Professor Mark D Szczelkun

B.Sc.(Liv.), Ph.D.(Soton)

  • BS8 1TD


Research output per year

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Personal profile

Research interests

The research focus of the group is the mechanistic analysis of DNA recognition and cleavage by prokaryotic defence systems such as Restriction-Modification and CRISPR. These enzymes protect bacteria from bacteriophages and thus moderate horizontal gene transfer. In addition, they are also important as the basis of many lab tools for manipulating DNA, such as the emergent genome editing technologies.

We use a dual experimental approach to studying DNA-protein interactions – combining single molecule microscopy with ensemble biochemistry, the latter including millisecond time-resolution rapid-mixing fluorescence spectroscopy, molecular biology and protein chemistry. More recently we have established collaborations to extend our studies to human cell culture.

DNA cleavage mechanisms in Restriction-Modification 

We have focussed our research efforts on Restriction-Modification enzymes that use ATP-dependent protein machines to evade virus infection, addressing how these "molecular motors" convert chemical energy into mechanical events that lead to DNA cleavage. We have been able to demonstrate alternative properties of the helicase-like motor domains of these enzymes, including dsDNA translocation or molecular switching. These activities allow the enzymes to interact with sites that are distant along a phage genome. We aim to understand the diversity of these mechanisms, and their potential fitness costs to the bacteria.

The CRISPR/Cas effector nucleases

The Clustered, Regularly Interspaced, Short Palindromic Repeats (CRISPR) and the CRISPR-associated (cas) genes comprise an adaptive immune system in bacteria and archaea.  Silencing of foreign nucleic acids by CRISPR/Cas systems relies on a small CRISPR RNA (crRNA), the latter derived by processing transcribed CRISPR repeat-spacer arrays. We have developed a single molecule assay that allows the crRNA-guided recognition of specific DNA sequences to be followed in real time. Understanding how CRISPR/Cas systems achieve specificity will be particularly important in the manipulation of these proteins as tools for genome surgery, where specificity is paramount. We are also adapting the CRISPR/Cas systems for use as gene editing or targeting tools in human mitochondria.


  • Nucleases, DNA cleavage mechanisms
  • Restriction-Modification
  • Helicases, molecular motors, ATPases
  • Phage avoidance strategies
  • Single molecule microscopy, magnetic and optical tweezers
  • Stopped flow fluorescence
  • Enzymology, kinetics
  • Modelling of kinetic data

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Research Output

  • 68 Article (Academic Journal)
  • 4 Chapter in a book
  • 1 Conference Contribution (Conference Proceeding)
  • 1 Comment/debate (Academic Journal)

Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes

Chand, M. K., Nirwan, N., Diffin, F. M., van Aelst, K., Kulkarni, M., Pernstich, C., Szczelkun, M. D. & Saikrishnan, K., 20 Oct 2015, In : Nature Chemical Biology. 11, p. 870-877 10 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
  • 9 Citations (Scopus)
    903 Downloads (Pure)

    Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

    Szczelkun, M. D., Tikhomirova, M. S., Sinkunas, T., Gasiunas, G., Karvelis, T., Pschera, P., Siksnys, V. & Seidel, R., 8 Jul 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 27, p. 9798-9803 6 p.

    Research output: Contribution to journalArticle (Academic Journal)

  • 195 Citations (Scopus)
    39 Downloads (Pure)

    The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA

    Schwarz, F. W., Tóth, J., van Aelst, K., Cui, G., Clausing, S., Szczelkun, M. D. & Seidel, R., 19 Apr 2013, In : Science. 340, 6130, p. 353-6 4 p.

    Research output: Contribution to journalArticle (Academic Journal)

  • 45 Citations (Scopus)


    British Biophysical Society Young Investigator Award

    Szczelkun, Mark D (Recipient), 2004

    Prize: Prizes, Medals, Awards and Grants

  • Mrs. Joyful Prize for Rafia Work

    Szczelkun, Mark D (Recipient), 1953

    Prize: Prizes, Medals, Awards and Grants

    Supervised Work

    The Engineering and Evaluation of Genome Editing Tools in Mitochondria

    Author: Mullally, G., 23 Jan 2019

    Supervisor: Szczelkun, M. (Supervisor) & Lane, J. (Supervisor)

    Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)