Searched for: author%3A%22Joo%2C+C.%22
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de Lannoy, C.V. (author), Filius, M. (author), Kim, S.H. (author), Joo, C. (author), de Ridder, Dick (author)
Förster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nanoscale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner but lack the flexibility...
journal article 2021
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Bastiaanssen, C.K.J.M.L. (author), Joo, C. (author)
Transposable elements have both detrimental and beneficial effects on their host genome. Tetrahymena is a unicellular eukaryote that deals with transposable elements in a unique way. It has a separate somatic and germline genome in two nuclei in a single cell. During sexual reproduction, a small RNA directed system compares the germline and...
review 2021
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Balci, Hamza (author), Globyte, V. (author), Joo, C. (author)
Clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, particularly Cas9, have provided unprecedented control on targeting and editing specific DNA sequences. If the target sequences are prone to folding into noncanonical secondary structures, such as G-quadruplex (GQ), the conformational states and...
journal article 2021
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Lerner, Eitan (author), Barth, A. (author), Hendrix, Jelle (author), Ambrose, Benjamin (author), Birkedal, Victoria (author), Blanchard, Scott C. (author), Börner, Richard (author), Joo, C. (author), Lee, Tae Hee (author)
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever- increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs...
review 2021
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Bohländer, P.R. (author), Filius, M. (author), van Kooten, Xander F. (author), Pomorski, A.K. (author), Schmid, S. (author), Dekker, C. (author), Eelkema, R. (author), Kim, S.H. (author), Joo, C. (author)
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside...
review 2021
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Filius, M. (author), Kim, S.H. (author), Severins, I.W.H. (author), Joo, C. (author)
Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object, which makes it difficult to apply single-molecule FRET for structural analysis of biomolecules. Here, we present an approach that allows for the...
journal article 2021
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Loeff, L. (author), Kerssemakers, J.W.J. (author), Joo, C. (author), Dekker, C. (author)
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step...
journal article 2021
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Cnossen, J.P. (author), Cui, Tao Ju (author), Joo, C. (author), Smith, C.S. (author)
Localization microscopy offers resolutions down to a single nanometer but currently requires additional dedicated hardware or fiducial markers to reduce resolution loss from the drift of the sample. Drift estimation without fiducial markers is typically implemented using redundant cross correlation (RCC). We show that RCC has sub-optimal...
journal article 2021
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Filius, M. (author), Cui, T.J. (author), Ananth, A.N. (author), Docter, M.W. (author), Hegge, Jorrit W. (author), van der Oost, John (author), Joo, C. (author)
Super-resolution imaging allows for the visualization of cellular structures on a nanoscale level. DNA-PAINT (DNA point accumulation in nanoscale topology) is a super-resolution method that depends on the binding and unbinding of DNA imager strands. The current DNA-PAINT technique suffers from slow acquisition due to the low binding rate of...
journal article 2020
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Breve, T. (author), Filius, M. (author), Araman, Can (author), van der Helm, M. (author), Hagedoorn, P.L. (author), Joo, C. (author), van Kasteren, Sander I. (author), Eelkema, R. (author)
Supramolecular encapsulation is known to alter chemical properties of guest molecules. We have applied this strategy of molecular encapsulation to temporally control the catalytic activity of a stable copper(I)–carbene catalyst. Encapsulation of the copper(I)–carbene catalyst by the supramolecular host cucurbit[7]uril (CB[7]) resulted in the...
journal article 2020
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Park, Kwang Hyun (author), Kim, S. (author), Lee, Su Jin (author), Cho, Jee Eun (author), Patil, Vinod Vikas (author), Dumbrepatil, Arti Baban (author), Song, Hyung Nam (author), Ahn, Woo Chan (author), Joo, C. (author)
The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA<sup>+</sup> ATPase family. Even though it was discovered more than two decades ago and has been widely used for aromatic hydrocarbon sensing, the activation mechanism of DmpR has remained elusive. Here, we show that phenol-bound...
journal article 2020
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Hegge, Jorrit W. (author), Swarts, Daan C. (author), Chandradoss, S.D. (author), Cui, T.J. (author), Kneppers, Jeroen (author), Jinek, Martin (author), Joo, C. (author), van der Oost, John (author)
Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated...
journal article 2019
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Restrepo Perez, L. (author), Huang, Gang (author), Bohländer, Peggy R. (author), Worp, N.M. (author), Eelkema, R. (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author)
While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in...
journal article 2019
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Cui, T.J. (author), Joo, C. (author)
Argonaute (Ago) proteins are of key importance in many cellular processes. In eukaryotes, Ago can induce translational repression followed by deadenylation and degradation of mRNA molecules through base pairing of microRNAs (miRNAs) with a complementary target on a mRNA sequence. In bacteria, Ago eliminates foreign DNA through base pairing of...
review 2019
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Cui, Thijs (author), Klein, M. (author), Hegge, Jorrit W. (author), Chandradoss, S.D. (author), van der Oost, John (author), Depken, S.M. (author), Joo, C. (author)
Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its complementary target sequences for specificity. To efficiently scan nucleic-acid chains for targets, Ago diffuses...
journal article 2019
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Zhao, Shidi (author), Restrepo Perez, L. (author), Soskine, Misha (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author), Aksimentiev, A. (author)
Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations....
journal article 2019
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Restrepo Perez, L. (author), Wong, C.H. (author), Maglia, Giovanni (author), Dekker, C. (author), Joo, C. (author)
Post-translational modifications (PTMs) of proteins play key roles in cellular processes. Hence, PTM identification is crucial for elucidating the mechanism of complex cellular processes and disease. Here we present a method for PTM detection at the single-molecule level using FraC biological nanopores. We focus on two major PTMs,...
journal article 2019
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Fareh, M. (author), van Lopik, J. (author), Katechis, I. (author), Bronkhorst, Alfred W. (author), van Eijkeren-Haagsma, A.C. (author), Van Rij, Ronald P. (author), Joo, C. (author)
RNA interference (RNAi) is an indispensable mechanism for antiviral defense in insects, including mosquitoes that transmit human diseases. To escape this antiviral defense system, viruses encode suppressors of RNAi that prevent elimination of viral RNAs, and thus ensure efficient virus accumulation. Although the first animal Viral Suppressor...
journal article 2018
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Restrepo Perez, L. (author), Joo, C. (author), Dekker, C. (author)
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example,...
review 2018
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Kim, S.H. (author), Ahn, Tak Kyoon (author), Cui, T.J. (author), Chauhan, S. (author), Sung, Jaeyoung (author), Joo, C. (author), Kim, Doseok (author)
At the core of homologous DNA repair, RecA catalyzes the strand exchange reaction. This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster grows to cover the single-stranded DNA but may leave 1- to 2-nucleotide (nt) gaps between the clusters due to three different...
journal article 2017
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