Alpha-2'-deoxyguanosine promotes highly stable anti-parallel G-quadruplex DNA structures with therapeutic potential via guided G-quadruplex assembly.

DNA and RNA G-quadruplexes (GQ) are non-canonical G-rich four-stranded structures with proven important roles in major cellular events. DNA GQs are highly polymorphic. Their topology and G-tetrad architecture are strongly influenced by numerous factors. Notable variations in topology and stability between different GQs arise partially from glycosidic bond syn-anti conformational isomerism. The use of unnatural nucleotide analogues with a preferred syn or anti configuration is an efficient approach to control GQ folding, G-tetrad architecture, and stability. Alpha-nucleosides are known to adopt preferably anti-configuration of glycosidic bond. Selective modification of GQs with alpha-2'-deoxyguanosine (αdG) provides a useful tool to manipulate GQ structural parameters and stability. In the GQ core, unnatural αdG residues mimic invariant syn-dG nucleotides and thus drastically reduce the range of possible conformational rearrangements. Understanding the role of αdG modification in controlling GQ architecture and stability requires further biophysical and structural studies of modified GQs. In this paper, we report the design and biophysical characterization of anti-parallel three-layer GQs with αdG-modified G-tetrads of the same polarity. Furthermore, we investigate the therapeutic potential of modified G-rich oligonucleotides in the context of induced formation of αdG-modified anti-parallel GQ. A highly specific termination of primer extension at selected position was induced at a short G3 run in the template strand via guided association with the three segment G-rich modified oligonucleotide.