Functionalization of 2 double prime -C-(Piperazinomethyl)-2',3' -BcNA (Bicyclic Nucleic Acids) with Pyren-1-ylcarbonyl Units

Herein, we describe the incorporation of 2 double prime -C-(piperazinomethyl)-2',3' -BcNA (Bicyclic Nucleic Acids) into oligonucleotides via phosphoramidite chemistry and their subsequent solid-phase functionalization with pyren-1-ylcarbonyl units after oligonucleotide synthesis. Thermal denaturation measurements showed that one modification led to increased thermal stability of the resulting duplex, and that two modifications could be incorporated in close proximity without decreasing the duplex stability (compared to the duplex stability of unmodified RNA). Fluorescence studies of the modified duplexes revealed that the structure and intensity of the fluorescence spectra were largely sequence-dependent. Furthermore, molecular-modeling studies showed that the pyrene moieties are placed in the major groove, and that the configuration at C(2 double prime ) is important for the thermal stability of the duplex.