Synthesis and characterization of a tetranucleotide analogue containing alternating phosphonate-amide backbone linkages

Abstract

Described herein is the synthesis and characterization of a tetranucleotide, 5′-dC- phosphonate-T- amide-T- phosphonate-dC ( III), in which the C-T and T-C steps contain a phosphonate backbone bond and T-T is a peptide nucleic acid dimer unit (neutral backbone). The 5′- and 3′-OH groups of the tetramer can be further derivatized and, thus, the compound is a potential building block for longer oligonucleotides which will contain alternating backbone modifications at designated positions. The synthesis involved first the preparation of two hybrid peptide-deoxyribose dinucleotides, CT-CO ( I) and N-CT ( II) (C and T are nucleobases; CO and N are carboxylic and amino terminal, respectively); each is linked through a phosphonate linkage. A condensation reaction between the two dimers, followed by deprotection, resulted in the formation of a peptide linkage to give the desired tetramer III. The reaction conditions used are mild to afford products in moderate to excellent yields. The DNA-PNA-DNA tetramer, d(CTTC), is a substrate for T4 kinase but fails to give a ligation product, even though NMR shows weak interactions between the tetramer III with its complementary sequence, d(GAAG).