Creation of Unique Nucleic Acid Structures Using Nucleic Acid Reaction Fields

Abstract

The unique nucleic acid structures such as threaded structures and interstrand crosslinking have high potential in chemical biology, nanotechnology and oligonucleotide therapeutics. For example, the noncovalent labeling and modification by the threaded structures are useful as new chemical biology and nanotechnology tools. The properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNA and siRNA. This paper introduces the creation of threaded structures, such as rotaxane-like structures and catenanes, and interstrand crosslinking with flip-out bases based on our hybridization-specific template reactions. In the hybridization-specific reaction fields, the reactions are accelerated by the proximity effect achieving efficient and selective creations. Regarding the creation of threaded structures, we designed pseudorotaxane-forming oligo DNAs (prfODNs) with reactive moieties and achieved automatic pseudorotaxane formation toward the target DNA and RNA by taking advantage of hybridization-specific reaction fields. The pseudorotaxane structures were also obtained using cyclized ODNs via the slipping process. The catenane structure was formed by the combination of pseudorotaxane formation with a 5’-end-phosphorylated RNA and enzymatic ligation. For crosslinking, we created the crosslinked DNA with flip-out bases using the base flipping-induced artificial bases and photoinduced [2+2+2] cycloaddition reaction among alkynes and molecular oxygen. From the viewpoint of organic chemistry, it is hoped that further creation of unique functional nucleic acids and structures will lead to the development of new concepts for oligonucleotide therapeutics, new tools for RNA research and DNA nanotechnology.