Origins of the specificity in the intercalation of ethidium into nucleic acids. A theoretical analysis.

The sequence preferences observed in the intercalative binding of ethidium to dinucleoside phosphates have been theoretically examined. This specificity is for pyrimidine (3'--5') purine sequences as compared to their purine (3'--5') pyrimidine sequence isomers. It is shown that the stacking energies between the ethidium cation and the base pairs are fairly constant for all combinations of bases at the intercalation site. In contrast, the energy of unwinding the double helix to assume the geometry of the intercalation complex shows substantial sequence differences. Thus, the specificity observed is more readily explained in terms of these conformation energy changes than by preferential stacking interactions. These results imply that there may be a large class of intercalating molecules which exhibit similar pyrimidine (3'--5') purine sequence specificity.