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.

Selective chemical reactions with DNA, such as its labelling, are very useful in many applications. In this paper, we discuss a new strategy for the selective alkylation of DNA using an oligonucleotide containing an abasic site and alkylating probes. We designed three probes consisting of 2-AVP as a reactive moiety and three kinds of binding moiety with high affinity to duplex DNA. Among these probes, Hoechst-AVP probe exhibited high selectivity and efficient reactivity to thymine bases at the site opposite an abasic site in DNA. Our method is potentially useful for inducing site-directed reactions aimed at inhibiting polymerase reactions.

Caffeoylquinic acids (CQAs) are a group of the phenylpropanoids produced by certain plant species, which have various biological activities including antioxidant, antibacterial, anticancer, and others. Several synthetic routes have been developed using quinic acids (QAs) and caffeic acid derivatives as starting materials. In this study, alternative pathways of 3-and 5-CQAs preparation using protected quinic acids are described. Both CQAs were achieved by removal of the protecting groups of compound 9 and 18 with acid hydrolysis using dilute HCl solution. These compounds (9 and 18) are novel, resulted from esterification reaction of diacetyl caffeoyl chloride and protected quinic acids. The hydroxyl groups of quinic acid in this case were protected with 2,2-dimethoxy propane or tert-butyldimethylsilyl (TBS) chloride.

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