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Project 33: The molecular mechanisms of DNA replication and repair on molecular level

Suitable Majors

Biochemistry and Molecular Biology, Computer Science, Molecular Biology

Research Area

Computation biology, Structural biology, Genetics

Internship Description

The proposed project is mainly focused on the molecular bases of substrate recognition by 5’nucleases. The project combines cutting-edge computational resources and state-of-the-art biophysical computational tools, including full-atom molecular dynamics (MD) simulations, to establish the conformational states and dynamics of bubble DNA structure and how they are influenced by the bubble size and DNA sequence.
These studies will be accompanied and verified side-by-side by the experimental results coming from the cutting-edge biophysical techniques, including the single-molecule FRET (smFRET) measurements and high-resolution multidimensional Nuclear Magnetic Resonance (NMR) experiments.

Prerequisites

This project is suitable for students with bioscience, physics, or engineering background.

Deliverables/Expectations

We offer the students participating in this project to learn:
- How to use the state-of-the-art biophysical techniques and design the workload;
- How to become self-reliant in the design, preparation, running and analysis of the molecular dynamics (MD) simulations of biologically essential macromolecular systems;
- How to analyze and integrate the results derived from different computational techniques with the experimentally derived information from the cutting-edge biophysical techniques, including smFRET and Bio-NMR.

To complete the above tasks we expect from the students:
- A positive approach and strong will to work in the interdisciplinary and international research team;
- The preparation of the final report in the article format;
- The preparation of presentation that will be given during the group meeting.

Other Comments

​Internship dates: 23 June to 29 August or 7 July to 14 September​

Division

Biological and Environmental Sciences and Engineering

Faculty Name

Mariusz Jaremko