Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

Abstract

The construction of functionalizable branched DNA (bDNA) relies on the designing of oligonucleotides and exploitation of their complementary chemistries. The stability of these structures largely depends on the hybridization specificity of the contributing oligonucleotides. However, most of the bDNA structures are not found suitable for in vivo application due to poor yield owing to uncharacterized hybridization efficiency and instability in biological fluids. In this report, our group has explored a mechanistic way for studying the hybridization pathway of genomic sequence derived oligonucleotides that are self-assembled to fabricate robust bDNA structures. The effect of change in nucleotide sequences on bDNA stability was studied by taking oligonucleotides derived from primers of different genes. Additionally, the stability of the bDNA in solutions with different pH, salts, and DNaseI which mimics physiological environment was reported. It was found that genomic sequence derived oligonucleotides self-assembled in a cooperative manner to yield the designed bDNAs, which are stable in physiological environment.

Self-Assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications

“…In the last decades, DNA and RNA oligonucleotides have emerged as intriguing molecular building blocks, due to their ability to create highly functional biocompatible nanostructured architectures with accurate control of the structural properties [179,180]. The oligonucleotides self-assembly approach is based on the circumstance that two strands of DNA can bond together by tuning the non-covalent interactions at each complementary base pair of nucleotide.…”

“…The oligonucleotides self-assembly approach is based on the circumstance that two strands of DNA can bond together by tuning the non-covalent interactions at each complementary base pair of nucleotide. Each secondary DNA multi-tiles with specific properties can further self-assemble to form higher-order, complex nanostructures ( Figure 15) [179,180]. Moreover, DNA tiles can be programmed according to specific instructions and algorithmic rules that allow a precise control of the successive layer of tiles.…”

Self-assembled DNA nanostructure containing oncogenic miRNA-mediated cell proliferation by downregulation of FOXO1 expression

“…The designing of bDNA structure was performed as described previously [22,23] and purchased from Integrated DNA Technology (IDT), USA without any modi cation or puri cation (Table S1). In brief, the bDNA monomeric structure composed of four oligonucleotides namely, strands A, B, C and D. The external region of strands B and C are complementary to each other, whereas the internal regions are complementary to strands A and D respectively (Fig.…”

miRNA-mediated alteration of sulfatase modifying factor 1 expression using self-assembled branched DNA nanostructures

“…Appropriate proportions of oligonucleotides were allowed to self-assemble in TAE/Mg 2+ buffer at 95 C for 10 min and then slowly cool down to 4 C using thermal cycler (Bio-Rad) facilitating the formation of bDNA scaffold. 30,32 The bDNA structures were checked for their integrity on 10% native polyacrylamide gel that was electrophoresed at 150 V for 1.5 h in TAE buffer. The gels were stained with ethidium bromide and imaged using the FluroChem E system (Cell Biosciences).…”

“…29 Biocompatible selfassembled bDNA nanostructures increase the efficiency and bioavailability of therapeutics like miRNA or antimiRNA by protecting from nuclease degradation and enhancing the halflife of oligonucleotides bound to the bDNA nanostructures. [30][31][32][33] Thus, in the current communication, we studied miRNA-mediated modication of SUMF1 expression in breast cancer using bDNA nanostructures. Particularly, the expression of miRNAs-106b-5p, 128-3p, and 148b-3p were thoroughly examined since the putative binding sites of these miRNAs were found at the 3 0 -UTR of SUMF1.…”