NMR studies of DNA structure and counterion behaviour

Abstract: DNA is a polymer of nucleotides, each nucleotide consisting of a negatively charged phosphate group, a ribose sugar unit, and a purine or pyrimidine base. The secondary structure of DNA is commonly a double-helix with Watson-Crick paired bases. Several secondary structures, all with these features, are observed for DNA. Due to the negative charge of DNA, it is always accompanied by cations, referred to as counterions. The concentration and charge, as well as the specific molecular details of the counterions, have a profound impact on the secondary structure of DNA. Also the activity of water in the system, which hydrate the molecules, comes into play. The thesis looks into some of these systems and their behavior, with nuclear magnetic resonance, NMR, as the main tool of investigation. The thesis is based on the following publications and manuscripts:Papers I-III deal with the unusual transition from the B- to the C-form of fibrous LiDNA as the water activity is lowered. A multiple-quantum NMR diffusion experiment is designed, and the diffusion of Li+ and Cs+ in oriented polymeric DNA measured using NMR. It is found that the Li+ diffusion is very slow compared to that of Cs+. Molecular dynamics simulations show strong complexation of Li+ with the charged DNA phosphate oxygens O1' and O2'. The phosphate orientations of the B- and C-forms of DNA with LiDNA are measured by 31P solid-state NMR, and a new model for the C-form is built. The new model involves a high degree of BII nucleotides, which could be of relevance to the DNA-protein recognition process.Papers IV-V set to investigate the behavior of the biologically interesting polyamines with oligomeric DNA in solution and oriented polymeric DNA fibers. The diffusion, measured by 1H NMR, of some polyamines with oligonucleotides in the Z-form and B-form, show a higher degree of association to the Z-form. 1H NMR NOE measurements show the association with DNA to be weak with both DNA forms, although a slightly shorter polyamine correlation time is observed with the Z-form. The transition of fibrous DNA from the B-form to the A-form with some polyamines but not with others is investigated. 1H NMR diffusion measurements show no unusual behavior, but some characteristic 2H spectral features are observed. No direct molecular reason for the differentent impacts on DNA structure by different polyamines can be isolated, and the effect is believed to be thermodynamic in origin.Paper VI shows that DNA complexed with the suspected intercalator bipyridyl(ethylenediamine)Pt(II)2+ remains in the B-form, meaning that the molecule does not interacalate fibrous DNA to a high degree. This is seen by application of a number of methods sensitive to the molecular conformation, amongst those extraction of the phosphate orientation using 31P solid-state NMR.