Projects / Programmes
Structures of tetrahelical nucleic acids adopted by tandem repeats
| Code |
Science |
Field |
Subfield |
| 1.04.02 |
Natural sciences and mathematics |
Chemistry |
Structural chemistry |
| Code |
Science |
Field |
| B002 |
Biomedical sciences |
Biophysics |
| Code |
Science |
Field |
| 1.04 |
Natural Sciences |
Chemical sciences |
nucleic acids, structure, NMR, regulatory regions
Researchers (9)
Organisations (2)
Abstract
DNA is known primarily for its role in carrying genetic instructions. This role in the living world can be explained by the well-known structure of the double helix. In the last few decades, knowledge of the DNA capability to adopt a large number of structures has emerged, including multistrand helices, which are associated with various biological functions ranging from the transmission of genetic information to catalysis and regulation. Many promoters include guanine-rich sequences, which can fold into quadruplex structures. G-quadruplex, a four-stranded secondary structure formed by guanine-rich nucleic acids is gaining increasing attention as means for therapeutic intervention. The basic building block of G-quadruplexes is a G-quartet in which four guanine bases are held together by eight Hoogsteen hydrogen bonds in a co-planar arrangement. AGCGA-quadruplexes are a new structural family that we have described only recently. It is of particular interest that G-rich tracts appear in loops and not in the core of the structure, as is the case of G-quadruplexes. Within the framework of the current proposal we intend to study structural features of G-rich genomic DNA sequences, which are expected to form G- and AGCGA-quadruplexes. The proposed research will help to broaden and deepen the knowledge of folding of DNA sequences involved in the regulation of expression (onco)genes. AGCGA-repeats were found in the regulatory regions of various human genes, which are related to brain development and neurological disorders, abnormal cartilage and bone formation, cancer as well as the regulation of basic cell processes. Knowledge of the structure-property relationship together with dynamic properties of molecules that can be obtained by NMR studies is vital. We are proposing studies of the structural characteristics of G-rich genomic DNA fragments, which we expect to form quadruplex structures. We will focus primarily on promoter regions associated with proteins that are important in neurological disorders, bone and cartilage development and cancer. Recent studies have shown that DNA regions with tandem repeats are involved in the pathogenesis of various diseases and are therefore an important target in drug development. This role can be attributed to their G-rich promoters and repressors that can potentially fold into the G- or AGCGA-quadruplex structures. Many findings confirm the hypothesis that the formation and development of G-quadruplex structures can be involved in the regulation of gene expression. Recent studies have shown that G-quadruplexes are highly polymorphic, which has been associated with specifics of oligonucleotide sequences as well as with solution conditions. We will devote special attention to the nature and sequence requirements of loops since their structure is very important in terms of interaction between the DNA molecule and ligands (potential drugs). An attractive therapeutic strategy to inhibit transcription of proteins is by the introduction of polycyclic aromatic hydrocarbon insertions such as Twisted Intercalating Nucleic Acids that stabilize G-quadruplexes and repress transcription. Decoy strategy is based on a hypothesis that oligonucleotides mimicking G-quadruplexes compete with the binding of transcription factors and thus inhibit its expression. To enhance their activity, decoy oligonucleotides should maintain the 3D structure recognized by the cognate transcription factor and exhibit enhanced resistance to nucleases. The primary research tool will be high-resolution NMR spectroscopy. We plan to complement the results by UV, CD and other biophysical methods. Using structure-guided design we expect to optimize the sequence position of intercalating nucleotide residues with pyrene chromophores. It is noteworthy that the main objectives of the proposed studies are qualitatively innovative despite building on earlier experience, and should not be considered in a simplified way as a continuation.
Significance for science
Results of the proposed studies will contribute to expansion and deepening of knowledge on folding of DNA sequences which are involved in regulation of expression of (onco)genes and can fold according to their oligonucleotide structures into G- or AGCGA-quadruplexes. Numerous promoters contain G-rich elements that can fold into quadruplexes. AGCGA repeat sequences have been located in regulatory regions of various human genes connected to neurodevelopment and neurological disorders, abnormal cartilage and bone formations, cancer and regulation of basic cellular processes. In order to understand the processes in nature it is vital to consider structure-property relationship, which in recent times includes knowledge of the dynamic properties of molecules that can be obtained by NMR studies. Up till now, very little is known about G-quadruplex structures adopted by G-rich regions found in promoter regions of oncogenes. AGCGA quadruplexes are a new structural family that we have described only recently. Knowledge of structural features is important for understanding the regulation of gene expression and can be of help in designing of novel organic molecules that could specifically stabilize certain quadruplex structures. This will help against various forms of cancer and many viral diseases. Alternatively, organic molecules with fluorescent properties can be used as in vivo probes. High-resolution 3D structures will provide much needed insight into the nature of interactions of aromatic groups of intercalating residues and G-quadruplexes. Currently it is difficult to rationalize affinities of intercalating residues due to the absence of appropriate data on geometry of interaction. Special consideration will be given to interaction of individual intercalating residues with loops and nearby G-quartets. The results of the proposed studies of structures and interactions will enable the prediction of new intercalating residues and their incorporation in the oligonucleotide decoys of transcription factors with improved properties. In co-operation with the foreign partner we are planning to test the guanine-rich oligonucleotide decoys and effectiveness of suppression of expression of genes in model animals. We will also contribute to the development of experimental methods for DNA structure elucidation. Novel 'in cell' NMR methods will be developed to facilitate DNA structure elucidation within confines of cell environment.
Significance for the country
Results of the proposed studies will contribute to expansion and deepening of knowledge on folding of DNA sequences which are involved in regulation of expression of (onco)genes and can fold according to their oligonucleotide structures into G- or AGCGA-quadruplexes. Numerous promoters contain G-rich elements that can fold into quadruplexes. AGCGA repeat sequences have been located in regulatory regions of various human genes connected to neurodevelopment and neurological disorders, abnormal cartilage and bone formations, cancer and regulation of basic cellular processes. In order to understand the processes in nature it is vital to consider structure-property relationship, which in recent times includes knowledge of the dynamic properties of molecules that can be obtained by NMR studies. Up till now, very little is known about G-quadruplex structures adopted by G-rich regions found in promoter regions of oncogenes. AGCGA quadruplexes are a new structural family that we have described only recently. Knowledge of structural features is important for understanding the regulation of gene expression and can be of help in designing of novel organic molecules that could specifically stabilize certain quadruplex structures. This will help against various forms of cancer and many viral diseases. Alternatively, organic molecules with fluorescent properties can be used as in vivo probes. High-resolution 3D structures will provide much needed insight into the nature of interactions of aromatic groups of intercalating residues and G-quadruplexes. Currently it is difficult to rationalize affinities of intercalating residues due to the absence of appropriate data on geometry of interaction. Special consideration will be given to interaction of individual intercalating residues with loops and nearby G-quartets. The results of the proposed studies of structures and interactions will enable the prediction of new intercalating residues and their incorporation in the oligonucleotide decoys of transcription factors with improved properties. In co-operation with the foreign partner we are planning to test the guanine-rich oligonucleotide decoys and effectiveness of suppression of expression of genes in model animals. We will also contribute to the development of experimental methods for DNA structure elucidation. Novel 'in cell' NMR methods will be developed to facilitate DNA structure elucidation within confines of cell environment.
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