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.