Fig. 2. Dependence of the intermolecular ligation efficiency on the length of complementary part in the 3′-OH side (DNA/RNA heteroduplex) of the nick. On the 5′-phosphate side of the nick, a DNA/DNA duplex is formed. (A) The sequences of RNA (blue) and DNA (red) were used to systematically change the length of stem in the 3′-OH side; (B) denaturing PAGE (12%) of the products by Rnl2 at 25 °C for 12 h. Lanes 1, 3, 5, 7 and 9: only DNA13, DNA15, DNA17, DNA19 and DNA21, respectively. Lanes 2, 4, 6, 8 and 10: Rnl2 ligation of L-8 in the presence of DNA13, DNA15, DNA17, DNA19 and DNA21, respectively. [RNA] = 2 μM, [DNA] = 1 μM and [Rnl2] = 0.4 U μL−1 in 1× buffer. The migration rate of L-29 was faster than L-27 because it involves a very stable stem-loop structure which is very difficult to be denatured.
