Novel insights into pH-dependent TWJ-DNA nanoparticles

Short single-stranded nucleic acids can form a structural motif called TWJ (three-way junction) DNA [1]. TWJs have considerable potential for a variety of biotechnology applications. Using the properties of another non-canonical structure - the i-motif - it‘s also possible to prepare TWJ-based nanoparticles sensitive to pH changes [2]. This sensitivity is achieved by the presence of C-rich overhangs in the individual sequences forming the TWJ structure. DNA i-motif is four-stranded non-canonical structure consisting of cytosine-rich sequences. Acidic conditions facilitate the formation of this motif due to the presence of cytosine-cytosine⁺ base pairs. pH-sensitivity of i-motif is widely used as pH switchers in nanotechnology and in other applications [3].

It´s well known, that synthetic metallosupramolecular helicate ligands with trigonal geometry could bind into the central cavity of TWJ DNA [4]. Therefore, ligands L1-L3 based on imine scaffold, N-coordinated to metal ion were prepared. These complexes stabilize TWJ structure. The second focus of our interest is to prepare and analyze fluorescent ligands targeted i-motifs formed on terminal overhangs of TWJ. These i-motif ligands could de/stabilize i-motif clamp between two subunits of TWJ. Such a macromolecular system represents a hydrogel that can be used even in very mildly acidic conditions close to neutral pH as pH-dependent fluorescent and/or colored sensors. Combinations of ligands targeting different regions of a single molecule could have significant applying potential in nanotechnologies.