meso-DNAs with homopurine sequences: analysis of their interaction with natural DNAs

Two homopurine sequences of meso-DNAs (DNAs having an alternating sequence of 2-deoxy-L-ribose and 2-deoxy-D-ribose in their sugar moieties), d(LADG)5 and d(LGDA)5, were prepared. Both d(LADG)5 and d(LGDA)5 interacted with the corresponding complementary natural DNAs, d(DCDT)5 and d(DTDC)5, respectively. In the interactions, pH-dependent duplex/triplex selectivity was observed, i.e., meso-d(Pu)10 formed a duplex at pH 7.5 and a triplex at pH 5.0 with the complementary D-d(Py)10. The meso-d(Pu)10/D-d(Py)10 complex showed a CD spectrum similar in shape to that of the natural complex, suggesting that meso/natural complexes form right-handed helices. At pH 7.5, ethidium bromide intercalated into both d(LADG)5/d(DCDT)5 and d(LGDA)5/d(DTDC)5 duplexes. A clear difference between d(LADG)5/d(DCDT)5 and d(LGDA)5/d(DTDC)5 was observed at pH 5.0. Addition of ethidium bromide did not affect the formed d(LADG)5/d(DCDT)5 triplex, and ethidium bromide did not intercalate into the triplex. On the other hand, d(LGDA)5 did not form a triplex with d(DTDC)5 in the presence of ethidium bromide even at pH 5.0, but it formed a duplex. Ethidium bromide intercalated into the duplex at pH 5.0.