Unveiling biomacromolecule interactions-NMR and optical spectroscopy studies on ligand binding to DNA and lysozyme
Doktorsavhandling, 2013

Studies on intercalation of bulky binuclear ruthenium compounds into DNA have attracted attention due to their slow dissociation rate and sequence selectivity. Previous results showed that dumb-bell shaped molecules of the type [μ-(bidppz)(L)4Ru2]4+, L=phenanthroline or bipyridine, bind rapidly on the surface of DNA prior to intercalation. Functional understanding of the intercalation mechanism may greatly gain from structural characterization of both surface bound and intercalation states. In this work the initial surface bound state has for the first time been structurally characterized by 2-D NMR in detail, showing the binuclear compound aligned into the minor groove. A structure close to the proposed following intercalated state was found by X-ray crystallography: one dppz moiety inserts into the DNA stack of a hexamer duplex through extrusion of an AT base pair while the second moiety make such complexes being dimerized by end-stacking. Optical spectroscopy results indicate that these interactions are present also in dilute solution. Minor groove binding to DNA was also studied with the classical drug Hoechst 33258. By a combination of 1D-NMR, calorimetry and optical spectroscopy, two drug molecules were found to bind to the minor groove of a consecutive A4T4 sequence, one after another, instead of a ‘sandwich’ conformation as previously proposed. Proteins are another type of essential biomacromolecules, and in this thesis, lysozyme, an antimicrobial enzyme is studied. Lysozyme was found to undergo domain wide structure rearrangements accompanying the deprotonation of Glu 35, involving helix movements, reorientation of binding site residues and variations of the hydrogen bond pattern near the active site. Similar structural changes are observed when short polysaccharides are bound. Interestingly, surface properties such as electrostatic potential and hydrophobic patches significantly modulate the interaction of a disaccharide with intermolecular contacts remote from the catalytic site, while binding affinity near the active site shows fewer variations. Both the dynamic behavior of the α-domain as well as the surface properties of all binding sites are critical factors in the design or optimization of lysozyme-based compounds for applications in food preservation and pharmaceutical usage.

ruthenium compounds


Hoechst 33258




structure rearrangements.



Opponent: Prof. Michael P. Williamson


Lisha Wu

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

DNA is a double-stranded helical macromolecule consisting of nucleotide monomers with backbone and four different bases adenine (A), cytosine (C), guanine (G) and thymine (T). In humans, DNA is located on the chromosomes in the nucleus of a cell, with a stretched length of about 2 meters. The total length of DNA present in all 1013 cells of an adult human is about 2 x 1013 meters, which equals to nearly 70 trips from earth to the sun and back. DNA encodes for proteins, and proteins act as ‘factory workers’ who actively carry out metabolic functions: for example, several different proteins are crucial in the process of DNA synthesis. These protein molecules make sure there is almost no error during DNA replication. Erroneous DNA carries altered genetic information, which can result in evolution, but also in cancer and genetic diseases. Ruthenium compounds are special synthetic molecules, which can mimic iron, selectively enter cancer cells, and thus are considered as new type candidates for anti-cancer pharmaceuticals. Dimeric ruthenium compounds that bind and insert into DNA selectively at AT region, blocking particular genes, thus prevent diseases, which may be interesting for future pharmaceutical development. Lysozyme, an antibacterial enzyme dissolves bacterial cell walls, leading to cell death. Structural rearrangements of human lysozyme upon pH variations were studied by NMR.


Biokemi och molekylärbiologi



Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie


Opponent: Prof. Michael P. Williamson