Projects / Programmes source: ARIS

NMR studies of the role of cations for folding and stabilization of DNA quadruplexes

Research activity

Code Science Field Subfield
1.04.00  Natural sciences and mathematics  Chemistry   

Code Science Field
P003  Natural sciences and mathematics  Chemistry 
NMR, structure, DNA, cations, interactions
Evaluation (rules)
source: COBISS
Researchers (2)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  10082  PhD Janez Plavec  Chemistry  Head  2008 - 2011  1,230 
2.  22575  PhD Primož Šket  Chemistry  Researcher  2008 - 2011  216 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,257 
DNA molecules can besides the well known B-type double helix adopt higher order structures such as G-quadruplexes. The importance of G-quadruplex structures, which are formed by guanine rich oligonucleotide sequences originates from the roles of these structures in several important biological processes and made them drug targets in the field of cancer, aging, diabetes, central nervous system and cardiovascular diseases. G-quadruplex structures are also interesting due to their applications in nanotechnology. Understanding of biological roles and function of G-quadruplexes is tightly correlated with the knowledge of their 3D structures and dynamic properties. NMR spectroscopy will provide insight into 3D structure with atomic resolution. The results will be useful in the design of molecules that stabilize G-quadruplexes by binding to specific structural elements. New structures will greatly assist the search for correlations between oligonucleotide sequence and their 3D structure. We will also focus on localization of cations which play important role in stabilization of G-quadruplexes. NMR spectroscopy provides insight into binding and dynamic processes of cation exchange within G-quadruplex and with bulk solution. Development of new NMR methods for studies of cation interactions with DNA will simultaneously provide data on 3D structure of coordination sites with atomic resolution and rate of movement amongst individual binding sites which will find applications in design of artificial ion channels and will be of help in understanding of conductance of nanowires made of DNA.
Significance for science
DNA is one of the most important molecules in our life. Besides the well known right-handed B-type double helix it can adopt numerous other structural forms. DNA molecules can fold into higher-order structures such as quadruplexes, which consist of four interacting strands originating from a single molecule or several molecules. Typically quadruplex structures are adopted by G-rich DNA sequences. Recently interest in G-quadruplexes has increased due to the roles of these structures in various important biological processes and due to their possible applications in therapeutics. G-quadruplexes play important biological roles in organism and are targets for biomedical applications. G-quadruplexes can be drugs themselves (e.g. antiviral compounds, diabetes, aptamers). The formation of G-quadruplexes at telomeric ends of DNA and their stabilization by specific ligands has been proved to inhibit telomerase in cancer cells. Our research is important in view of development of novel therapeutic agents based on structural details of G-quadruplexes as well as potential application of these structures in other fields such as supramolecular chemistry and nanotechnology. In the framework of the project we have collected novel data on folding and stabilization of G-quadruplexes. 3D structure and function of nucleic acids in organism are tightly correlated with the presence of metal ions. G-quadruplexes are special example of this tight correlation and can due to strong interaction serve as an excellent model system to study interaction of nucleic acids with metal ions. 15N isotopically labeled ammonium ions are utilized to improve our understanding of localization of binding sites for monovalent cations within structures of G-quadruplexes. Ammonium ions are involved in slow exchange on the NMR time-scale. NMR studies have enabled insight into the strength of interaction of cations to specific binding site as well as into dynamics of exchange of individual ions within G-quadruplex and with bulk solution.
Significance for the country
Spectrum of biological processes which involve G-quadruplexes has broadened recently. G-quadruplexes are potential targets in cancer therapies as their formation inhibits telomerase activity. It is thus not surprising that many research efforts are directed into screening of ligands that can selectively bind G-quadruplexes and stabilize them. Knowledge of structural motifs that are available to these structures is of big importance as it enables design of more effective ligands for stabilization of G-quadruplexes, which are potential anticancer drugs. Stability of G-quadruplexes greatly depends on the nature of present metal cations that are present in solution, which implies that our results have contributed to the development of novel potential drugs. Controlled change of solution conditions can lead to structural changes in G-quadruplex into desired direction which could be exploited in the design of molecular switches and nano-devices. Our structural studies have shown that not all structural motifs are known even for relatively simple oligonucleotide sequences. We have demonstrated that even a small change in oligonucleotide sequence or in nature of metal ions can lead to dramatic structural changes. New structural data will be useful in the design of novel anticancer drugs which could be of potential interest for pharmaceutical industry in Slovenia. Studies of metal ion binding to G-quadruplexes have expanded our knowledge on the interactions of cations with nucleic acids in general. This represents a complex problem as it is hard to get direct information on cation binding. G-quadruplexes represent an excellent model system for such studies as they allow localization of cations to a given binding sites in solution with the use of NMR methods. Our results were published in internationally recognized journals and presented at international meetings and conferences and thus presented to the public. Development of NMR methodology for studies of G-quadruplexes has contributed to the advance of NMR spectroscopy and Slovenian NMR centre which actively and tightly collaborates with Slovenian industry.
Most important scientific results Annual report 2008, 2009, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2008, 2009, final report, complete report on dLib.si
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