Conformation of P‐form DNA

The P‐Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P‐form has little or no hydrogen bonding, while the data from EM show that the P‐form has a condensed tertiary structure. In earlier work, we demonstrated that the P‐form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P‐Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P‐form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non‐hydrogen‐bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P‐form that have been observed.