Quadruplex and pentaplex self-assemblies of oligonucleotides containing short runs of 8-aza-7-deaza-2 `-deoxyisoguanosine or 2 `-deoxyisoguanosine

Abstract

Oligonucleotides containing 8-aza-7-deaza-2 ` -deoxyisoguanosine (4) were investigated regarding their self-assembly in aqueous solution. The aggregation of 4 was compared with that of oligonucleotides containing 2 ` -deoxyisoguanosine (2b) and 2 ` -deoxyguanosine (1b). For this purpose the phosphoramidite of 4 was synthesized which was protected by a dibutylaminomethylidene residue at the amino group and a diphenylcarbamoyl residue at the 2-oxo function. Solid-phase synthesis furnished oligonucleotide containing short runs of the nucleoside 4. The self-assembly of the oligonucleotide 5 ` -d(T(4)4(4)T(2)) was studied by ion-exchange chromatography. The formation of a pentaplex was observed in the presence of Cs+, while a tetraplex is formed when the counter ion is Na+ or Rbl. The cation selectivity of the oligonucleotide 5 ` -d(T(4)4(4)T(2)) was found to be different from the parent 5 ` -d(T(4)isoG(4)T(2)) Which was forming the tetraplex as well as a pentaplex in aq RbCl solution.