Synthetic oligodeoxynucleotide

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. 

Both bacterial DNA and synthetic oligodeoxynucleotides (ODNs) containing CpG motifs have been shown to induce or enhance the stimulation of a variety of immune cells (Figure 22.2). This stimulation includes ... 

Jones, T.R., Obaldia III, N., Gramzinski, R.A., Charoenvit, Y., Kolodny, N., Kitov, S. et al. (1999) Synthetic oligodeoxynucleotides containing CpG motifs enhance immunogenicity of a peptide malaria vaccine in Aotus monkeys. Vaccine, 17, 3065-3071. 

This approach has been extensively applied to small subunit rRNA, and sequences of synthetic oligodeoxynucleotides that can serve as universal primers for this molecule have been reported previously.9 Owing to its... 

Oumouna, M., L. Jaso-Friedmann and D.L. Evans. Activation of nonspecific cytotoxic cells (NCC) with synthetic oligodeoxynucleotides and bacterial genomic DNA binding, specificity and identification of unique immunostimulatory motifs. Dev. Comp. Immunol. 26 257-269, 2002. 

Karamychev VN, Reed MW, Neumann RD, Panyutin IG. Distribution of DNA strand breaks produced by iodine-123 and indium-111 in synthetic oligodeoxynucleotides. Acta Oncol 2000 39 687-692. 

Wang H, Rayburn E, Zhang R (2005). Synthetic oligodeoxynucleotides containing deoxycytidyl-deoxyguanosine dinucleotides (CpG ODNs) and modified analogs as novel anticancer therapeutics. Curr. Pharmaceu. Des. 11 2889-2907. 

A synthetic oligodeoxynucleotide mismatched at a single nucleotide to a specific complementary site on a wild-type circular < >X174 DNA can be used to produce a defined point mutation, thus in vitro incorporation into a closed circular duplex DNA by elongation with DNA polymerase and ligation followed by transfection... 

Saito and co-workers investigated a series of photoligation reactions of DNA using native and terminus-functionalized oligonucleotides. As illustrated in Scheme 1.17, synthetic oligodeoxynucleotides 88a and 88b, which bear a cytosine at the 3 -end and a 5-vinyldeoxyuridine at the 5"-end, are complementary to an oligodeoxynucleotide tern-... 

Dinucleoside H-phosphonate dimers have been used as intermediates for the synthesis of phosphorothioates (10), phosphoramidates (10), phosphate triesters (10), and methyl phosphonates (15) (Fig. 3). This method has been extended to the synthesis of polynucleoside phosphorothioates (7,12,13) and phosphoramidates (7,10,11,16). Much of this chapter is devoted to the coupling and the oxidation reactions. The coupling step is very sensitive to overactivation by acyl chlorides, and thus, precautions must be taken to avoid the consequent side reactions. The oxidation reaction is important because of the fact that all linkages are oxidized at once, and care must be taken at this step to ensure complete oxidation, yet prevent the alkaline hydrolysis of the backbone. Often, poor quality of synthetic oligodeoxynucleotide is the result of hydrolysis of the backbone or incomplete oxidation, not inadequate chain elongation. 

In the past few years the demand for synthetic oligodeoxynucleotides has increased enormously because of their usefulness in many areas of the life sciences. They arell needed ... 

Stationary phase. The classical example of a mixed mode column packing material is the low-pressure resin RPC-5 (13). It consists of non-porous Plaskon or Teflon particles to which aliphatic quaternary ammonium salts are adsorbed. RPC-5 has been applied successfully to the separation of tRNAs. tRNA fragments and more recently to the isolation of restriction fragments (14). RPC-5 itself is not commercially available. A RPC-5 analogue, however, has been developed, NACS, which can be purchased from BRL. NACS-12 has been used for mixed mode HPLC of DNA, DNA fragments and synthetic oligodeoxynucleotides. 

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