Synthesis and pairing properties of oligoribonucleotide analogues containing a metal-binding site attached to beta-D-allofuranosyl cytosine

A method for the facile preparation of oligoribonucleotide analogues containing beta-d-allofuranosyl nucleosides with additional functional groups tethered to the 6'-O positions is presented. It is based on the synthesis of two protected nucleosides carrying a 6'-O -bromopentyl and a 6'-O -methylaminopentyl substituent. By a simple two-step procedure, these key intermediates were transformed into two phosphoramidites carrying a 1-aza-18-crown-6 and a triethyleneglycol group, respectively, each capable of complexing metal ions. By automated synthesis, these functionalized nucleoside analogues were efficiently incorporated into short oligoribonucleotides. Under physiological conditions (150 mM NaCl, 2 mM MgCl2, pH 7.4), incorporation of a single allofuranosyl cytosine substituted with a triethyleneglycol moiety led to a significant enthalpic stabilization of an A-type RNA duplex. This observation is in agreement with a metal ion-mediated stabilizing interaction between the two pairing strands.