Structure of photoreactive binary system of oligonucleotide conjugates assembled on the target nucleotide sequence

Recently we have developed an approach to superspecific photomodification o f nucleic acids by binary systems of oligonucleotides conjugated to precurs or groups capable of assembling into photoactivatable structure upon simult aneous binding of the: conjugates to the target. We have investigated the s olution structure of a model binary system 1:2:3, where 1 is the target 12- mer 5'-pdCTATCAGTTTCT, 2 is the photoreactive conjugate 5'-dAGAAACpNH(CH2)( 2)NH-Az and 3 is the sensitizing conjugate 5'-Pyr-pdTGATAC (Az is p-azidote trafluorobenzoyl group and Pyr is the pyrenyl-1-methylannino group). The ph otoreaction within this complex results in crosslinking of reagent 2 with N 7-position of the G7 residue of the target thus indicating that the photore active Az residue is located in the major groove near the G7 residue. The c enter-to-center distances between the Pyr and Az moieties in complex 1:2:3 independently determined by the Pyr-group fluorescence quenching and the At -group sensitized photodecomposition were 11.2 and 12.6 Angstrom, respectiv ely.