Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2 0 -deoxyuridines and their application in DNA triplex formation

The incorporation of C5-amino-modified 20-deoxy-uridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four dif-ferent C5-amino-modified 20-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pKa values were deduced using 1H NMR. All of them display the expected anti-conformation of the nucleoside with 20-endo sugar puckers for the deoxyribose ring.