Publications

KEY ARTICLES * corresponding authorship

See also papers we published as contributing authors § equal contribution

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" (submitted)

J. W. Hegge, D. C. Swarts, S. D. Chandradoss, T. J. Cui, J. Kneppers, M. Jinek, C. Joo, J. van der Oost, "DNA-guided DNA cleavage at moderate temperatures by prokaryotic Argonaute" (submitted)

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) (paper)

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)

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)

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

M. Fareh and 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)

JoVE

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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