formation of transcriptional modulators using non-canonical DNA i-motifs.

Non-canonical DNA i-motifs and G-quadruplexes are postulated as genetic switches for the transcriptional regulation of proto-oncogenes. However, in comparison to G-quadruplexes, the therapeutic potential of i-motifs is less explored. The development of i-motif selective ligands by conventional approaches is challenging due to the structural complexity of i-motifs. The target guided synthetic (TGS) approach involving cycloaddition could provide specific ligands for these dynamic DNA structures. Herein, we have used i-motif forming C-rich DNA and their complementary G-quadruplex forming DNA sequences of and promoter regions as well as a control self-complementary duplex DNA sequence as the templates to generate selective ligands from a pool of reactive azide-alkyne building blocks. In our approach, thiolated DNA targets are immobilized on the surface of gold-coated iron nanoparticles to enable efficient isolation of the newly generated ligands from the solution mixture by simple magnetic decantation. The combinatorial cycloaddition generated cell-membrane permeable triazole leads for respective DNA targets ( and i-motifs and G-quadruplexes) that selectively promote their formation. cellular studies reveal that the i-motif and G-quadruplex leads downregulate gene expression whereas the i-motif lead upregulates and the G-quadruplex lead represses gene expression. The TGS strategy using i-motif DNA nanotemplates represents a promising platform for the direct formation of i-motif specific ligands for therapeutic intervention.