Oligonucleotide containing 3-cyanovinylcarbazole (K-CNV) can crosslink to a pyrimidine base in complementary DNA/RNA by a few seconds of irradiation. The effect of 5-substitution of the uracil base in DNA photocrosslinking using K-CNV was evaluated. Each uracil analog base had diverse photoreactivity with K-CNV, and there was good correlation with the photo reactivity and LUMO level of the target uracil base in duplex DNA.