Comparative Circular Dichroism and Fluorescence Studies of Oligodeoxyribonucleotide and Oligodeoxyribonucleoside Methylphosphonate Pyrimidine Strands in Duplex and Triplex Formation

An analogue of the homopyrimidine oligodeoxyribonucleotide d(CT)₈ has been synthesized. This analogue, d(CT)₈ contains nonionic methylphosphonate internucleoside linkages. The pH-dependent conformational transitions of d(CT)₈ have been studied and its ability to form duplexes and triplexes with the normal homopurine oligonucleotide d(AG)₈ has also been investigated as a function of pH. Circular dichroism spectroscopy and ethidium bromide fluorescence enhancement have been used to monitor pH-dependent conformational transitions driven by the protonation of cytosine residues, and the different behavior of d(CT)₈ and d(CT)₈ has been compared. It was possible to form self-associated complexes by using either d(CT)₈ or d(CT)₈, and both compounds combined with d(AG)₈ to form duplex or triplex DNA. At neutral pH, the CD spectrum of d(AG)₈·d(CT)₈ duplex was quite different from the CD spectrum of d(AG)₈·d(CT)₈ duplex, reflecting most likely a difference in conformation. The duplex to triplex transition characteristic of this DNA sequence occurred at a lower pH when d(CT)₈ was substituted for d(CT)₈; however, at pH 4.2, triplex containing d(CT)₈ was similar in conformation to triplex containing d(CT)₈. Several of these observations can be related to the alterations in electrostatic and steric interactions that occur when the negatively charged phosphodiester backbone of d(CT)₈ is replaced with a nonionic methylphosphonate backbone.