Synthesis and Biochemical Activity of New Oligonucleotide Analogs

Abstract

Borane phosphonate deoxyoligonucleotides are synthesized from 5′-O-benzhydroxybis(trimethylsilyloxy)silyl-2′-deoxynucleoside-3′-phosphoramidites. The exocyclic amines of adenine and cytosine are protected with dimethoxytrityl and trimethoxytrityl, respectively, whereas guanine protection is with N2-(9-fluorenylmethoxycarbonyl) or N2-trimethoxytrityl. Thymine is protected with N3-anisoyl. Using these synthons and under standard conditions via activation with tetrazole, condensations in excess of 99% are observed. Oxidation with either THF·BH₃ or a peroxyanion solution followed by cleavage of the silyl ether with fluoride completes a cycle. Following synthesis of an appropriate oligomer, protecting groups are removed using sequentially acetic acid, a dithiolate and ammonium hydroxide. Oligodeoxynucleotide 10 mers and 12 mers having any combination of borane phosphonate and phosphate internucleotide linkages as well as all four 2′-deoxynucleotides are synthesized in isolated yields of 70–80% and characterized by phosphorus NMR and mass spectrometry.

Keywords:

• Borane phosphonate DNA

Acknowledgments

This work was supported by the University of Colorado. The technical assistance of Richard Shoemaker in the NMR Laboratory is gratefully acknowledged.

Notes

^a Peroxyanion Solution: Solution A = 3% (w/v) aqueous LiOH (10 mL), 1.5 M 2-amino-2-methyl-1-propanol in water (15 mL), and dioxane (17.5 mL). Solution B = m-chloroperbenzoic acid (1.78 g), dioxane (32.5 mL), and aqueous 30% hydrogen peroxide (12 mL). Equal volumes are mixed just prior to synthesis.

^a p = phosphate; b = borane phosphonate. ^b Perseptive Biosystems Voyager Biospectrometry Workstation using a previously published procedure.