Highly Efficient Synthesis of a Phosphoramidite Building Block of C8-Deoxyguanosine Adducts of Aromatic Amines

Abstract

The synthesis of 5′-O-DMTr-3′-O-phosphoramidite-C8-arylamine-dG adducts 11 and 12 is described. The compounds are potential building blocks for the automated synthesis of site-specifically modified oligonucleotides. The C8-adducts were synthesized by a palladium-catalyzed cross-coupling reaction.

Pd-cross coupling - amination - nucleoside adducts - protecting groups - phosphoramidites

References

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Rac-BINAP is much less expensive than the biphenyl ligand.

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23

Amination of N ²-i-Butyryl-O ⁶-benzyl-8-bromo-3′,5′-bis(t-butyldimethylsilyl)-2′-deoxyguanosine: 450.0 mg (0.61 mmol) 8-Bromo-2′-deoxyguanosine, 156.0 mg (0.73 mmol) K₃PO₄, 56.1 mg (61.0 µmol) tris(dibenzylideneacetone)di-palladium(0) (Pd₂dba₃), 114.4 mg (0.18 mmol) racemic-2,2′-bis(diphenylphosphino)-1,1′-binaphthyl (BINAP) and 131.2 mg (1.22 mmol) of p-toluidine was solubilized in
15 mL dry 1,2-DME in an inert atmosphere and stirred at 80 °C until the reaction was complete (TLC analysis). After cooling to r.t., 1 mL of sat. sodium bicarbonate solution was added. After addition of 10 mL of brine the layers were separated and the aq layer was extracted three times with
10 mL of ethyl acetate. The combined organic layers were washed twice with 10 mL of brine and once with a mixture of 10 mL brine and 2 mL water. The organic layer was dried (Na₂SO₄) and the solvent was removed in vacuo. Purification by chromatography on silica gel, eluting with 20% ethyl acetate in hexane afforded 350 mg (75%) of the desired product as a light-yellow foam.

24

N ²-i-Butyryl-8-N-(4-methylphenylamino)-O3′-[(2-cyano-ethoxy)-(N,N-diisopropylamino)phosphinyl]-O5′-dimeth-oxytrityl-2′-deoxyguanosine: 200.0 mg (0.27 mmol) of N ²-i-butyryl-8-N-(4-methylphenylamino)-O5′-dimethoxytrityl-2′-deoxyguanosine were dissolved in 7 mL dry CH₂Cl₂ and treated subsequently with 234 µL (1.34 mmol) of DIPEA and 113 µL (0.51 mmol) of (2-cyanoethoxy)-(N,N-diiso-propylamino)-chlorophosphine. After stirring for 1 h at r.t., the reaction was stopped by adding 0.5 mL of methanol. The solution was diluted with 50 mL of CH₂Cl₂ and washed with 5% aq NaHCO₃ followed by brine. The organic layer was dried and concentrated to dryness. The residue was purified by chromatography on silica gel, eluting with CH₂Cl₂/ace-tonitrile and CH₂Cl₂/methanol to give 215.7 mg (85%) as a light-yellow solid.

25 It should be added that a synthesis of a C8-N-acetylamino-fluorene (AAF) adduct phosphoramidite has been published before. However, the initial synthesis of the adduct gave very low yields and the protecting group chemistry was different to ours, ref. and: Zhou Y. Chládek S. Romano LJ. J. Org. Chem.  1994,  59:  556