pH - responsive, reversible A-motif based DNA hydrogels: synthesis and biosensing applications

Abstract

Functional DNA hydrogels using various motifs and functional groups require perfect sequence designing to avoid cross-bonding interference with self or other structural sequences. The present work reports an A-motif functional DNA hydrogel that does not require any sequence design. A-motif DNA is a non-canonical parallel DNA duplex structure comprises homopolymeric deoxyadenosines (poly-dA) strands that undergo conformational changes from single strands at neutral pH to a parallel duplex DNA helix at acidic pH. Despite many advantages over other DNA motifs like no sequence, design is required and no cross-bonding interference with other structural sequences, A-motif has not been explored much. We successfully synthesized DNA hydrogel utilizing A-motif as a reversible handle to polymerize DNA three-way junction (3WJ). The composed A-motif hydrogel was first characterized by EMSA, & DLS, which shows the formation of higher-order structures. Further, we utilized imaging techniques like atomic force microscopy (AFM) and scanning electron microscope (SEM) validating its hydrogel like highly branched morphology. pH-induced conformational transformation from monomers to gel is quick and reversible, and was analysed for multiple acid-base cycles. The sol-to-gel transitions and gelation properties is further examined using rheological studies. The use of A-motif hydrogel in the visual detection of pathogenic target nucleic acid sequence is demonstrated for the first time using the capillary assay. Moreover, the pH-induced hydrogel formation is observed in-situ as a layer over the mammalian cells. The proposed A-motif DNA scaffold has enormous potential in designing stimuli-responsive nanostructures that can be utilized for many biological applications.