Disrupting DNA G-quadruplex secondary structures to revert premature ageing
Lead Research Organisation:
Imperial College London
Department Name: Chemistry
Abstract
The underlying cause of aging remains one of the central mysteries of biology. Recent studies in several different biological models suggest that not only can the rate of aging be modified by environmental and genetic factors, but also that the aging clock can be reversed, restoring characteristics of youthfulness to aged cells and tissues.
DNA packaging and organisation in the cell nucleus has been shown to be significantly altered thorough ageing and some accelerating ageing disorders. Treatment with small molecule ligands can interfere with nuclear organisation and revert premature ageing sings in patient-derived cells. DNA non-canonical structures, in particular DNA G-quadruplex structures, have also shown to play a role in DNA packaging in some accelerating ageing syndromes. Indeed, mutation of specific G-quadruplex unwinding proteins and accumulation of these DNA structures have been shown to be the underlying cause of accelerating ageing syndromes, such as Cockayne syndromes. Targeting DNA and its structural feature to both further our understating in fundamental ageing biology and explore potential for therapeutic intervention of rare accelerating ageing disorders, is an unexplored opportunity that needs to be investigated.
Here, I will exploit a range of chemical biology tools to both investigate the fundamental role of DNA G-quadruplex structures in ageing biology, and explore the potential for therapeutic intervention of rare accelerating ageing syndromes by developing small molecules to target and disrupt these structures. Specifically, I will combine my experience with DNA G-quadruplex targeting and genome-wide mapping with a G-quadruplex selective live-cell imaging methodology that has been developed at the chemistry department of Imperial College London in collaboration with Dr. Vilar. I intend to address these specific questions:
1) What are the global changes in G-quadruplex prevalence genome-wide in accelerating ageing disorders and how is DNA packaging affected by their formation?
2) Can targeting and disrupting the G-quadruplexes that accumulate via ageing be used to revert the ageing phenotypes by restoring correct DNA packaging?
3) What are the dynamics in living cells, with respect to transcription and replication of DNA, that cause G-quadruplex formation thorough ageing?
Addressing these questions will further our understanding of the cause and effect relationship between DNA secondary structure formation and gene mis-regulation that cause ageing. This will pave the way towards the development of novel therapeutic agents which will ultimately increase health-span and treat rare accelerating ageing syndromes.
DNA packaging and organisation in the cell nucleus has been shown to be significantly altered thorough ageing and some accelerating ageing disorders. Treatment with small molecule ligands can interfere with nuclear organisation and revert premature ageing sings in patient-derived cells. DNA non-canonical structures, in particular DNA G-quadruplex structures, have also shown to play a role in DNA packaging in some accelerating ageing syndromes. Indeed, mutation of specific G-quadruplex unwinding proteins and accumulation of these DNA structures have been shown to be the underlying cause of accelerating ageing syndromes, such as Cockayne syndromes. Targeting DNA and its structural feature to both further our understating in fundamental ageing biology and explore potential for therapeutic intervention of rare accelerating ageing disorders, is an unexplored opportunity that needs to be investigated.
Here, I will exploit a range of chemical biology tools to both investigate the fundamental role of DNA G-quadruplex structures in ageing biology, and explore the potential for therapeutic intervention of rare accelerating ageing syndromes by developing small molecules to target and disrupt these structures. Specifically, I will combine my experience with DNA G-quadruplex targeting and genome-wide mapping with a G-quadruplex selective live-cell imaging methodology that has been developed at the chemistry department of Imperial College London in collaboration with Dr. Vilar. I intend to address these specific questions:
1) What are the global changes in G-quadruplex prevalence genome-wide in accelerating ageing disorders and how is DNA packaging affected by their formation?
2) Can targeting and disrupting the G-quadruplexes that accumulate via ageing be used to revert the ageing phenotypes by restoring correct DNA packaging?
3) What are the dynamics in living cells, with respect to transcription and replication of DNA, that cause G-quadruplex formation thorough ageing?
Addressing these questions will further our understanding of the cause and effect relationship between DNA secondary structure formation and gene mis-regulation that cause ageing. This will pave the way towards the development of novel therapeutic agents which will ultimately increase health-span and treat rare accelerating ageing syndromes.
Technical Summary
The aim of this project is to investigate the role of DNA packaging and DNA G-quadruplex secondary structure thorough ageing and accelerating ageing disorders.
G-quadruplexes are stable non-B DNA structures that form in guanine-rich DNA sequences, acting as knots and posing a threat for polymerases processivity during transcription and replication. G-quadruplex prevalence is highly dependent on chromatin architecture and recent findings have suggested that is the lack of resolution of DNA G-quadruplex structures, particularly those formed within the guanine-rich ribosomal DNA, the underlining cause of accelerating ageing in Cockayne syndrome. However, a clear cause-effect between the buildup of unresolved G-quadruplex structures, chromatin structure alteration and ageing biology remains yet to be elucidated. Investigating chromatin architecture variation thorough lifespan and targeting age-dependent DNA structural features to revert ageing phenotypes is an unexplored opportunity that could radically improve our understanding of ageing biology.
I will develop molecular probes to target, visualise and disrupt G-quadruplex structures to study their prevalence and influence on chromatin structures during ageing, leveraging on cell-models derived from patients affected by accelerating ageing disorders. The use of these probes, in combination with live-cell imaging techniques established at Imperial College and genome-wide mapping methodologies, will provide a unique platform to unravel the changes in chromatin architecture and DNA secondary structures formation that are linked with ageing. This work will pave the way towards the targeting of DNA and chromatin structural features to revert ageing associated conditions/phenotypes and treat rare accelerating ageing disorders.
G-quadruplexes are stable non-B DNA structures that form in guanine-rich DNA sequences, acting as knots and posing a threat for polymerases processivity during transcription and replication. G-quadruplex prevalence is highly dependent on chromatin architecture and recent findings have suggested that is the lack of resolution of DNA G-quadruplex structures, particularly those formed within the guanine-rich ribosomal DNA, the underlining cause of accelerating ageing in Cockayne syndrome. However, a clear cause-effect between the buildup of unresolved G-quadruplex structures, chromatin structure alteration and ageing biology remains yet to be elucidated. Investigating chromatin architecture variation thorough lifespan and targeting age-dependent DNA structural features to revert ageing phenotypes is an unexplored opportunity that could radically improve our understanding of ageing biology.
I will develop molecular probes to target, visualise and disrupt G-quadruplex structures to study their prevalence and influence on chromatin structures during ageing, leveraging on cell-models derived from patients affected by accelerating ageing disorders. The use of these probes, in combination with live-cell imaging techniques established at Imperial College and genome-wide mapping methodologies, will provide a unique platform to unravel the changes in chromatin architecture and DNA secondary structures formation that are linked with ageing. This work will pave the way towards the targeting of DNA and chromatin structural features to revert ageing associated conditions/phenotypes and treat rare accelerating ageing disorders.
Planned Impact
The fundamental insights gained from this project will directly benefit scientists engaged in the study of nucleic acids function, gene regulation and ageing biology.
The deliverables will include insights into molecular targets and their cognate small molecule ligands, which will provide starting points for the development of therapeutic agents that act via G-quadruplex recognition. The tools and methodologies that will be developed will have broader use in future chemical biology approaches to study and interfere with ageing-dependent chromatin remodelling for both diagnostics and therapeutic applications.
Ultimately this research aims to further the knowledge of fundamental ageing biology for increasing health-span, having a direct impact on the wider public.
The deliverables will include insights into molecular targets and their cognate small molecule ligands, which will provide starting points for the development of therapeutic agents that act via G-quadruplex recognition. The tools and methodologies that will be developed will have broader use in future chemical biology approaches to study and interfere with ageing-dependent chromatin remodelling for both diagnostics and therapeutic applications.
Ultimately this research aims to further the knowledge of fundamental ageing biology for increasing health-span, having a direct impact on the wider public.
People |
ORCID iD |
Marco Di Antonio (Principal Investigator / Fellow) |
Publications
Balcerowicz M
(2021)
Monitoring Real-time Temperature Dynamics of a Short RNA Hairpin Using Förster Resonance Energy Transfer and Circular Dichroism.
in Bio-protocol
Minard A
(2019)
The unexplored potential of quinone methides in chemical biology.
in Bioorganic & medicinal chemistry
Weber J
(2019)
An Activatable Cancer-Targeted Hydrogen Peroxide Probe for Photoacoustic and Fluorescence Imaging.
in Cancer research
Monti L
(2023)
G-Quadruplexes as Key Transcriptional Regulators in Neglected Trypanosomatid Parasites.
in Chembiochem : a European journal of chemical biology
Raguseo F
(2020)
Chemical-biology approaches to probe DNA and RNA G-quadruplex structures in the genome.
in Chemical communications (Cambridge, England)
Liano D
(2022)
Long-range DNA interactions: inter-molecular G-quadruplexes and their potential biological relevance.
in Chemical communications (Cambridge, England)
Minard A
(2020)
A short peptide that preferentially binds c-MYC G-quadruplex DNA.
in Chemical communications (Cambridge, England)
Rauchhaus J
(2022)
G-quadruplexes Mark Sites of Methylation Instability Associated with Ageing and Cancer.
in Genes
Robinson J
(2024)
Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy.
in Journal of the American Chemical Society
Liano D
(2021)
Cockayne Syndrome B Protein Selectively Resolves and Interact with Intermolecular DNA G-Quadruplex Structures.
in Journal of the American Chemical Society
Description | I have started my own group at Imperial College London (Chemistry Department) in September 2018, after being awarded this Biotechnology and Biology Research Council (BBSRC) David Phillips Fellowship to study the role of G-quadruplex (G4) structures in epigenetic changes associated with ageing. During this time, I have published 10 manuscripts as a corresponding author, despite the challenges posed by the COVID-19 pandemic, demonstrating how timely and impactful my research vision is. Specifically, I have discovered, inspired by the endogenous G4-binding protein DHX36, a short peptide that selectively recognises a DNA G4 structure formed in the promoter region of the undruggable oncogene MYC (Minard et al. Chem. Commun. 2020). More recently, I have reported the first example of a human protein that recognises with exquisite selectivity and affinity multimolecular G4s (Liano et al. J. Am. Chem. Soc. 2021), hinting at a biological relevance of these neglected secondary structures. I have also developed a platform to rationally design disruptors of targeted G4s structures (Chowdhury et al. Nucleic Acids Res. 2022,, and exemplified their use to study the biology of these structures in cells. |
Exploitation Route | Our findings can be used at many level by both other academics and industry. In terms of academic development, the discovery of CSB as a selective intermolecular-G4 binder can lead to structural biology studies where its mechanism of action is unraveled, which can be of relevance to fundamental chromatin biology and epigenetics. Given the proven link of CSB and G4-formation with ageing, industries might leverage our findings to design novel drugs to prevent or slow down ageing related diseases. |
Sectors | Education,Healthcare,Pharmaceuticals and Medical Biotechnology |
URL | https://www.imperial.ac.uk/news/232394/long-range-four-stranded-dna-structures-found-play/ |
Description | Responsive Mode |
Amount | £709,350 (GBP) |
Funding ID | BB/W016710/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2023 |
End | 12/2025 |
Description | Andrew Jamieson collaboration on short peptides targeting G4s |
Organisation | University of Glasgow |
Department | School of Chemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have teamed up with Dr Andrew Jamieson from the Chemistry Department of Glasgow University to characterise the binding interaction of certain short peptides that they have generated against a panel of G-quadruplex forming sequences. Our contributions have been both intellectual in selecting the substrate to be tested, and practical in measuring the binding affinity of the peptides for the structures tested using a variety of biochemical and biophysical methods. |
Collaborator Contribution | The Jamieson group has designed short peptides taking inspiration from published crystal structures and has executed the synthesis of those peptides. Hence, their contributions include both the intellectual design of the peptides and their synthetic preparation, which have both been pivotal for the identification of novel MYC selective G4-binding peptides. |
Impact | This is a multidisciplinary activity with the Jamieson group providing peptide synthesis expertise and the Di Antonio group providing biochemical and biophysical expertise. A publication has been produced from this collaboration: DOI: 10.1039/d0cc02954h |
Start Year | 2019 |
Description | Optical Tweezer collaboration |
Organisation | Kent State University |
Country | United States |
Sector | Academic/University |
PI Contribution | We have partnered up with Hanbin Mao to leverage his optical tweezer platform to characterise the LNA-based probed we developed as G4-disruptor |
Collaborator Contribution | The collaborator has provided key measurement for the characterisation of our probes in the form of single-molecule measurement |
Impact | We have a manuscript currently under consideration in Nucleic Acids Research |
Start Year | 2021 |
Description | Presentation to the online RSC Nucleic Acids Forum |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | The PDRA hired on this project delivered a talk about our research to postgrad students and initiate discussion about ageing biology |
Year(s) Of Engagement Activity | 2021 |
Description | School Visit St. Paul's Girl School |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | I have inspired young girl to undergo a career in STEM |
Year(s) Of Engagement Activity | 2022 |
Description | TEDxYouth talk London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Delivered a TED talk to young STEM students |
Year(s) Of Engagement Activity | 2022 |
Description | Talk at Latimer School (London) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Inspired young students to work in cancer and ageing research and explained our BBSRC-funded work and its impact. |
Year(s) Of Engagement Activity | 2022 |