Oligodeoxynucleotides,

Fig. 11. The amidite method for synthesizing oligodeoxynucleotides, where B and represent one of the protected bases thymine, A/ -benzoylcytosine,...

Synthesis of 3 -C- and 4 -C-branched oligodeoxynucleotides and the development of locked nucleic acids (LNA) 99ACR301. 

Probe A molecule used to detect the presence of a specific fragment of DNA or RNA in, for instance, a bacterial colony that is formed from a genetic library or during analysis by blot transfer techniques common probes are cDNA molecules, synthetic oligodeoxynucleotides of defined sequence, or antibodies to specific proteins. 

Single-stranded oligodeoxynucleotides were even more effective than dA at preserving the reactivity of QMP11 in an aqueous solution. A mere 3 pM of 5 -d... 

Only after the oligodeoxynucleotide component of the conjugate was replaced with d(T)io could the adducts of external nucleophiles be observed. This alternative oligodeoxynucleotide was chosen based on the lack of detectable reaction between T and the parent ortho-QMS 1 Aqueous incubation of the d(T)10 QM conjugate in the absence and presence of 2-mercaptoethanol yielded the water and 2-mercaptoethanol adducts, respectively, as characterized by HPLC and mass spectroscopy.71... 

SCHEME 9.23 An oligodeoxynucleotide-bis(quinone methide) conjugate was designed for cross-linking duplex DNA by initial triplex formation but resulted at best in only monoalkylation of its target. 

Caruthers, M. H., Synthesis of oligonucleotides and oligonucleotide analogues, in Oligodeoxynucleotides — Antisense Inhibitors of Gene Expression, Cohen, J. S., Ed., CRC Press, Boca Raton, FL, 1989, 7. 

Imidazolides, 1,2,4-triazolides, or tetrazolides of arylsulfonic acids have been used as condensing agents in expedient syntheses of oligodeoxynucleotides. 

Short reviews of die synthesis of oligodeoxynucleotides with mesitylenesulfonyl- or triisopropylbenzenesulfonyltetrazoles as coupling agents are provided in references [26] and [27],... 

Finally a few sentences are deserved for the vast area of DNA photochemistry. Thymine dimerization is the most common photochemical reaction with the quantum yield of formation in isolated DNA of all-thymine oligodeoxynucleotides 2-3% [3], Furthermore, a recent study based on femtosecond time-resolved transient absorption spectroscopy showed that thymine dimers are formed in less than 1 ps when the strand has an appropriate conformation [258], The low quantum yield of the reaction in regular DNA is suggested to be due to the infrequency of these appropriate reactive conformations. 

Okamoto A, Ichiba T, Saito I (2004) Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J Am Chem Soc 126 8364—8365... 

In protozoa this problem is solved by the addition of preexisting oligodeoxynucleotide blocks to the 3 ends of DNA. These blocks are composed of tandemly repeated units of (T2G4)n or (T4G4)n, where n is approximately 50. The enzyme that adds these polymers requires a primer but not a template. These oligonucleotide block polymers are called telomers. Another DNA polymerase,... 

Standifer K, Chien C, Wahlstedt C, Brown G, Pasternak G. Selective loss of delta opioid analgesia and binding by antisense oligodeoxynucleotide to a delta opioid receptor. Neuron 1994 12 805-810. 

Tomita N, Azuma H, Kaneda Y, Ogihara T, Morishita R (2004) Application of decoy oligodeoxynucleotides-based approach to renal diseases. Curr Drug Targets 5 717-733... 

Gaur, R., Sharma, S., and Gupta, K.C. (1989) A simple method for the introduction of thiol group at 5 -termini of oligodeoxynucleotides. Nucleic Acids Res. 17, 4404. 

Kiyama, H., Emson, P.C., and Tokyama, M. (1992) In situ hybridization histochemistry using alkaline phosphatase-labeled oligodeoxynucleotide probe. In Methods in Molecular Biology, Protocols in Molecular Neurobiology, (A. Longstaff, and R Revest, eds.), Vol. 13, pp. 167-179. Humana Press, Totowa, New Jersey. 

Alvarez-Salas, L.M., Benitez-Hess, M.L., and DiPaolo, J.A. 2003. Advances in the development of ribozymes and antisense oligodeoxynucleotides as antiviral agents for human papillomaviruses. Antiviral Therapy 8(4), 265-278. 

The translation of the sequence of the cDNA encoding deacetylvindoline 4-O-acetyltransferase compared to other putative plant acetyltransferases revealed a conserved region near the carboxy terminus of the proteins. This sequence was used to design a degenerate antisense oligodeoxynucleotide primer for PCR. The sense primer was based upon an internal peptide sequence of salutaridinol 7-0-acetyltransferase. This approach finally yielded a partial cDNA that encoded salutaridinol 7-O-acetyltransferase. The full-length clone was obtained by RACE-PCR and was functionally expressed in S. frugiperda Sf9 cells.28 The amino acid sequence of salutaridinol 7-O-acetyltransferase is most similar (37% identity) to that of deacetylvindoline acetyltransferase of C. roseus.27... 

KOHRER, K., KUTCHAN, T.M., DOMDEY, H., Specific oligodeoxynucleotide probes obtained through RNA sequencing, DNA, 1989,8,143-147. 

Shirota, H. et al., Regulation of murine airway eosinophilia and Th2 cells by antigen-conjugated CpG oligodeoxynucleotides as a novel antigen-specific immunomodulator, J Immunol, 164, 5575, 2000. 

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