Publications

* corresponding authorship

§ equal contribution

J. Alfaro*, ... , A. Meller*, C. Joo*, "The emerging landscape of single-molecule protein sequencing technologies" Nature Methods (free access)

L. Loeff, J. W. J. Kerssemakers, C. Joo*, C. Dekker*, "AutoStepfinder: a fast and automated step detection method for single-molecule analysis" Patterns (open access)

H. Balci*, V. Globyte, C. Joo*, "Targeting G-quadruplex Forming Sequences with Cas9", ACS Chemical Biology (open access)

M. Filius, S. H. Kim, I. Severins, C. Joo*, "High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)", Nano Letters (BioRxiv, open access)

M. Klein, T. J. Cui, I. MacRae, C. Joo*, M. Depken*, "Skipping and sliding to optimize target search on protein-bound DNA and RNA", (BioRxiv)


C. Bastiaanssen and C. Joo*, "Small RNA-directed DNA elimination: the molecular mechanism and its potential for genome editing", RNA Biology (2021) (open access)

K. H. Park§ , S. Kim§ , S. J. Lee, J. E. Cho, V. V. Patil, A. B. D., H. N. Song, W. C. Ahn, C. Joo* , S. G. Lee, V. Shingler, E. J Woo* "Tetrameric architecture of phenol-bound DmpR, a single-component AAA+ ATPase transcriptional regulator", Nature Communications (2020) (open access)

M. Filius§, T. J. Cui§, A. N. Ananth, M. W. Docter, J. W. Hegge, J. van der Oost, C. Joo*, "High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT" Nano Letters (2020) (open access)

S. Kim§,*, L. Loeff§, S. Colombo, S. J.J. Brouns, C Joo*, "Selective prespacer processing ensures precise CRISPR-Cas adaptation" Nature (2020) (BioRxiv, open access) (animation)

- Featured content for Nobel Prize in Chemistry 2020
- Highlighted in CORDIS
- Highlighted in The CRISPR Journal
- News in TU Delft

L. Restrepo-Pérez, C. H. Wong, G. Maglia, C. Dekker*, C. Joo*, "Label-free detection of post-translational modifications with a nanopore" Nano Letters (2019) (open access)

T. J. Cui, M. Klein, J. W. Hegge, S. D. Chandradoss, J. van der Oost, M. Depken*, C. Joo*, "Argonaute bypasses cellular obstacles without hindrance during target search" Nature Communications (2019) (BioRxiv, open access)

L. Restrepo-Pérez, G. Huang, P. Bohländer, N. Worp, R. Eelkema, G. Maglia, C. Joo*, C. Dekker* "Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore" ACS Nano (2019) (open access)

T. J. Cui, C. Joo*, "Facilitated diffusion of Argonaute-mediated target search" RNA Biology (2019) (free access)

- Editorial in RNA Biology

L. Loeff, C. Joo*, "Biophysics of RNA-guided CRISPR immunity", Springer, (2019) (book chapter)

S. Zhao§, L. Restrepo-Pérez§, M. Soskine, G. Maglia, C. Joo*, C, Dekker*, A. Aksimentiev*, "Electro-mechanical conductance modulation of a nanopore using a removable gate" ACS Nano (2019) (open access)

V. Globyte§, S. H. Lee§, T. Bae, J.-S. Kim*, C. Joo*, "CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion" EMBO Journal (2018) (paper) (bioRxiv)

- Highlighted in EMBO Journal

I. Severins§, M. Szczepaniak§*, C. Joo* "Multiplex single-molecule DNA barcoding using an oligonucleotide ligation assay" Biophysical Journal (2018) (paper) (bioRxiv)

L. Restrepo-Pérez, C. Joo*, C. Dekker* "Paving the way to single-molecule protein sequencing" Nature Nanotechnology (2018) (paper) (open access)

V. Globyte, S. H. Kim, C. Joo*, "Single-molecule view of small RNA-guided target search and recognition" Annual Review of Biophysics (2018) (open access)

L. Loeff, S. J. J. Brouns*, C. Joo* "Repetitive DNA reeling by the Cascade-Cas3 complex in nucleotide unwinding steps" Molecular Cell (2018) (paper) (bioRxiv)

- News in TU Delft (Cas3: a fishing rod and a shredder rolled into one)

J. van Ginkel, M. Filius, M. Szczepaniak , P. Tulinski , A. S. Meyer*, C. Joo* "Single-molecule peptide fingerprinting" Proceedings of the National Academy of Sciences (2018) (paper) (bioRxiv) (YouTube)

- Comment by Nature Biotechnology

M. Fareh, J. van Lopik, I. Katechis, A. W. Bronkhorst, A. C. Haagsma, R. P. van Rij*, C. Joo* "Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA" Nucleic Acids Research (2017) (open access)

Figure from http://blog.healthgenie.in/

S. M. Klum§, S. D. Chandradoss§, N. T. Schirle, C. Joo*, I. J. MacRae* "Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition" EMBO Journal (2017) (open access)

L. Restrepo-Pérez§, S. John§, A. Aksimentiev*, C. Joo*, C. Dekker*, "SDS-assisted protein transport through solid-state nanopores" Nanoscale (2017) (open access) (simulations)

D. C. Swarts§, M. Szczepaniak§, G. Sheng§, S. D. Chandradoss, Y. Zhu, E. M. Timmers, Y. Zhang, J. Lou, Y. Wang*,C. Joo*, & J. van der Oost* "Autonomous generation and loading of DNA guides by bacterial Argonaute" Molecular Cell (2017) (paper) (PMC free text)

- Highlight in Molecular Cell

M. Klein§, S. D. Chandradoss§, M. Depken*, C. Joo* "Why Argonaute is needed to make microRNA target search fast and reliable" Seminars in Cell & Developmental Biology (2017) (open access)

M. Fareh, K. H. Yeom, A. C. Haagsma, S. Chauhan, I. Heo, & C. Joo* "TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments" Nature Communications 7:13694 (2016) (open access)

N. T. Schirle, J. Sheu-Gruttadauria, S. D. Chandradoss, C. Joo*, & I. J. MacRae* “Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.” eLife 4:e07646 (2015) (open access)

Y. Yao, M. Docter, J. van Ginkel, D. de Ridder*, & C. Joo* "Single-molecule protein sequencing through fingerprinting: computational assessment" Physical Biology, 12(5):055003 (2015) (open access) (data)

S. D. Chandradoss, N. T. Schirle§, M. Szczepaniak§, I. J. MacRae*, & C. Joo* “A dynamic search process underlies microRNA targeting” Cell, 162(1):96-107 (2015) (paper) (PMC free text)

- Highlight in Molecular Cell

B. Kim§, M. Ha§, L. Loeff§, H. Chang, D. K. Simanshu, S. Li, M. Fareh, D. J. Patel, C. Joo*, & V. N. Kim* "TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms" EMBO Journal, 34(13):1801-15 (2015) (open access)

T. R. Blosser§, L. Loeff§, E. R. Westra, M. Vlot, T. Kunne, M. Sobota, C. Dekker, S. J. J. Brouns*, & C. Joo* "Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex" Molecular Cell, 58(1):50-60 (2015) (paper) (PMC free text)

C. Joo*, M. Fareh, V. N. Kim "Bringing single-molecule spectroscopy to macromolecular protein complexes" Trends in Biochemical Sciences, 38(1):30-37 (2013) (paper) (PMC free text)

K. H. Yeom, I. Heo, J. Lee, S. Hohng, V. N. Kim*, & C. Joo*, "Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation" EMBO Reports, 12, 690-696 (2011) (paper) (PMC free text)

Key Protocols

See also protocols we published as contributing authors

V. Globyte & C. Joo*, “Single-molecule FRET studies of Cas9 endonuclease” Methods in Enzymology, 616:313-335 (2019)

M. Fareh & C. Joo "Probing RNA-Protein Interactions with Single-Molecule Pull-Down Assays" Methods in Molecular Biology, 1814:267-285 (2018) (PDF)

M. Fareh, L. Loeff, M. Szczepaniak, A. C. Haagsma, K. H. Yeom, C. Joo* "Single-molecule pull-down for investigating protein—nucleic acid interactions" Methods, 105:99-108 (2016) (PDF) (PMC free text)

- Published in a special series of Single-molecule probing by fluorescence and force detection

S. D. Chandradoss, A. C. Haagsma, Y. K. Lee, J. H. Hwang, J. M. Nam, & C. Joo* "Surface passivation for single-molecule protein studies" Journal of Visualized Experiments, (86), e50549, doi:10.3791/50549 (2014) (open access)

Book

C. Joo and D. Rueda, “Biophysics of RNA-Protein Interactions: A Mechanistic View” Springer, 2019 (online)

Springer

Patents

C. Joo, M. Filius, C. de Lannoy, D. de Ridder, "Single-molecule FRET for protein characterization", WO2021049940

L. Restrepo-Pérez, C. Dekker, C. Joo, "Protein current trace signal acquisition using a nanopore", NL2023062

C. Joo, C. Dekker, H. G. T. M. van Ginkel, A. S. Meyer, "Single-molecule protein sequencing", WO2014014347