Structure-based rational design of oligonucleotide-mediated chemical ribonucleases

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Non-scientific Summary:The highly specific action of synthetic, robust catalytic molecules that can cleave and process nucleic acids not only underlies the essence of cellular life and the translation of the genetic message of an individual into their physical make-up, but also provides a substantial portion of the tools of modern chemical biology. The development of novel man-made chemical compounds imitating the active centre of some natural enzymes that are capable of damaging messenger RNA provides a basis for generating new useful tools of modern chemical biology, perhaps even drugs, affecting specific messenger RNAs and viral genetic material. Recently a considerable effort has been made in the creation of chemical ribonucleases, catalytic molecules capable of damaging RNA molecules irreversibly at desired positions. These compounds can potentially be applicable to a range of problems in biomedical areas and public healthcare and also in various areas of life sciences and chemical biology. However, the problem of unsatisfactory biological performance of metal-free chemical ribonucleases remains unsolved. Recently, in the frame of our collaborative work with a Russian research group, a new type of chemical nuclease, showing very unusual biological properties, was discovered. These novel compounds were constructed by chemical fusion of short, synthetic protein-like molecules with synthetic DNA fragments. The most remarkable feature of these novel catalytic molecules was that the short DNA fragment enormously enhanced the biological activity of a previously inactive protein-like molecule. Our preliminary study showed that the merger of these two chemical entities seems to produce a new, hybrid type of molecule that can synergistically combine the individual properties of the two components to yield a new and unusual biological ability. The DNA-like component seems to induce an `active` structure of the protein-like fragment and hence significantly enhance its catalytic performance. However, the basic, fundamental processes behind this unusual discovery have never been studied. The great challenge is therefore to provide an understanding at the molecular level of how these functionally significant entities (i.e. the short synthetic protein-like molecule and the short DNA fragment) interact with each other and mutually change their functions. The aim of this proposal is therefore to determine the structural rules and molecular mechanisms which govern biological activity of these novel synthetic catalysts and control whether these molecules can recognize and specifically cleave another molecule. Success in this area will provide us with a chemical means to develop novel tools for chemical biology, such as catalysts with increased activity, altered specificity and improved storage properties compared to natural enzymes. We already have obtained experimental evidence that the molecules we are designing can provide specific and efficient cleavage, but now we need to understand the fine molecular mechanisms managing these processes. To achieve this we have to put this research onto a solid experimental basis through high resolution structural studies and a high-level computational approach.