Oligonucleotides, hybridization based

An advantage of the ASO method is that it can be used to simultaneously test samples for several different mutations by the use of multiple probes bound to a solid matrix. In practice, the success of this method relies on precisely establishing conditions for optimal oligonucleotide hybridization in order to ensure specific probe hybridization, and so multiplex ASO assays can be difficult to develop. Molecular diagnostic kits for use in genetic disorders based on ASO methods are available (14). 

Jaeske, A., Fuertste, J. P., Erdmann, V. A., and Cech, D. (1994). Hybridization-based affinity partitioning of nucleic acids using PEG-coupled oligonucleotides. Nucleic Acids Res. 22, 1880 1884. 

Table III shows that the luminescent lifetimes and the relative luminescent intensities for the covalently bound duplex and its noncovalent analogue are similar. As with [Ru(phen)2(dppz)]2+, a biexponential decay in emission is observed for the ruthenated oligonucleotide hybridized to its complement. A small shift in the wavelength of maximum emission is also observed compared to the noncovalent complex. This shift likely reflects the sensitivity in emission to the stacking of the oriented dppz ligand a dependence of the maximum emission wavelength on base...

Moore P, Clayton J (2003) To affinity and beyond. Nature 426 725-731 Budach W, Abel AP, Bruno AP et al (1999) Planar waveguides as high performance sensing platforms for fluorescence-based multiplexed oligonucleotide hybridization assays. Anal Chem 71 3347-3355... 

OLA. The OLA uses an enzymatic reaction to increase the specificity of a hybridization-based approach. Three very specific oligonucleotide probes are used in OLA one specific for the wild-type allele, one specific for the variant allele, and a common probe that carries a fluorescent label. PCR is used to create amplicons containing the polymorphic site. When the PCR products are incubated with all three probes, the 5 region of the common probe anneals just downstream of the polymorphic site. The 3 end of either of the allele specific probes anneals adjacent to the 5 end of the common probe. In the presence of thermostable DNA ligase, the two probes will join only if there is a perfect match. The results of the assay can be observed either by gel... 

Wei, X., Dai, G., Marcucci,G Liu,Z Hoyt, D Blum, W and Chan, K.K. (2006) A specific picomolar hybridization based ELISA assay for the determination of phosphor othioate oligonucleotides in plasma and cellular matrices. Pharmaceutical Research, 23, 1251 1264. 

The ability to synthesize short oligonucleotide DNA probes with an acridinium ester attached at any defined position within the sequence (A16, N5) has allowed for the use of such probes in hybridization-based assays for RNA and DNA target sequences. Two techniques have recently emerged, together with a combination of the two (for enhanced sensitivity). 

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