Effect of base mismatch on the electronic properties of DNA–DNA and LNA–DNA double strands: Density-functional theoretical calculations

The electronic properties of double-stranded octametric DNA–DNA and LNA–DNA with a single-base mismatch were compared with those having fully complementary base pairs to quantify the effect of the base mismatch on hybridization energies (HE). A single T-G mismatch in the LNA–DNA gives rise to a significant reduction in HE, which is consistent with a significant lowering of the melting temperature for mismatched LNA–DNA. By contrast, the hybridization strength of the mismatched DNA–DNA depends strongly on local hydrogen-bonding arrangements in the mispaired T-G. The difference in HE is explained in terms of variation in charge distributions around the hydrogen-bonded base pairs.