The enthalpy of the “bulge” defect of imperfect nucleic acid helices

The Enthalpy of the "Bulge" Defect of Imperfect Nucleic Acid HelicesImperfections in base pairing are frequently encountered among the naturally occurring ribonucleic acids and in DNA's reconstituted by hybridization.Such imperfections, when they consist of one or a small number of bases that are extruded from and interrupt a helical region on one strand of a helix, may be termed "bulge" defects.'Model nucleic acid complexes containing such bulges may be obtained by selective oxidation of various fractions of the adenine bases (A) in polyadenylate (poly A) to the adenine-Nl-oxide form (A*) followed by addition to polyuridylate (poly U).The product consists of helical regions of poly A-poly U interrupted by single or clusters of A*, which cannot hydrogen bond with U. On the other hand, all the bases U remain paired with ' ' ' A A A AA* A A' ' ' 2,s The method for calculating the free energy of forma-