Optimising translocation of Hel308 helicase for improved nanopore DNA sequencing

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 Project Title: Optimising translocation of Hel308 helicase for improved nanopore DNA sequencing

Project summary:

DNA helicases play key roles in the replication, recombination and repair of DNA. Hel308 is a DNA helicase that was identified by its ability to process DNA structures that occur in homologous recombination, a conserved mechanism that is used to repair DNA double-strand breaks. Hel308 helicases are found in higher eukaryotes (where they are known as HELQ) and in archaea, but not in lower eukaryotes or bacteria. Hel308 helicases are used in biotechnological applications, where they help to translocate DNA through the nanopore of DNA sequencing flowcells.

We have found that amino acid substitutions in a conserved region of Hel308 lead to hyperactive DNA binding and DNA annealing activities in vitro, and result in vivo in a substantial increase in non-crossover recombination – but without any impact on cell growth or the repair of DNA lesions. Such changes in helicase activity are consistent with an altered ability to translocate along DNA, and indicate that this conserved region of Hel308 may hold the key to improvements in nanopore DNA sequencing technologies.

The initial phase of the project will use the extensive set of genetic tools available for the model archaeon Haloferax volcanii to screen for variants of Hel308 that display altered activities in vivo. The genetic screen will be used to identify residues that when mutated, lead to potential changes in helicase translocation activity. For example, elevated (or reduced) rates of genetic exchange are indicative of altered helicase translocation, and will be identified via high-throughput GFP-heteroallele recombination assays. This part of the project will be led by Professor Thorsten Allers.

In the second phase of the project, residues identified in the genetic screen will be targeted for amino acid substitutions in the Hel308 helicase from the archaeon Methanothermobacter thermautotrophicus. Proteins from this model archaeal species are tractable for biochemical analysis. Purified Hel308 proteins will be studied in gel-based and single-molecule FRET assays, to determine their altered DNA binding and DNA annealing activities in vitro. This part of the project will be led by Dr Ed Bolt.

In the final phase of the project, Hel308 candidates will be further investigated for their DNA translocation activity. Single-molecule picometer-resolution nanopore tweezers, which are based on a MinION flowcell platform, will be used to monitor the translocation of individual Hel308 enzymes along a DNA template, and thereby determine sequence-specific enzyme kinetics. This part of the project will be carried out in conjunction with the partner organisation, Oxford Nanopore Technologies.

To apply and check your eligibility, please click go to https://www.nottingham.ac.uk/bbdtp/apply/how-to-apply.aspx and you can find further information about how to apply to our programme.

Informal enquiries may be addressed to Thorsten.allers@nottingham.ac.uk or Ed.Bolt@nottingham.ac.uk or bbdtp@nottingham.ac.uk

Funding details:

Home and international students are welcome to apply for this opportunity. Funding is available for four years from late September 2023. The award covers tuition fee (£4,596) at the home rate plus an annual stipend which was (£17,668) for 2022. This is set by the Research Councils. Please note that successful international candidates will be put forward for a University Fees Difference Scholarship to cover the difference between the home and international fee.

 Apply online here by noon on Tuesday 17^th January 2023.