Oligonucleotide conjugates

The synthesis and characterisation of photocleavable peptide-DNA conjugates have been studied. The peptide portions have been used as mass tags, released during ionisation by UV-MALDI to identify unique DNA sequences. The conjugates were evaluated as hybridisation probes, and the photocleavable peptide had no effect on the thermal stability of DNA duplexes. 

The attachment of DNA to the backbone of defined organic polymers derived from ring-opening metathetic polymerisation (ROMP) has been reported. Starting from the norbornenol derivative (157), polymerisation of the ring-strained olefin was carried out, and the product converted into its phos-phoramidite derivative and conjugated to DNA. 

The fluorescent ddA 5 -triphosphate derivative (163) was shown to be an effective substrate for terminal transferase, and various DNA polymerases. The resultant DNA could then be detected by fluorescence spectroscopy. A molecular beacon DNA probe incorporating a donor and a quencher dye has been reported, which shows high sensitivity and dynamic range. Such molecular beacons are anticipated to have use in DNA/RNA and pro-tein/DNA/RNA interactions. 

A set of fluorophores derived from naphthalene, phenanthrene, pyrene, phenazine and fluorene have been conjugated to the 5 -ends of DNA and RNA to compare their physico-chemical properties. Decreasing the Ji-electron density led to an enhancement in thermal stability, attributable to more favourable Jt-Ji interactions. Stability is further enhanced by using nitrated fluorophores. Fluorescent labelling of ODNs using oxyamino modified fluorescein has been reported by the incorporation into DNA of aldehyde functions. The aldehyde function was attached either at the 5 -end via a phosphate linker or internally via 8-mercaptobutanal. Reduction of the resulting oxime was not necessary. 

A method for labelling ODNs with radioactive halogens has been reported using the conjugate (166). The reaction of ODNs containing a 3 -phos-phorothioate with the conjugate occurs in moderate yield. 

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The aqueous Diels-Alder reaction has also been used for bioconjugate studies. A Diels-Alder reaction of diene oligonucleotides with maleimide dieneophiles was used to prepare oligonucleotide conjugates in aqueous media under mild conditions (Eq. 12.39).102 A Diels-Alder-type cycloaddition of an electronically matched pair of saccharide-linked conjugated dienes and a dienophile-equipped protein was the... 

Pagels, P., Starke, D., Kramer, W., Hepatobiliary transport of bile add amino add, bile add peptide, and bile acid oligonucleotide conjugates in rats, Hepatology 1999, 30, 1257-1268. 

Geselowitz, D.A., and Neumann, R.D. (1995) Quantitation of triple-helix formation using a photo-cross-linkable aryl azide/biotin/oligonucleotide conjugate. Bioconjuate Chem. 6, 502-506. 

Marchan, V., Ortega, S., Pulido, D., Pedroso, E., and Grandas, A. (2006) Diels-Alder cycloadditions in water for the straightforward preparation of peptide-oligonucleotide conjugates. Nucleic Acids Res. 34(3), e24. 

M. Nakayama, T. Ihara, K. Nakano, and M. Maeda, DNA sensors using a ferrocene-oligonucleotide conjugate. Talanta 56, 857-866 (2002). 

A. S. Boutorine, M. Takasugi, C. Helene, H. Tokuyama, H. Isobe, E. Nakamura, Fullerene-oligonucleotide conjugates-photoinduced sequence-specific DNA cleavage, Angewandte Chemie International Edition in English, vol. 33, pp. 2462-2465,1994. 

A multiplexed immrmoassay has likewise been introduced based upon the ArrayPlate format in which antibody-oligonucleotide conjugates are assembled by hybridization to complementary capture probes. Beckman Coulter introduced the A MicroArray System in March 2004. The A squared or A (array of arrays) approach involves the printing of a capture oligonucleotide "zip code" in the bottom of a rounded square 96-well... 

Bongartz, J.P., Aubertin, A.M., Milhaud, P.G., Lebleu, B. (1994). Improved biological activity of antisense oligonucleotides conjugated to a fusogenic peptide. Nucleic Acids Res., 22, 4681 1688. 

Warren, W. J., and Vella, G. (1994). Analysis and purification of synthetic oligonucleotides by high-performance liquid chromatography. In Protocols for Oligonucleotide Conjugates (S. Agrawal, ed.), pp. 233-265. Humana Press, Totowa, NJ. 

Figure 1.50. Diastereoisomeric Cgo-oligonucleotide conjugates 239/240 including the racemic fullerene-alcohol buliding block ( )-215 (Scheme 1.18).

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. 

Nesterova, I.V. et al. MetaUo-phthalocyanine near-IR fluorophores oligonucleotide conjugates and their applications in PCR assays. Bioconjugate Chem. 2007, 18, 2159-2168. 

Privat E, Melvin T. Asseline U, Vigny P. Oligonucleotide conjugated thiazole orange probes as Tight-up probes for mes-senge RNA molecules in living cells. Photochem. Photobiol. B. 2001 74 532-541. 

Privat E, Asseline U. Synthesis and properties of oligonucleotide-conjugated thiazole orange. Bioconjugate Chem. 2001 12 757-769. 

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