THEORY OF MELTING OF CHEMICALLY-MODIFIED DNA WITH INTERSTRAND CROSS-LINKS

Melting of chemically modified, cross-linked DNA is considered within the framework of the Poland-Fixman-Freire formalism. Recurrent equatio ns are derived and an algorithm designed for calculating the melting c urves in such systems. The theory permits analysis of DNA complexes wi th compounds acting concurrently via different mechanisms: (i) binding to separate nucleotides, (ii) formation of short intrastrand links, a nd (iii) interstrand cross-linking. For assessing the effects of the t hird mechanism on DNA stability ''ideal links'' are envisaged that do not affect the stability of the directly involved base pairs but only prevent strand separation in DNA melting.