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Filius, M. (author), van Wee, R.G. (author), de Lannoy, C.V. (author), Westerlaken, I. (author), Li, Zeshi (author), Kim, S.H. (author), de Agrela Pinto, C. (author), Wu, Yunfei (author), Boons, Geert-Jan (author), Pabst, Martin (author), de Ridder, Dick (author), Joo, C. (author)
Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and...
journal article 2024
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Kim, S.H. (author), Severins, I.W.H. (author), Brandenburg, Frank (author), Bastiaanssen, C.K.J.M.L. (author), Joo, C. (author)
journal article 2023
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Shin, D. (author), Kim, Hakseong (author), Kim, S.H. (author), Cheong, Hyeonsik (author), Steeneken, P.G. (author), Joo, C. (author), Lee, Sang Wook (author)
The inherent properties of 2D materials—light mass, high out-of-plane flexibility, and large surface area—promise great potential for precise and accurate nanomechanical mass sensing, but their application is often hampered by surface contamination. Here we demonstrate a tri-layer graphene nanomechanical resonant mass sensor with sub-attogram...
journal article 2023
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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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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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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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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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Kim, B. (author), Ha, M. (author), Loeff, L. (author), Chang, H. (author), Simanshu, D.K. (author), Li, S. (author), Fareh, M. (author), Patel, D.J. (author), Joo, C. (author), Kim, V.N. (author)
Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the...
journal article 2015
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Kim, T.J. (author), Joo, C. (author), Seong, J. (author), Vafabakhsh, R. (author), Botvinick, E.L. (author), Berns, M.W. (author), Palmer, A.E. (author), Wang, N. (author), Ha, T. (author), Jakobsson, E. (author), Sun, J. (author), Wang, Y. (author)
It is unclear that how subcellular organelles respond to external mechanical stimuli. Here, we investigated the molecular mechanisms by which mechanical force regulates Ca2+ signaling at endoplasmic reticulum (ER) in human mesenchymal stem cells. Without extracellular Ca2+, ER Ca2+ release is the source of intracellular Ca2+ oscillations induced...
journal article 2015
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Kim, S.H. (author), Park, J. (author), Joo, C. (author), Kim, D. (author), Ha, T. (author)
RecA proteins form a long stable filament on a single-stranded DNA and catalyze strand exchange reaction. The stability of RecA filament changes dramatically with pH, yet its detailed mechanism is not known. Here, using a single molecule assay, we determined the binding and dissociation rates of RecA monomers at the filament ends at various pH....
journal article 2015
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Kim, SH (author), Joo, C. (author), Seong, A (author), Vafabakshsh, A (author), Botvinick, A (author), Berns, A (author), Palmer, TA (author), Wang, Z. (author), Ha, Seungkyu (author), Jakobsson, ME (author), Sun, M (author)
It is unclear that how subcellular organelles respond to external mechanical stimuli. Here, we investigated the molecular mechanisms by which mechanical force regulates Ca2+ signaling at endoplasmic reticulum (ER) in human mesenchymal stem cells. Without extracellular Ca2+, ER Ca2+ release is the source of intracellular Ca2+ oscillations induced...
journal article 2015
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Kim, S.H. (author), Joo, C. (author), Ha, T. (author), Kim, D. (author)
A is a DNA-dependent ATPase and mediates homologous recombination by first forming a filament on a single-stranded (ss) DNA. RecA binds preferentially to TGG repeat sequence, which resembles the recombination hot spot Chi (5'-GCTGGTGG-3') and is the most frequent pattern (GTG) of the codon usage in Escherichia coli. Because of the highly dynamic...
journal article 2013
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