Prof.dr. Chirlmin Joo

Research Theme(s): Single-molecule biophysics

Research Interests: Single-molecule protein sequencing, Next-generation single-molecule techniques, CRISPR biology, MicroRNA



Chirlmin Joo has advanced single-molecule techniques by innovating new tools including single-molecule multi-color FRET, single-molecule protein pull-down, and single-molecule protein sequencing. he is applying the single-molecule techniques to mechanistic studies of many biological systems. He uses fluorescence in his research and his main research interests are:

  • Mechanistic understanding of biological systems: Joo is deepening the understanding of the mechanistic properties of many proteins and systems, including those in the CRISPR and Argonaute families. His group has unraveled the target search of Argonaute and Cas9 proteins and demonstrated how microRNA biogenesis and CRISPR adaptation work at the single-molecule level.
  • Technique development: He is developing a first-ever massively parallel single-molecule fluorescence method that integrates next-generation DNA sequencing with single-molecule fluorescence. It will allow for genome-wide single molecule kinetic studies of gene regulation (microRNA) and genome engineering (CRISPR)
  • Protein sequencing: Recognizing the need of a platform for highly sensitive protein analysis tool, he is aiming at developing high-resolution single-molecule techniques that can, for the first time, determine protein sequences at the single-molecule level. Using single-molecule fluorescence and nanopores, his team is exploring the biophysics of protein translocation and will utilize it to develop a novel technology to determine the sequence of proteins. The new technologies will be the first to create the opportunity for single-cell proteomics and real-time screening for on-site medical diagnostics.


  • 2019 Human Frontier Science Program - Research Grant ($750k)
  • 2018 ERC Consolidator Grant, 1.8 M euros
  • 2017 NWO-FOM Vrije Programme, 2.3M euros
  • 2015 NWO talent grant Vidi, 800k euros
  • 2012 ERC Starting Grant, 1.5 M euros 


For information regarding current projects and research, visit Joo Lab


Current Projects

For information regarding the current open projects visit Joo Lab.

Highlight Publications

1. Selective loading and processing of prespacers for precise CRISPR adaptation.

Kim S, Loeff L, Colombo S, Jergic S, Brouns SJJ, Joo C.

Nature doi: 10.1038/s41586-020-2018-1


2. Argonaute bypasses cellular obstacles without hindrance during target search

Cui TJ, Klein M, Hegge JW, Chandradoss SD, van der Oost J, Depken M, Joo C.

Nat Commun. 10(1):4390. doi: 10.1038/s41467-019-12415-y


3. Paving the way to single-molecule protein sequencing

Restrepo-Pérez L, Joo C, Dekker C.Nat

Nanotechnol  (9):786-796. doi: 10.1038/s41565-018-0236-6. Epub 2018 Sep 6. Review 


4. Single-molecule peptide fingerprinting.

van Ginkel J, Filius M, Szczepaniak M, Tulinski P, Meyer AS, Joo C.

Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3338-3343. doi: 10.1073/pnas.1707207115. Epub 2018 Mar 12. 

5. A Dynamic Search Process Underlies MicroRNA Targeting.

Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ, Joo C.Cell. 2015 Jul 2;162(1):96-107. doi: 10.1016/j.cell.2015.06.032

Full Professor

Chirlmin Joo

Management Assistant

Tracey de Ruijter