Imaging Approaches to Monitor and Optimise Solid Phase Oligonucleotide Synthesis

Key facts

• Opens: Tuesday 14 January 2025
• Deadline: Sunday 16 February 2025
• Number of places: 1
• Duration: 36 months
• Funding: Home fee, Stipend, Travel costs

Eligibility

An upper second-class UK Honours degree in Chemistry or Chemical Engineering is required. A Masters-level degree is desirable but not essential. If English is not your first language, you must have an IELTS score of at least 6.5 with no component below 5.5.

Note: you do not need to see yourself as having ‘ticked all the boxes’ or being a direct fit for this role. We are keen to welcome and support candidates eager to learn and grow!

Project Details

Your PhD project presents the opportunity to focus your postgraduate research towards addressing the lack of process analytical technology (PAT) available to monitor solid phase oligonucleotide synthesis (SPOS).

As a PhD researcher in our team, you'll investigate non-invasive imaging approaches to identify colorimetric and shape-based signatures that track each key step in the SPOS cycle.

You'll also investigate object detection methods to enable the dynamic swelling properties of the solid supports used in SPOS. In the service of industrial partners developing new therapeutics, you will be helping us understand the potential uses of our team’s ground-breaking kinetic imaging software, Kineticolor, to:

• monitor kinetics of detritylation, coupling, oxidation/sulfurization, and capping
• develop a complementary understanding of imaging-enabled kinetics for SPOS operations (inc. base deprotection and resin cleavage)
• characterise dynamic SPOS resin swelling properties as a function of oligomer growth
• investigate the use of video analysis to track optimal aging of key reagents

Background

SPOS is widely used for the automated assembly of oligonucleotides, which are among the most sought-after therapeutic modalities. The process involves sequential addition of nucleotide residues to a growing chain anchored to an insoluble support. Each cycle consists of a series of reactions – including detritylation, phosphoramidite coupling, P-sulfurization or P-oxidation, and unreacted 5’-OH capping – that must occur with high efficiency to produce the desired sequence (figure right). While SPOS is critical in enabling the rapid, scalable production of oligonucleotides, real-time monitoring of reaction progress remains a challenge. Innovations in PAT could thus enhance the precision and yield of SPOS, particularly for complex sequences or modified nucleotides.

Research problem

As rates of approval for oligonucleotide (“oligo”) therapeutics rise, so too do the challenges to achieve sustainable manufacturing. A primary challenge in SPOS is the meticulous control of myriad variables (~30-50 depending on the oligo) required to prevent the formation of complex and unwanted impurities.

Reagents such as the phosphoramidite monomers are prone to fast degradation. Conversely, sulfurizing reagents require variable “ageing” times before use. In-line control of these events has the potential to enhance the robustness of the synthesis, but current state-of-the-art PAT requires intervention that is not compatible with manufacturing operations.

During SPOS, the reagents are pushed through a fix bed reactor generating a concentration gradient that, on larger scales, results in uneven distribution of reagents. Such variations can lead to batch inhomogeneity, compromising the commercial value of the oligo product.

The current in-line techniques (UV and conductivity) used to monitor SPOS are not sensitive enough to reliably detect heterogeneity. While some of the more recent PAT development efforts for SPOS – including mid-IR,2 NMR, and refractive index – have demonstrated valuable progress, there remains a lack of available non-contact PAT, and PAT that can monitor reaction bulk in complement to molecular specifics. Without a sufficient suite of PAT to monitor SPOS, batch homogeneity can only be assessed after the synthesis is completed, leading to avoidable waste and high process mass intensity (PMI).

Your role

As a PhD Researcher in our team, you will lead both publishable and patentable research, working under the supervision of Dr Marc Reid (Senior Lecturer/Associate Professor and UKRI Future Leaders Fellow).

You'll join an exciting team of chemists, chemical engineers, and computer scientists working together. As part of this close-knit team, you will have the opportunity to develop innovative real-time reaction monitoring methods for aligned industrial partners across the Chemical sector. The early successes of our emerging research programme will give you exposure to knowledge exchange and commercial activity, as well as pioneering fundamental research that can be (and has been) published in a suite of high-impact and direct-to-end-user journals.

Training

This project addresses a timely need for digital chemists, equipping you with skills in synthesis, kinetics, and advanced imaging technologies. Your lab-based training includes NMR, UV-vis kinetics, and EasySampler-enabled HPLC profiling, alongside the use of project management tools like Basecamp to foster leadership and planning skills.

The project involves lab-based video recording of SPOS reactions and statistical analysis to validate the imaging-based approach as a viable PAT method. Correlations between video data and traditional analytics (e.g., UV-vis and HPLC) will be explored to support this validation.

With support from a prestigious UKRI Future Leaders Fellowship, recently renewed with £567k in funding, your PhD position includes a project budget for consumables, travel to conferences, and possible project placements with aligned industrial project partners.

Funding details

The funding covers home fees (UK students only) and an annual stipend of £20,199.

With support from a prestigious UKRI Future Leaders Fellowship, recently renewed with £567k in funding, your PhD position includes a project budget for consumables, travel to conferences, and possible project placements with aligned industrial project partners.

While there is no funding in place for opportunities marked "unfunded", there are lots of different options to help you fund postgraduate research. Visit funding your postgraduate research for links to government grants, research councils funding and more, that could be available.

Dr Marc Reid

Senior Lecturer Pure and Applied Chemistry

Professor Craig Jamieson

Head Of Department Pure and Applied Chemistry

Apply

Please send a two-page CV and one-page cover letter, detailing your reasons for applying, directly to Dr Marc Reid ( marc.reid.100@strath.ac.uk ) before the application deadline.

Number of places: 1

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Contact us

marc.reid.100@strath.ac.uk

Research areas