Triazole-Linked Dumbbell Oligodeoxynucleotides with NF-κB Binding Ability as Potential Decoy Molecules

Abstract

Triazole-cross-linked oligodeoxynucleotides were synthesized with use of the Cu(I) catalyzed alkyne-azide cycloaddition (CuAAC) with oligodeoxynucleotides possessing N-3-(azidoethyl)thymidine and N-3-(propargyl)thymidine at the 3'- and 5'-termini. The newly synthesized oligodeoxynucleotides were thermally stable and their global structures retained those of non-cross-linked oligodeoxynucleotides. The newly synthesized dumbbell oligodeoxynucleotides showed excellent stability against snake venom phosphodiesterase (3'-exonuclease) and high thermal stability, which are necessary for decoy molecules to achieve biological responses leading to alteration of gene expression. Moreover, dumbbell oligodeoxynucleotides have the ability to bind to NF-kappaB p50 homodimer within a similar range to that of a control double-stranded decoy oligodeoxynucleotide. This strategy allows us to prepare triazole-linked dumbbell oligodeoxynucleotides with a range of loop lengths, and we found that the greater the number of the thymidine residues constituting the loop region, the higher the binding affinity of the dumbbell oligodeoxynucleotides to the nuclear factor kappaB. This means that a protein binding ability of the dumbbell oligodeoxynucleotides could be modulated by altering the loop size. This study clearly shows that cross-linking by the triazole structure does not prevent the dumbbell oligodeoxynucleotides from binding to the nuclear factor kappaB transcription factor. Therefore, the results obtained conclusively demonstrate that the triazole cross-linked dumbbell oligodeoxynucleotides could be proposed as powerful decoy molecules.

Furan‐Oxidation‐Triggered Inducible DNA Cross‐Linking: Acyclic Versus Cyclic Furan‐Containing Building Blocks—On the Benefit of Restoring the Cyclic Sugar Backbone

“…Next to increased antisense activity through irreversible binding to the target for specific knock down of particular mRNAs or miRNAs, [24] the interest of synthesis methods for the preparation of selectively cross-linked, small, double-stranded DNA sequences can further be found in the sequence-specific regulation of transcription factors by so-called decoy ODNs. ICLs have been shown to enhance decoy stability [25,26] and have the possibility to constrain the decoys into a more active conformation towards the target transcription factor. [27] Finally cross-linking of DNA can serve various purposes in structural biology and nanotechnology.…”

Postsynthetic DNA Modification through the Copper‐Catalyzed Azide–Alkyne Cycloaddition Reaction

“…[26] This group prepared a dsODN that binds to the kB transcription factor as a decoy molecule to inhibit in vitro and ex vivo transcription. Then propargyl and azidoethyl linkers on the N3-position of thymidine were introduced.…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…40 Cyclic oligonucleotides have also been prepared by Click chemistry using an N 3 -propargyl-dT and N 3 -azidoethyl-dT at the termini of the oligonucleotides. 41 The masked phosphate (6) has been incorporated into DNA to study the role of telomeric RNA in telomerase activity. 42 Photoirradiation of (6) generates a nitrene that can be used for trapping of proximal RNA of the telomerase region by crosslinking to it.…”