Critical Effect of Base Pairing of Target Pyrimidine
on the Interstrand Photo-Cross-Linking of DNA via 3‑Cyanovinylcarbazole
Nucleoside
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Abstract
To evaluate the effect of base pairing
of the target pyrimidine
on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole
nucleoside (<sup>CNV</sup>K), a complementary base of target pyrimidine
was substituted with noncanonical purine bases or 1,3-propandiol (S).
As the decrease of the hydrogen bonds in the base pairing of target
C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold),
it can be concluded that the number of hydrogen bonds in the base
pairing, i.e., the stability of base pairing, of the target pyrimidine
plays a critical role in the interstrand photo-cross-linking reaction.
In the case of G to S substitution, the highest photoreactivity toward
C was observed, whose photoreaction rate constant (<i>k</i> = 2.0 s<sup>–1</sup>) is comparable to that of <sup>CNV</sup>K toward T paired with A (<i>k</i> = 3.5 s<sup>–1</sup>). This is the most reactive photo-cross-linking reaction toward
C in the sequence specific interstrand photo-cross-linking. This might
facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides
for various target sequences