Final Report Summary - FAR-QUAD (FoldAmeRs: a new family of G-QUADruplex ligands)
Project objectives
It has been known that G-rich nucleic acids have a propensity to form four stranded structures called quadruplexes in vitro. Recently, it has been discovered that they do indeed play a general physiological role and are highly relevant targets for cancer therapy. Many different ligands have been synthesised so far, however, their common feature is their flatness which allows stacking on the top of quadruplex platform. This project was initiated by the serendipitously discovery that helically folded molecule, called foldamers, could strongly interact with the human telomeric quadruplex, suggesting a different mechanism. The main objectives of this project were:
i) to develop new G-quadruplex ligands having high affinity and specificity and
ii) to understand the elements responsible for specific interaction of the ligand by the structure determination of quadruplex-foldamer complex by X-ray diffraction.
Description of the work performed since the beginning of the project
The work performed consisted in:
i) the chemical synthesis of a consequent number of foldamers without various modifications, including backbone and side chains variations;
ii) their biophysical studies with six different biologically relevant quadruplex sequences;
iii) the selection of DNA sequences against the best foldamer and
iv) cristallogenesis of quadruplexes in absence or presence of foldamers.
The main results achieved so far
1) Almost all of our new macrocycles and foldamers 1-12 showed significant potential for quadruplexes stabilisation without any evidence of duplex stabilisation.
2) Biophysical studies revealed that the octacationic foldamer 8 is the best ligand for stabilising quadruplexes DNA known so far.
3) Structure activity relationships allowed us to determine features required for a foldamers to be a good quadruplex ligand (backbone, side chains and nature of extremities).
4) Using SELEX technology, we discovered that foldamer 8 selected oligonucleotides with a G-quadruplex conformation, which clearly indicates the high affinity of this foldamer for this DNA folded structure.
5) Complex formation between quadruplex and foldamers is specific from this latest, depending on its helicity, as demonstrated by tethering a correct chiral group at one extremity.
The expected final results and their potential impact and use
As foldamer 8 is the best ligand for G-quadruplex structures known up-to-date, promising application will be considered. We will take advantage of its lack of sequence specificity to use it as detection probe of G-quadruplex structure within the genome. In the same, we are still optimistic to obtain a X-ray structure of a complex and then get access to of interaction between the two partner. This will allow us to start designing foldamers for sequence specific recognition of quadruplex.
It has been known that G-rich nucleic acids have a propensity to form four stranded structures called quadruplexes in vitro. Recently, it has been discovered that they do indeed play a general physiological role and are highly relevant targets for cancer therapy. Many different ligands have been synthesised so far, however, their common feature is their flatness which allows stacking on the top of quadruplex platform. This project was initiated by the serendipitously discovery that helically folded molecule, called foldamers, could strongly interact with the human telomeric quadruplex, suggesting a different mechanism. The main objectives of this project were:
i) to develop new G-quadruplex ligands having high affinity and specificity and
ii) to understand the elements responsible for specific interaction of the ligand by the structure determination of quadruplex-foldamer complex by X-ray diffraction.
Description of the work performed since the beginning of the project
The work performed consisted in:
i) the chemical synthesis of a consequent number of foldamers without various modifications, including backbone and side chains variations;
ii) their biophysical studies with six different biologically relevant quadruplex sequences;
iii) the selection of DNA sequences against the best foldamer and
iv) cristallogenesis of quadruplexes in absence or presence of foldamers.
The main results achieved so far
1) Almost all of our new macrocycles and foldamers 1-12 showed significant potential for quadruplexes stabilisation without any evidence of duplex stabilisation.
2) Biophysical studies revealed that the octacationic foldamer 8 is the best ligand for stabilising quadruplexes DNA known so far.
3) Structure activity relationships allowed us to determine features required for a foldamers to be a good quadruplex ligand (backbone, side chains and nature of extremities).
4) Using SELEX technology, we discovered that foldamer 8 selected oligonucleotides with a G-quadruplex conformation, which clearly indicates the high affinity of this foldamer for this DNA folded structure.
5) Complex formation between quadruplex and foldamers is specific from this latest, depending on its helicity, as demonstrated by tethering a correct chiral group at one extremity.
The expected final results and their potential impact and use
As foldamer 8 is the best ligand for G-quadruplex structures known up-to-date, promising application will be considered. We will take advantage of its lack of sequence specificity to use it as detection probe of G-quadruplex structure within the genome. In the same, we are still optimistic to obtain a X-ray structure of a complex and then get access to of interaction between the two partner. This will allow us to start designing foldamers for sequence specific recognition of quadruplex.