Two-dimensional NMR, structural analysis and physical properties of dithiophosphate DNA analogs

The disclosure of biomolecular structure is critical to understanding biological function. By using two dimensional nuclear magnetic resonance spectroscopy techniques, we are able to fully study the structural components of reasonably large biomolecules in their solution state. Using this type of study we have investigated the structural parameters, and physical properties of two separate deoxyribonucleic acid (DNA) systems. Both of the systems under study are of interest to biological science because they represent modified structures which may be capable of acting as antisense gene therapy agents. The dithiophosphate modifications in the DNA backbone have been shown to induce significant perturbations in the stability and local conformational parameters. In one system, a palindromic, doubly dithiophosphate modified decamer, the oligonucleotide was shown to preferentially adopt a hairpin DNA conformation. This behavior was unlike its non-modified parent structure which exists preferentially as a duplex. A duplex form of this modified decamer was also stabilized and the structural parameters investigated. In the other system, a non-palindromic, homopurine-homopyrimidine, singly dithiophosphate modified octa-mer, the duplex structure was found to be less stable than its non-modified parent analog and was shown to adopt a structure unlike either B-form or A-form DNA. The structures presented were determined by an iterative hybrid matrix procedure using nuclear Overhauser enhancement volumes as interproton distance constraints