Oligodeoxyribonucleotides

The fundamental problem of oligodeoxyribonucleotide synthesis is the efficient formation of the intemucleotidic phosphodiester bond specifically between C-3 and C-5 positions of two adjacent nucleosides. Any functional group (NH of nucleic base the other OH of deoxy-... 

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

C. Oligo- and Poly-nucleotides.—The stepwise enzymatic synthesis of internucleotide bonds has been reviewed. A number of polynucleotides containing modified bases have been synthesised " in the past year from nucleoside triphosphates with the aid of a polymerase enzyme, and the enzymatic synthesis of oligodeoxyribonucleotides using terminal deoxynucleotidyl transferase has been studied. Primer-independent polynucleotide phosphorylase from Micrococcus luteus has been attached to cellulose after the latter has been activated with cyanogen bromide. The preparation of insolubilized enzyme has enabled large quantities of synthetic polynucleotides to be made. The soluble enzyme has been used to prepare various modified polycytidylic acids. ... 

As mentioned in last year s Report, aromatic phosphoramidates have been used to protect 5 -phosphoryl groups in the stepwise synthesis of oligodeoxyribonucleotides. The appropriate monomer units are coupled with DCC and the phosphoramidate protecting group is removed when required with isoamyl nitrite. A rapid and general preparative method for oligonucleotides has been developed based on phosphoramidates of the highly lipophilic 4-aminophenyltriphenylmethane (25). Purification of... 

A variety of methods for modified oligonucleotide preparations have been reported including (1) the C5 and C4 positions for the pyramidines, (2) the exocyclic amino groups and the C8 positions of the purines, and (3) the 2 -hydroxyl group of the carbohydrate residue. Every method should be important as the basis for new immobilization chemistry, however, we especially focused our attention on the use of oligodeoxyribonucleotide phos-phorothioates (Fig. 3). 

As described in the subsequent section, we have reported the use of an oligodeoxyribonucleotide having five successive phosphorothioates for modified electrode preparations [19]. The IR-RAS spectrum for an Au substrate treated with the oligodeoxyribonucleotide (Fig. 4) confirmed that the formed surface phase reflects the intended adsorbate. Recently, Willner et al. also reported the use of an oligodeoxynucleo-... 

Puma, P., Duffey, D., and Dawidczyk, P., U.S. Patent appl. 94,944, Purification of oligodeoxyribonucleotide phosphorothioates using DEAE-5PW anion ion-exchange chromatography and hydrophobic interaction chromatography, 1994. 

Ozaki, H., Wada, H., Takeuchi, T., Makino, K., Fukui, T., and Kato, Y., Behaviour of single-stranded oligodeoxyribonucleotides on a DEAE-5PW anion-exchange column, /. Chromatogr, 322, 243, 1985. 

Sawai, H., Analysis and purification of synthetic large oligodeoxyribonucleotides by HPLC on RPC-5 like resin, Nucleic Acids Res., 17, 113, 1986. 

Another convenient phosphitylating reagent for use in an oligodeoxyribonucleotide synthesis based on the phosphoramidite approach is bis(tetrazolyl)morpholinophosphine. This is generally prepared in situ from morpholinophosphordichloridite containing di-isopropylethylamine and two equivalents of tetrazole in dichloromethane/pyridine at... 

Using method a, oligodeoxyribonucleotides were synthesized from di- to deca-deoxyribonucleotides by means of mesitylenesulfonylimidazole and mesitylenesulfonyl-1,2,4-triazole. With triisoproylbenzenesulfonylimidazole die condensation took place more slowly.11121 Compared widi the corresponding arylsulfonyl chlorides, imidazolides induced intemucleotide condensation much more slowly, but caused no darkening of the reaction mixture, did not affect acid-sensitive bonds in trityl protected nucleotides, and did not sulfonate the 3 -hydroxy groups.11111 The reaction conditions were room temperature, 5—6 days, and pyridine as solvent.11111... 

Instead of the isolated arylsulfonic acid azolides, mixtures of arylsulfonic acid chlorides and azoles have also been used for phosphorylation on a nucleoside 5 -OH or as coupling agents in the synthesis of oligodeoxyribonucleotides. 94 133 1371... 

Urdea, M.S., Warner, B.D., Running, J.A., Stempien, M., Clyne, J., and Horn, T. (1988) A comparison of non-radioactive hybridization assay methods using fluorescent, chemiluminescent and enzyme-labeled synthetic oligodeoxyribonucleotide probes. Nucleic Acids Res. 16, 4937-4956. 

The readily prepared immobilized phosphoramidite could be used to efficiently synthesize oligodeoxyribonucleotides with modified thymidine residues. Whereas the effect of microwave irradiation on the deprotection by exposing the strand to tet-rakis-triphenylphosphine palladium(O) and diethylammonium bicarbonate was only small using dichloromethane as solvent, complete removal of the alloc group was achieved in N,N-dimethylformamide within 10 min at 80 °C (Scheme 7.30). After the reaction, the solid-supported product was washed with N,N-dimethylformamide and dichloromethane and dried, before being subjected to acylation. The coupling... 

If a deoxyribonucleoside 5 -monophosphate is first esterified with a bulky apolar group, and then used as the 5 -terminus for synthesis of an oligodeoxyribonucleotide, reaction products may conveniently be isolated by solvent-extraction techniques, up to about the tetranucleotide stage. 2-(4-Tritylphenyl)thioethanol (69) and 2-(4-tritylphenyl)sulphonylethanol (70) have been used for this purpose.119 For deblocking, (69) is first oxidized to (70) with iV-chlorosuccinimide and then removed with alkali. 

G. Goodarzi, M. Watabe, K. Watabe, Organ Distribution and Stability of Phosphorothi-oated Oligodeoxyribonucleotides in Mice , Biopharm. Drug Dispos. 1992,13, 221 -227. 

R. H. Negative ionization micro electrospray mass spectrometry of oligodeoxyribonucleotides and their complexes. Rapid Commun Mass Spectrom 1996, 10, 47-50. 

Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res 31 2097-2107... 

Metal ions, especially Zn(II), play an important role in many enzyme-catalyzed reactions involving nucleic acids, such as DNA cleavage by zinc nuclease. Therefore, the binding of Zn(II) to a 19-mer double-stranded oligodeoxyribonucleotide was investigated to understand the role of zinc in DNA cleavage catalyzed by mung bean nuclease [107]. 

Diazafluorenes such as 129 have found use as cognition enhancers <1995USP5424430> and biologically active cyclobutane oligodeoxyribonucleotides such as 130 have been prepared using a photochemical cycloaddition reaction <2003W0070741>. 

Stemmer, W.P.C., Crameri, A., Ha, K.D., Brennan, T.M., and Heyneker, H.F. (1995). Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 49-53. 

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