Publications

* corresponding authorship

§ equal contribution

I. Severins*, J. van Noort, C. Joo "Point set registration for combining fluorescence microscopy methods" (BioRxiv)

S. Kim*, Y.-G. Choi, K. Janssen, C. Bull, B. S. Joshi, A. Pomorski, V. Raz, M. E. Tanenbaum, P. Miesen*, Z. Li*, C. Joo* "N-glycosylated molecules act as a co-precipitant in RNA purification" (BioRxiv)

D. H. Shin, S. H. Kim, K. Coshic, K. Watanabe, T. Taniguchi, G. Verbiest, S. Caneva, A. Aksimentiev, P. G. Steeneken*, C. Joo* "Diffusion of DNA on Atomically Flat 2D Material Surfaces (BioRxiv)

C. Bastiaanssen§, P. B. Ugarte§, K. Kim§, Y. Feng§, G. Finocchio§, T. A. Anzelon, S. Köstlbacher, D. C. Tamarit, T. J. G. Ettema, M. Jinek, I. J. MacRae, C. Joo*, D. C. Swarts*, F. Wu* "RNA-guided RNA silencing by an Asgard archaeal Argonaute" Nature Communications (open access) (BioRxiv)

B. Joshi, C. V. de Lannoy, M. Howarth, S. H. Kim*, C. Joo*, "iMAX FRET (Information Maximized FRET) for multipoint single-molecule structural analysis" Nano Letters (open access) (BioRxiv)

M. Filius, R. van Wee§, C. V. de Lannoy§, I. Westerlaken, Z. Li,  S. H. Kim, C. de Agrela Pinto, Y. Wu,  G.-J. Boons, M. Pabst, D. de Ridder, C. Joo*, "Full-Length Single-Molecule Protein Fingerprinting" Nature Nanotechnology (2024) (web, pdf) (BioRxiv) (behind the paper)

News and View: Topographic fingerprinting of single proteins and proteoforms (Nature Nanotechnology)

I. Severins, C. Joo*, J. van Noort*, "Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics", Molecular Cell (2022) (green open access)

C. Joo, A. Meller, "Leaders of the field: What does the future hold for single-molecule technology", iScience (2021) (open access)

C. de Lannoy, M. Filius, R. van Wee, C. Joo*, D. de Ridder*, "Evaluation of FRET X for Single-Molecule Protein Fingerprinting", iScience (2021) (open access)

C. de Lannoy, M. Filius, S. H. Kim, C. Joo, D. de Ridder, "FRETboard: semi-supervised classification of FRET traces", Biophysical Journal (2021) (pdf) (BioRxiv) (manual)

R. van Wee, M. Filius, C. Joo*, "Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging", Trends in Biochemical Sciences (2021) (PDF)

J. Alfaro*, ... , A. Meller*, C. Joo*, "The emerging landscape of single-molecule protein sequencing technologies" Nature Methods (2021) (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 (2021) (open access)

H. Balci*, V. Globyte, C. Joo*, "Targeting G-quadruplex Forming Sequences with Cas9", ACS Chemical Biology  (2021) (open access)

M. Filius, S. H. Kim, I. Severins, C. Joo*, "High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)", Nano Letters (2021) (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. Jergic, 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)

News and View: Cas9 slide‐and‐seek for phage defense and genome engineering (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)

c7nr02450a4.mpg

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

M. Filius, R. van Wee, C. Joo, "Single-Molecule FRET X" Methods in Molecular Biology 2694:203-213 (2024)

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)

50549_JOO_Low.mov

Book

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

Springer

Patents

C. Joo, M. Filius, R. G. van Wee, "Single-molecule aptamer FRET for protein identification and structural analysis", WO2024049290

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