Minimum number of oligonucleotide-based stable monomeric branched DNA nanostructure: Biochemical and biophysical study

Abstract

DNA has been employed as building blocks of nanomaterial construction due to their programmability and wide range applications. The functional branched DNA (bDNA) nanostructure is largely dependent on the sequence and structural symmetry. Despite the discovery of different structures, the synthesis of bDNA nanostructures from optimal number of oligonucleotides is yet to be explored. In the current study, for the first time we demonstrate the designing of stable monomeric bDNA structures using two or three oligonucleotides. Furthermore, the stability of bDNA nanostructures was thoroughly investigated in presence of different pH, cations, fetal bovine serum and DNaseI. The thermodynamic parameters indicate that hydrogen bonding and van der Waals interaction played a major role during binding of bDNA oligonucleotides. From the gel retardation assay, we confirmed the binding of complementary oligonucleotides to the bDNA nanostructures, thus can be explored for target specific transcript regulation. In conclusion, the self-assembled DNA structures developed from optimal oligonucleotides are stable in physiological environment and can be used for biomedical applications.