Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids

Abstract

The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease...

Formation of Direction-Controllable Pseudorotaxane and Catenane Using Chemically Cyclized Oligodeoxynucleotides and Their Noncovalent RNA Labeling

“…In nucleic acid chemistry, interlocked and threaded molecular structures have been studied for DNA nanotechnology, − topological labeling, , and complex stabilization. , Since nucleic acids are substrates for ligases, ligase reactions enabled the formation of numerous interlocked structures. Further, template-assisted chemical strand ligations via [2 + 2] photocyclization, , amidation, and click reaction ,, have been used to expand the applications of interlocked nucleic acids …”

“…Further, template-assisted chemical strand ligations 50 via [2 + 2] photocyclization, 51,52 amidation, 53 and click reaction 33,54,55 have been used to expand the applications of interlocked nucleic acids. 56 Following these studies, we previously developed automatic pseudorotaxane-forming oligo DNAs with reactive moieties for S N 2 and strain-promoted azide−alkyne cycloaddition (SPAAC) reactions. 57,58 Additionally, we found that the chemically cyclized oligodeoxynucleotides (cyODNs) with a double tail formed a pseudorotaxane structure with the target DNA and RNA via the slipping process (Figure 1).…”

“…59 Thus, we proposed a twostep mechanism for this slipping formation; this mechanism comprises the pre-equilibrium and threading steps (Figure 1A). 56,59 The formation of a nonthreaded intermediate in the pre-equilibrium step would facilitate the approaching and threading of the ring part to the end of the target. In this study, we designed a simple cyclized pseudorotaxane-forming ODN (prfODN) to further study cyclized prfODNs (Figure 1B).…”

Programmable DNA Interstrand Crosslinking by Alkene–Alkyne [2 + 2] Photocycloaddition

“…1−4 The formation of a covalent bond between correctly oriented functional groups in single strands leads to the formation of an interstrand crosslink (ICL). 5 ICLs are of interest in biology because they inhibit replication and transcription, leading to cellular toxicity. 6 Examples of small-molecule-induced ICL are formed by anticancer drugs such as cisplatin 7 and nitrogen mustards.…”

“…The DNA double helix is an outstanding scaffold for the guided arrangement of functional groups. Precise control of chromophores or reactive groups in DNA can lead to functional materials that offer new opportunities for chemical biology and nanotechnology. − The formation of a covalent bond between correctly oriented functional groups in single strands leads to the formation of an interstrand crosslink (ICL) . ICLs are of interest in biology because they inhibit replication and transcription, leading to cellular toxicity .…”