Oligonucleotides forming an i-motif: the pH-dependent assembly of individual strands and branched structures containing 2′-deoxy-5-propynylcytidine

Abstract

Non-branched and branched oligonucleotides incorporating consecutive runs of 2′-deoxy-5-propynylcytidine residues (2) instead of 2′-deoxycytidine (1) were synthesized. For this, phosphoramidite building blocks of 2′-deoxy-5-propynylcytidine (3a–c) were prepared using acetyl, benzoyl or N,N-di-n-butylaminomethylidene protecting groups. The formation of the i-motif assemblies incorporating 2′-deoxy-5-propynylcytidine residues was confirmed by temperature-dependent CD- and UV-spectra as well as by ion-exchange chromatography. The low pK_a-value of nucleoside 2 (pK_a = 3.3) compared to dC (pK_a = 4.5) required strong acidic conditions for i-motif formation. Branched oligonucleotide residues with strands in a parallel orientation lead to a strong stabilization of the i-motif allowing aggregation even at non-optimal pH conditions (pH = 5). The immobilization of oligonucleotides incorporating multiple residues of 2 on 15 nm gold nanoparticles generated DNA–gold nanoparticle conjugates which are able to aggregate into i-motif structures at pH 5.