Hybridization of oligonucleotides

R. Drmanac, Z. Stresoska, I. Labat, S. Drmanac, and R. Crkvenjakov, Reliable hybridization of oligonucleotides as short as six nucleotides. DNA Cell Biol. 9, 527-534 (1990). 

Novagen (ProteoPlex ), S S (FAST Quant), BioSource (Cartesian Array ), and BD Biosciences (BD Clontech Ab Microarrays) have introduced or will soon introduce protein microarray slide formatted products in which antibodies are directly immobilized. Beckman Coulter s protein array products for performing micro-ELlSAS in standard 96-well plate formats are based upon the self-assembly (by hybridization) of oligonucleotide-antibody conjugates to complementary oligonucleotides arrayed in individual wells. HTG s protein array technology was described previously. 

Algar, W. R., and Krull, U. J. (2006), Adsorption and hybridization of oligonucleotides on mercaptoacetic acid-capped CdSe/ZnS quantum dots and quantum dot-oligonucleotide conjugates, Langmuir, 22,11346-11352. 

Wallace, R. B., et al. 1981. The use of synthetic oligonucleotides as hybridization probes. II Hybridization of oligonucleotides of mixed sequence to rabbit P globin DNA. Nucl. Acids Res. 9 879-887. 

The dependence of the plasmon band on the dielectric constant of the surrounding medium in metal nanocrystals had been used to detect binding events taking place at the ligand shell. Thus, Au nanocrystals could colorimetrically determine the successful hybridization of oligonucleotide strands bound to its surface [83, 86]. It has been proposed that colorimetric sensing of heavy metal ions could be obtained by the use of carboxylic acid terminated bifunctional... 

Chu, H., Yan, J.,et al. Electrochemiluminescent detection of the hybridization of oligonucleotides using an electrode modified with nanocomposite of carbon nanotubes and gold nanoparticles. Microchimica Acta,175(3), 209-216 (2011). 

Tokareva and E. Hutter, Hybridization of oligonucleotide-modified silver and gold nanoparticles in aqueous dispersions and on gold films. /. Am. Chem. Soc., 126,15784-15789 (2004). 

Drmanac, R.T. Crkvenjakov, R.B. Method of Sequencing by Hybridization of Oligonucleotide Probes, United States Pat. No. 5695940, June 5,1995. 

FIGURE 10.1 Schematic representation of a molecular beacon, a hair pin-shaped molecule containing a fluorophore, and a quencher at its two ends. On excitation of the fluorophore, it is possible to observe emissions from the quencher because of EET. However, when a target nucleotide sequence is added, the fluorophore and the quencher are separated, and the fluorescence of the fluorophore is recovered. The process can be used to probe the hybridization of oligonucleotides. 

Gamper HB Jr, Arar K, Gewirtz A, Hou YM (2006) Unrestricted hybridization of oligonucleotides to structure-free DNA. Biochemistry 45 6978-6986... 

Kasamatsu A, Endo Y, Uzawa K, Nakashima D, Koike H, Hashitani S, et al. Identification of candidate genes associated with salivary adenoid cystic carcinomas using combined comparative genomic hybridization and oligonucleotide microarray analyses. Int J Biochem Cell Biol 2005 37 1869-80. 

Cyanine dyes also are used as labels for oligonucleotide probes. Unlike the hydrophilic cyanine dyes valuable for protein labeling, the use of dye-phosphoramidite compounds to synthesize DNA or RNA probes typically requires the use of more hydrophobic dye structures to make them compatible with the solvents and reactions of oligonucleotide synthesis. Thus, indol cyanines containing few or no sulfonates are used in these applications to label oligos for applications such as array detection, hybridization assays, and RT-PCR. 

Ghosh, S.S., Kao, P.M., McCue, A.W., and Chappelle, H.L. (1990) Use of maleimide-thiol coupling chemistry for efficient syntheses of oligonucleotide-enzyme conjugate hybridization probes. Bioconjugate Chem. 1, 71-76. 

Oerther DB, Danalewich J, Dulekgurgen E (1998) Bioaugmentation of sequencing batch reactors for biological phosphoms removal comparative rRNA sequence analysis and hybridization with oligonucleotide probes. Wat Sci Technol 37 469 173... 

All DNA hybridization assays are subject to cross-hybridization, in which an oligonucleotide that is not a perfect sequence match hybridizes with the capture probe. The cross-hybridization in the OFRR was investigated using samples of oligonucleotides with either 0-, 1-, 2-, 5-, or 25-base mismatches when compared with the 25 base-pair biorecognition capture probe. The resulting resonant mode spectral shifts for the respective mismatch are plotted in Fig. 14.7b. The measurements show a difference of 1.3 pm and 2.8 pm for one and two base-pair... 

At the EM level, detection usually involves using a probe (oligonucleotide) in which a hapten has been incorporated. Incorporation of the hapten does not interfere with the hybridization of the complementary sequences. The next step is the binding of a reporter (may be an antibody) to the hapten. The reporter is then subjected to a binding molecule (may be a secondary antibody) that is coupled with an electron-dense material such as colloidal gold for visualization. Nonetheless, the many affinity-detection and immunodetection systems developed for immuno-cytochemistry may now with ingenuity be applied to molecular biology at the EM level. 

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