pH‐Responsive and Reversible A‐Motif‐Based DNA Hydrogel: Synthesis and Biosensing Application

• Published in: Chembiochem : a European journal of chemical biology 2023-05, Vol.24 (10), p.e202300067-n/a
• Main Authors: Morya, Vinod, Shukla, Ashish Kumar, Ghoroi, Chinmay, Bhatia, Dhiraj
• Format: Article
• Language: English
• Subjects: A-motifs; Animals; Atomic force microscopy; Biosensors; Bonding; capillary assays; Conformation; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA biosynthesis; DNA hydrogels; DNA structure; Electrophoretic mobility; Functional groups; Hydrogels; Hydrogels - chemistry; Hydrogen-Ion Concentration; Imaging techniques; Interference; Light scattering; Mammalian cells; Mammals; Monomers; Nanostructures - chemistry; Nucleic acids; Nucleotide Motifs; Nucleotide sequence; pH effects; pH-responsive; Photon correlation spectroscopy; poly-dA; Rheological properties; Scanning electron microscopy; Sol-gel processes; Strands; Target detection
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.202300067

Functional DNA hydrogels with various motifs and functional groups require perfect sequence design to avoid cross‐bonding interference with themselves or other structural sequences. This work reports an A‐motif functional DNA hydrogel that does not require any sequence design. A‐motif DNA is a noncanonical parallel DNA duplex structure containing homopolymeric deoxyadenosines (poly‐dA) strands that undergo conformation changes from single strands at neutral pH to a parallel duplex DNA helix at acidic pH. Despite this and other advantages over other DNA motifs like no cross‐bonding interference with other structural sequences, the A‐motif has not been explored much. We successfully synthesized a DNA hydrogel by using an A‐motif as a reversible handle to polymerize a DNA three‐way junction. The A‐motif hydrogel was initially characterized by electrophoretic mobility shift assay, and dynamic light scattering, which showed the formation of higher‐order structures. Further, we used imaging techniques like atomic force microscopy and scanning electron microscope to validating its hydrogel like highly branched morphology. pH‐induced conformation 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 were further examined in rheological studies. The use of the A‐motif hydrogel in the visual detection of pathogenic target nucleic acid sequence was demonstrated for the first time in a capillary assay. Moreover, pH‐induced hydrogel formation was 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 used for many biological applications. Poly‐dA can form noncanonical duplexes at acidic pH. DNA three‐way junctions with poly‐dA stretches can form supramolecular hydrogels under acidic conditions thereby providing a pH‐responsive, reversible DNA hydrogel that can be used for sensing foreign nucleic acid strands.