Selective alkylation of T–T mismatched DNA using vinyldiaminotriazine–acridine conjugate

Abstract

The alkylation of the specific higher-order nucleic acid structures is of great significance in order to control its function and gene expression. In this report, we have described the T–T mismatch selective alkylation with a vinyldiaminotriazine (VDAT)–acridine conjugate. The alkylation selectively proceeded at the N3 position of thymidine on the T–T mismatch. Interestingly, the alkylated thymidine induced base flipping of the complementary base in the duplex. In a model experiment for the alkylation of the CTG repeats DNA which causes myotonic dystrophy type 1 (DM1), the observed reaction rate for one alkylation increased in proportion to the number of T–T mismatches. In addition, we showed that primer extension reactions with DNA polymerase and transcription with RNA polymerase were stopped by the alkylation. The alkylation of the repeat DNA will efficiently work for the inhibition of replication and transcription reactions. These functions of the VDAT–acridine conjugate would be useful as a new biochemical tool for the study of CTG repeats and may provide a new strategy for the molecular therapy of DM1.

Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids

“…The obtained alkylation yields were then graphed versus the alkylation time (Figure 9C and Supplementary Figure S16). The result clearly showed the effectivity to the T-T mismatch target, while such an effectivity was not followed in the U-U mismatch target, similar to what we observed in our previous result with VDAT (27). This alkylation efficiency of the T-T mismatch was higher than that of VDAT.…”

“…The purified alkylated thymidine VQ-dT** 1 H-NMR and HMBC NMR were then recorded and assigned to reveal the exact position of the adduct (Supplementary Figure S5). We previously reported the NMR spectra recorded for the vinyldiaminotriazine (VDAT) acridine conjugate reacted with the thymidine at the N3 position (27). Referring to the recorded COSY, edited-HSQC and HMBC NMR from this particular previous report, we could then assign the position of the carbon at the thymidine's carbonyl group, C 2 and C 4 as well as the proton H a from one of the ethylene protons between the quinazolinone and thymine base.…”

Alkyne–Alkyne Photo-cross-linking on the Flipping-out Field

“…(C) Structure of phenylcarbamoyl-modified dA . (D) Structure of thymine base modified with an acridine-conjugated triazine . (E) Structures of Ph and An bases.…”

An 111In-labelled bis-ruthenium(ii) dipyridophenazine theranostic complex: mismatch DNA binding and selective radiotoxicity towards MMR-deficient cancer cells

“…This includes a bis-naphthalene macrocycle "threading" molecule, 45 a triaminotriazine-acridine conjugate which acts by intercalation of the acridine group along with hydrogen bonding 46 and a vinyldiaminotriazine-acridine conjugate for the selective alkylation of TT mismatched DNA. 47 Although our study was limited to a short hairpin and TT mismatch-containing 10-mer duplex, it would be interesting to examine the stabilisation of a greater range of mismatch-containing duplex sequences by these Ru(II) complexes. Considering X-ray crystal structures of RPC-DNA co-crystals have proven invaluable in understanding binding geometries and specicities, Although the In-chelator H 3 [2] 4+ does bind DNA, it had negligible cytotoxicity and does not generate signicant intracellular DNA damage, which is advantageous in its use as a benign carrier of 111 In to the target DNA molecule.…”