Exploring potential of i-motif DNA formed in the promoter region of GRIN1 gene for nanotechnological applications

Abstract

The tandem repeat stretches of cytosine residues fold to construct intercalated motif (i-motif) structures over an acidic pH range. Several advancements have been made to understand the biological role of i-motif DNA. Potential i-motif structures found in gene promoters are involved in positive transcriptional regulation and sequence specific DNA binding. Herein, a 27-mer C-rich DNA stretch present at the promoter region of (Glutamate Ionotropic Receptor NMDA type subunit 1) GRIN1 gene, named GRIN1c was studied to investigate its structural status using biophysical and biochemical techniques. The gel electrophoresis, circular dichroism spectroscopy and pH-dependent monophasic UV-thermal melting data revealed that GRIN1c sequence adapts a bimolecular i-motif structure. Two alternative structural models are suggested for the bimolecular i-motif structure with typical C·C+ base pairing and significant Watson-Crick base pairing. Possibility of co-existence of non-Watson-Crick and Watson-Crick base pairing in the formation of i-motif expands the repertoire of various topologies of i-motif structures. Extensive applications of i-motif structure in the areas of nanotechnology, analytical and biomedical systems and many more have made it essential to explore these multistranded structures. Nanodevices-based on i-motif structure found applications as biosensors and drug release platform, and also serve as proof for their in vivo existence.