (May 2003)</i><br /><br />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. Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection. RM Anthony AR Schuitema AB Chan PJ Boender PR Klatser L Oskam Biotechniques, Vol. 34, No. 5. (May 2003) 2007-11-02T23:08:16-00:00 2003 Biotechniques 0736-6205 34 5 a_poly a_top