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Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping

Fujimoto, Kenzo, Yamada, Asuka, Yoshimura, Yoshinaga, Tsukaguchi, Tadashi, Sakamoto, Takashi
Journal of the American Chemical Society 2013 v.135 no.43 pp. 16161-16167
DNA, cis-trans isomers, fluorescence, genotyping, image analysis, isomerization, nucleosides, reversed-phase high performance liquid chromatography, rice, single nucleotide polymorphism, thermodynamics
To clarify the cis–trans isomeric effect on the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside (CᴺⱽK) in the DNA duplex, which gives a single photodimer on the reversed-phase HPLC chromatogram, the kinetics of the cis–trans photoisomerization of CᴺⱽK in double-stranded DNA was evaluated. Since the photoisomerization rate constant for cis to trans isomerization in double-stranded DNA was significantly larger than that for trans to cis isomerization, and the thermodynamic stability of the trans isomer was higher than that of the cis isomer, it was strongly suggested that the trans isomer of CᴺⱽK is a reactive species of the photo-cross-linking reaction. ¹H–¹H NOESY analysis of the photoadduct consisting of CᴺⱽK and T also supported the trans-mediated photo-cross-linking reaction of CᴺⱽK. By using this ultrafast photo-cross-linking reaction for the molecular beacon-based SNPs typing, four individual Japanese rice strains were clearly distinguishable with simple photoirradiation and fluorescence imaging using double-stranded target DNAs.