ABSTRACT
PURPOSE: Telomeres are specialized DNA-protein complexes found at the ends of eukaryotic chromosomes. In normal somatic cells these become shorter with each cell division and appear to control their replicative lifespan. However almost all tumours show activation of the enzyme telomerase, a specialised reverse transcriptase/DNA polymerase, that can add new telomeric repeats to the ends of chromosomes and this appears to be a key factor in the cell immortalization process. Consequently there is much current interest in the potential for inhibitors of telomere extension in the treatment of cancer. Several groups have found that it is possible to produce inhibitory molecules that target the telomeric repeat (substrate) DNA rather than the telomerase enzyme itself. This is thought to work because it has been found that in vitro, these DNA sequences can fold up into a four-stranded (quadruplex) structure that the drugs recognise and stabilize, but which is not recognised by the enzyme. However, while medicinal chemists continue to base rational design programs on this hypothesis, there is currently very little evidence that these structures form in vivo, and that in vivo the drugs work by binding to them. To have incontrovertible evidence of where and how these telomerase inhibitors and DNA interact is therefore a pressing concern for a basic understanding of their mechanism of action and effective drug development. MATERIALS AND METHODS: Radioprobing represents a valuable new approach to the study of DNA structures. Recently we have shown through computer simulations of radioprobing that the technique is a remarkably sensitive probe of quite fine details of DNA conformation. Here we report on our simulations of the binding of a radiolabelled telomerase inhibitor, related to a class of novel inhibitors under development at Nottingham, to a variety of possible structures for telomeric DNA. RESULTS AND CONCLUSIONS: The predicted cleavage patterns prove to be very sensitive to the DNA structure, and the mode of binding of the drug. These results suggest that radioprobing experiments should be able to provide unambiguous evidence as to the 'true' nature of the telomere-drug complexes, and so aid the rational design programme.
Subject(s)
Crystallography/methods , Drug Design , Molecular Probe Techniques , Radioisotopes , Telomere/chemistry , Telomere/metabolism , Animals , Antineoplastic Agents/administration & dosage , Binding Sites , Drug Delivery Systems/methods , Humans , Models, Molecular , Molecular Conformation , Neoplasms/diagnostic imaging , Neoplasms/drug therapy , Neoplasms/metabolism , Radionuclide Imaging , Structure-Activity Relationship , Telomere/drug effects , Telomere/ultrastructureABSTRACT
We model and analyze a short section of a DNA chain with a defect, with the aim of understanding how the frequency, amplitude, and localization of breathing events depend on the strength of the bonds between base pairs, both along the chain and between the chains. Our results show that the presence of a defect in the chain permits the existence of a localized breather mode. The models we analyze are linear and hence solvable, with solvability extending to the statistical mechanics formulation of the problem. Parameter values for the interaction energy of a base with its nearest neighbors are obtained from AMBER. The results indicate good agreement with both the amplitude and the number of base pairs affected by defect-induced breathing motion.
