Publications


KEY ARTICLES                                                                                                                                          
* corresponding authorship
See also papers we published as contributing authors                                                                     
§ equal contribution

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



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

CRISPR memory update



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)
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)

SDS-coated Titin dimer translocation



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

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)


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)

JoVE



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

Springer

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

Protein Fingerprinting


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