Oligonucleotide hybridization detection

T.-Y. Lee and Y.-B. Shim, Direct DNA hybridization detection based on the oligonucleotide-functionahzed conductive polymer. Ainal. Chem. 73, 5629—5632 (2001). 

The subsequent explosion of array technologies has been sparked by two key inno-vations. The first is the use of non-porous solid support, such as glass, which has facilitated the miniaturization of the array and the development of fluorescence-hybridization detection (16, 17, 18). The second critical iimovation has been the development of methods for high-density spatial synthesis of oligonucleotides, which allows the analysis of thousands of genes at the same time. Because DNA cannot bind directly to the glass, the surface is first treated with silane to covalently attach reactive amine, aldehyde, or epoxies groups that allow stable attachment of DNA, proteins, and other molecules. 

Taton et al. used gold nanoparticles functionalized with thiol-modified oligonucleotides to detect the presence of its complementary sequence hybridized on a transparent substrate (Fig. 13.9).16 In comparison to conventional fluorophore probes, this technique is three times more sensitive in discriminating an oligonucleotide sequence with a single basepair mismatch. In addition, signal amplification by reduction of silver ions on the nanoparticles drastically increased the sensitivity of... 

The one-base extension method [73], rolling circle amplification (RCA) method [74]and Taqman PCR method [75], have been applied to SNP detection. Also a DNA chip which anchored oligonucleotide on the substrate has been developed as a simple hybridization detection tool [76-82], For SNP detection, it is not easy to determine the difference of one base mismatch with this hybridization detection method due to unstable hybridization between probe and SNP and nonspecific adsorption. 

Hakala, H., and Lonnberg, H. (1997) Time resolved fluorescence detection of oligonucleotide hybridization on a single microparticle covalent immobilization of oligonucleotides and quantitation of a model system. Bioconjugate Chemistry, 8, 232 237. 

Algar WR, Krull UJ. Towards multi-colour strategies for the detection of oligonucleotide hybridization using quantum dots as energy donors in FRET. Anal Chim Acta2007 581 193-201. 

Pham M. C., Piro B., Tran L. D., Ledoan T., and Dao L. H., Direct electrochemical detection of oligonucleotide hybridization on poly(5-hydroxy-l,4-naphthoquinone-co-5-hydroxy-3-thioacetic acid-l,4-naphthoquinone) film, Anal Chem., 75(23), 6748-6752, 2003. 

A PCR sequence was used related to Hepatitis B (HBV) virus genome. Optimization of hybridization detection was performed with 17-mer short oligonucleotides. Carbon paste electrodes (CPE) and hanging mercury drop electrodes (HMDE) were used as sensor surface, CV and DPV transduction of MDB accumulated after hybridization between 23-mer capture probe and HBV-PCR amplicon was monitored for the detection. By using MDB indicator. Herpes simplex (HSV) virus genome detection and discrimination of HSV type I and type II viruses were performed in PCR amplicon... 

Using this method, several fluorescein- and biotin-tagged oligonucleotidic hybridization probes (a probe for the detection of genes encoding cysteine proteases of Fasciola hepatica, a probe for the detection of human papillomavirus (type 16)) have been synthesized and successfully used in biological studies. 

A fluorimetric detection of oligonucleotide hybridization is also possible since the fluorescence of polythiophenes is quenched in the planar, aggregated form [37, 38]. For instance, at 55 °C, the yellow form... 

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