Doctorate

23.09.2021: Faculty of Biosciences, Heidelberg University. Magna cum laude [Thesis 1.0, overall 1.2]

01/10/2019 – 23/09/2021: Lab of Prof. Dr. Rebecca C. Wade, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany

01/11/2016 – 30/09/2019: Lab of Late Prof. Dr. Jörg Langowski (deceased May 2017, lab headed by Dr. Katalin Tóth), Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany

Thesis: “The effects of the linker-DNA on linker histone positioning: a single-pair FRET study from mono to trichromatosomes”

Supervisors: Prof. Rebecca C. Wade (primary), Prof. Karsten Rippe (secondary)

Research interest

  1. Chromatin organisation, nucleosomes
  2. DNA-protein interaction, molecular machines,
  3. single-molecule spectroscopy, FRET, NMR
  4. Biophysics and Structural biology

Selected presentations

  1. 10/03/2021: Fragile Nucleosome Seminar series [online]: https://www.youtube.com/watch?v=t0iKzh5vhuU
  2. 31/03/2019-05/04/2019: Multiscale modelling of Chromatin: Bridging Experiments with Theory. Biophysical Society Thematic Meeting, Les Houches, France
  3. 27/02/2020: Heidelberg Chromatin Club, Germany

Research outputs

1. M. De, M. Würtz, G. Müller, K. Tóth, R. C. Wade, Effect of A-tract-mediated linker histone orientation on trinucleosome compaction, bioRxiv. (2021). doi: https://doi.org/10.1101/2021.08.13.456082 [Submitted for publication]

2. M. De, M.A. Öztürk, S. Isbaner, K. Tóth, R.C. Wade, DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study, Biophysical Journal. (2021). https://doi.org/10.1016/j.bpj.2021.07.012

3. M.A. Öztürk, M. De, V. Cojocaru, R.C. Wade, Chromatosome Structure and Dynamics from Molecular Simulations, Annu. Rev. Phys. Chem. 71 (2020) 101–119. https://doi.org/10.1146/annurev-physchem-071119-040043

4. PDB ID: 5B81. M. De, S. Chatterjee, Bose Institute, Kolkata, India (2016). Novel mismatched DNA that partially preserves thermodynamic properties of canonical B-DNA by staggered base pairing. doi: 10.2210/pdb5b81/pdb.

Awards/Fellowships

  1. 16/11/2018: DKFZ PhD Poster prize and travel grant
  2. 17/02/2018 – 21/02/2018: Travel grant for 62nd Biophysical Society Meeting, San Francisco, USA
  3. 01/11/2016 – 31/10/2019: Helmholtz PhD Fellowship, DKFZ, Heidelberg, Germany
  4. 18/02/2016 – 21/02/2016: Best Student Poster award, 22nd conference of National Magnetic Resonance Society, India
  5. 01/09/2015 – 31/08/2016: CSIR-JRF (NET) scholarship, Bose Institute, Kolkata, India
  6. 01/08/2013 – 21/08/2015: Bose Institute Masters Fellowship, Kolkata, India

Expertise

Experimental

Spectroscopic techniques: single-molecule Förster Resonance Energy Transfer, Fluorescence Correlation, ensemble Absorbance/Fluorescence (incl. anisotropy), Nuclear Magnetic Resonance, Circular dichroism.

Molecular biology: cloning and expressing recombinant proteins in bacterial vectors, Polymerase Chain Reaction, Golden-Gate assembly.

Protein biochemistry: Protein purification and fluorescence labeling using ‘click’ chemistry.

Computational

Structural modeling: normal mode analysis, FRET modeling using FPS, molecular dynamics simulations using AMBER software suite, docking, modeling using UCSF Chimera, PyMol, VMD.

Data analysis: MATLAB, Igor Pro.

Conference organisation

  1. 06/06/2019 – 07/06/2019: Organising committee, 6th Heidelberg Forum for Young Life Scientists, “Zooming Out: from Molecules to Patients”, Heidelberg, Germany.
  2. 03/02/2011 – 04/02/2011: Organising committee: National seminar on “Modern trends in Spectroscopy”, 2011, IACS, Kolkata, India

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