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

Described herein is the synthesis and characterization of a tetranucleotide , 5'-dC-(phosphonate)-T-(amide)-T-(phosphonate) (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 tetram er can be further derivatized and, thus, the compound is a potential buildi ng block for longer oligonucleotides which will contain alternating backbon e modifications at designated positions. The synthesis involved first the p reparation 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 termin al, respectively); each is linked through a phosphonate linkage. A condensa tion reaction between the two dimers, followed by deprotection, resulted in the formation of a peptide linkage to give the desired tetramer III. The r eaction conditions used are mild to afford products in moderate to excellen t yields. The DNA-PNA-DNA tetramer, d(CTTC), is a substrate for T4 kinase b ut fails to give a ligation product, even though NMR shows weak interaction s between the tetramer III with its complementary sequence, d(GAAG). (C) 20 00 Elsevier Science Lctd. All rights reserved.