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Title: Evaluation of discriminating capability of planar rRNA-based oligonucleotide microchips
Keywords: discrimination index, dissociation temperatures, hybridization, mismatch, non-equilibrium dissociation, perfect match
Issue Date: 11-Dec-2003
Citation: LI SZE YING, EMILY (2003-12-11). Evaluation of discriminating capability of planar rRNA-based oligonucleotide microchips. ScholarBank@NUS Repository.
Abstract: This study examined the performance of three types of commercially available 2-dimensional substrate-coated slides using an approach that compares non-equilibrium dissociation profiles and dissociation temperatures (Tds) of all probe-target duplexes simultaneously. Both the conventional Td approach and a discrimination index (D.I.) approach were used to optimize discrimination between perfect and mismatch duplexes. Maximal discrimination indexes for duplexes with 2 and 1 internal MM occurred at temperatures 5 and 10A?C higher, respectively, than Td of the PM duplexes. Hybridization conducted using guanidithiocyanite (GuSCN)-based buffer produced duplexes with Tds slightly lower than that using formamide (FA)-based buffer. Salt concentration in the wash buffer, probe length, MM number, MM position, but not MM type, significantly affected dissociation profiles and Tds. Reusability potential of aldehyde-coated microchips was also demonstrated by subjecting printed microarrays to seven cycles of hybridization, washing and stripping. Finally, a mathematical model was proposed to systematically compute the probability of occurrence of microbial species of interest on microarrays.
Appears in Collections:Master's Theses (Open)

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