High-throughput synthesis and selection of DNA G-quadruplex optical probes

Lead Research Organisation: Imperial College London
Department Name: Chemistry


Specific guanine-rich sequences of DNA can fold into four-stranded structures known as G-quadruplexes (G4s), which are thought to be involved in a range of essential biological functions in healthy cells and are implicated in diseases. However, their detection in live biological samples remains very challenging. Recently, we have suggested a novel way of monitoring G4 formation in live cells, based on detection of the fluorescence lifetime of small optical probes [Nature Commun 2015, 6, 8178]. Despite this successful proof of concept study, our probes require further modification and optimization, in order to achieve high contrast signal upon binding to G4 DNA. Multiple possible variations in the probe structure, as well as the variations in DNA topology and concentration, mean that testing of new probes will be time consuming and laborious if performed using standard synthetic procedures and fluorescence lifetime analysis. Here we propose a strategy for high throughput synthesis and analysis of a large number of derivatives of thiazole orange (TO), a molecule which showed significant promise as a G4 DNA sensor in our proof of concept studies. This project will develop a novel methodology for high throughput synthesis and statistical testing of results in a fully automated way, allowing us to select ideal optical probes for G4 that are not accessible through standard routes within the timeframe of a PhD.

Keywords: DNA optical probes, high throughput synthesis and analysis, fluorescence lifetime, molecular rotors, automation, data-driven optimisation

Planned Impact

Academic impact:
Recent advances in data science and digital technology have a disruptive effect on the way synthetic chemistry is practiced. Competence in computing and data analysis has become increasingly important in preparing chemistry students for careers in industry and academic research.

The CDT cohort will receive interdisciplinary training in an excellent research environment, supported by state-of-the-art bespoke facilities, in areas that are currently under-represented in UK Chemistry graduate programmes. The CDT assembles a team of 74 Academics across several disciplines (Chemistry, Chemical Engineering, Bioengineering, Maths and Computing, and pharmaceutical manufacturing sciences), further supported by 16 industrial stakeholders, to deliver the interdisciplinary training necessary to transform synthetic chemistry into a data-centric science, including: the latest developments in lab automation, the use of new reaction platforms, greater incorporation of in-situ analytics to build an understanding of the fundamental reaction pathways, as well as scaling-up for manufacturing.

All of the research data generated by the CDT will be captured (by the use of a common Electronic Lab Notebook) and made openly accessible after an embargo period. Over time, this will provide a valuable resource for the future development of synthetic chemistry.

Industrial and Economic Impact:
Synthetic chemistry is a critical scientific discipline that underpins the UK's manufacturing industry. The Chemicals and Pharmaceutical industries are projected to generate a demand for up to 77,000 graduate recruits between 2015-2025. As the manufacturing industry becomes more digitised (Industry 4.0), training needs to evolve to deliver a new generation of highly-skilled workers to protect the manufacturing sector in the UK. By expanding the traditional skill sets of a synthetic chemist, we will produce highly-qualified personnel who are more resilient to future challenges. This CDT will produce synthetic chemists with skills in automation and data-management skills that are highly prized by employers, which will maintain the UK's world-leading expertise and competitiveness and encourage inward investment.

This CDT will improve the job-readiness of our graduate students, by embedding industrial partners in our training programme, including the delivery of training material, lecture courses, case studies, and offers of industrial placements. Students will be able to exercise their broadened fundamental knowledge to a wide range of applied and industrial problems and enhance their job prospects.

The World's population was estimated to be 7.4 billion in August 2016; the UN estimated that it will further increase to 11.2 billion in the year 2100. This population growth will inevitably place pressure on the world's finite natural resources. Novel molecules with improved effectiveness and safety will supersede current pharmaceuticals, agrochemicals, and fine chemicals used in the fabrication of new materials.

Recent news highlights the need for certain materials (such as plastics) to be manufactured and recycled in a sustainable manner, and yet their commercial viability of next-generation manufacturing processes will depend on their cost-effectiveness and the speed which they can be developed. The CDT graduates will act as ambassadors of the chemical science, engaging directly with the Learned Societies, local council, general public (including educational activities), as well as politicians and policymakers, to champion the importance of the chemical science in solving global challenges.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/S023232/1 31/03/2019 29/09/2027
2278942 Studentship EP/S023232/1 30/09/2019 31/12/2023 Aatikah Majid