Density-functional calculations on DNA-DNA, PNA-DNA and PNA-PNA double strands

Electronic properties of hybridized B-form DNA-DNA, PNA-DNA and PNA-PNA double strands with common base sequences were theoretically investigated by molecular orbital calculations based on the density functional theory. The computed hybridization energy in PNA-DNA is greater by about 5 kcal/mol than that in the DNA-DNA double strand. The origin of the larger stability of B-form PNA-DNA double strand is ascribed to the presence of greater positive charge on the hydrogen atoms involved in H-bonding, leading to stronger hybridization. The results suggest higher sensitivity in a PNA-DNA array sensor than in its DNA-DNA counterpart.