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Single-molecule studies of eukaryotic DNA replication

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  • Full or part time
    Dr H Yardimci
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

This 4-year PhD studentship is offered in Dr Hasan Yardimci’s Group based at the Francis Crick Institute (the Crick).

Before a cell divides it has duplicate its genome so that two identical copies of the DNA content can be partitioned into daughter cells. In eukaryotic cells, DNA replication is initiated at thousands of origins on the DNA, each resulting in the assembly of two replisomes that travel away from the initiation site in opposite directions. Complete and high-fidelity duplication of the genome is essential for faithful transmission of genetic information. When DNA replication goes awry, the result could be cells with mutations, missing or extra genetic material a hallmark of the genomic instability seen in most cancers.

We investigate processes involved in eukaryotic replication using conventional biochemistry and single-molecule imaging tools. A significant advantage of single-molecule methods is that one can directly observe individual proteins that provide new insight into their dynamics and reaction mechanisms. To study eukaryotic replication at the single-molecule level we use a number of model systems including Xenopus egg extracts [1-3], SV40 replication system [4], and purified proteins yeast. Using novel methodologies that combine single-molecule imaging and DNA nanomanipulation in extract-based systems and conventional bulk assays, we previously differentiated between different models of unwinding by the replicative helicases MCM2-7 [2-3] and SV40 large T-antigen [4], and discovered how large T-antigen deals with replication barriers [4]. In the future, we aim to gain a comprehensive understanding of the overall architecture and dynamics of the eukaryotic replisome by fluorescently labeling individual components of the replisome and visualizing labeled proteins in real-time during replication. The goal of this project is to understand how the eukaryotic replisome deals with replication barriers such as DNA-protein crosslinks [5] and DNA interstand-crosslinks.

Consideration will be given to talented and motivated students from various backgrounds including biochemistry, biophysics, physics, and biology. During the course of graduate studies, the student will develop skills in molecular biology such as cloning, expression and purification of proteins and single-molecule techniques including total internal fluorescence microscopy and magnetic tweezers.

Talented and motivated students passionate about doing research are invited to apply for this PhD position. The successful applicant will join the Crick PhD Programme in September 2019 and will register for their PhD at one of the Crick partner universities (Imperial College London, King’s College London or UCL).

Applicants should hold or expect to gain a first/upper second-class honours degree or equivalent in a relevant subject and have appropriate research experience as part of, or outside of, a university degree course and/or a Masters degree in a relevant subject.


Funding Notes

Successful applicants will be awarded a non-taxable annual stipend of £22,000 plus payment of university tuition fees. Students of all nationalities are eligible to apply.


1. Yardimci, H., Loveland, A. B., van Oijen, A. M. and Walter, J. C. (2012)
Single-molecule analysis of DNA replication in Xenopus egg extracts.
Methods 57: 179-186. PubMed abstract
2. Fu, Y. V., Yardimci, H., Long, D. T., Ho, T. V., Guainazzi, A., Bermudez, V. P., Hurwitz, J., van Oijen, A., Schärer, O. D. and Walter, J. C. (2011)
Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase.
Cell 146: 931-941. PubMed abstract
3. Yardimci, H., Loveland, A. B., Habuchi, S., van Oijen, A. M. and Walter, J. C. (2010)
Uncoupling of sister replisomes during eukaryotic DNA replication.
Molecular Cell 40: 834-840. PubMed abstract
4. Yardimci, H., Wang, X., Loveland, A. B., Tappin, I., Rudner, D. Z., Hurwitz, J., van Oijen, A. M. and Walter, J. C. (2012)
Bypass of a protein barrier by a replicative DNA helicase.
Nature 492: 205-209. PubMed abstract
5. Duxin, J. P., Dewar, J. M., Yardimci, H. and Walter, J. C. (2014)
Repair of a DNA-protein crosslink by replication-coupled proteolysis.
Cell 159: 346-357. PubMed abstract

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