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Page 1
Full-length single-molecule protein fingerprinting.
Filius M, van Wee R, de Lannoy C, Westerlaken I, Li Z, Kim SH, de Agrela Pinto C, Wu Y, Boons GJ, Pabst M, de Ridder D, Joo C. Filius M, et al. Among authors: joo c, kim sh. Nat Nanotechnol. 2024 May;19(5):652-659. doi: 10.1038/s41565-023-01598-7. Epub 2024 Feb 13. Nat Nanotechnol. 2024. PMID: 38351230
Here we demonstrate fluorescence resonance energy transfer (FRET)-based single-molecule protein fingerprinting to map the location of individual amino acids and post-translational modifications within single full-length protein molecules. Our data show that both int …
Here we demonstrate fluorescence resonance energy transfer (FRET)-based single-molecule protein fingerprinting to map the loca …
The emerging landscape of single-molecule protein sequencing technologies.
Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C. Alfaro JA, et al. Among authors: joo c, dekker c, kim sh. Nat Methods. 2021 Jun;18(6):604-617. doi: 10.1038/s41592-021-01143-1. Epub 2021 Jun 7. Nat Methods. 2021. PMID: 34099939 Free PMC article. Review.
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 innovations in mass spectrometry t …
While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here w …
Single-molecule structural and kinetic studies across sequence space.
Severins I, Bastiaanssen C, Kim SH, Simons RB, van Noort J, Joo C. Severins I, et al. Among authors: joo c, kim sh. Science. 2024 Aug 23;385(6711):898-904. doi: 10.1126/science.adn5968. Epub 2024 Aug 22. Science. 2024. PMID: 39172834
At the core of molecular biology lies the intricate interplay between sequence, structure, and function. Single-molecule techniques provide in-depth dynamic insights into structure and function, but laborious assays impede functional screening of large sequence libr …
At the core of molecular biology lies the intricate interplay between sequence, structure, and function. Single-molecule techn …
Single-Molecule View of Small RNA-Guided Target Search and Recognition.
Globyte V, Kim SH, Joo C. Globyte V, et al. Among authors: joo c, kim sh. Annu Rev Biophys. 2018 May 20;47:569-593. doi: 10.1146/annurev-biophys-070317-032923. Epub 2018 Mar 29. Annu Rev Biophys. 2018. PMID: 29595998 Review.
Several proteins achieve that with the help of short RNA strands known as guides. This review focuses on single-molecule advances studying the target search and recognition mechanism of Argonaute and CRISPR (clustered regularly interspaced short palindromic repeats) …
Several proteins achieve that with the help of short RNA strands known as guides. This review focuses on single-molecule advan …
Characterization of Noise in a Single-Molecule Fluorescence Signal.
Lee J, Kim SH, Se T, Kim D. Lee J, et al. Among authors: kim sh, kim d. J Phys Chem B. 2022 Feb 17;126(6):1160-1167. doi: 10.1021/acs.jpcb.1c08621. Epub 2022 Feb 7. J Phys Chem B. 2022. PMID: 35129336
Single-molecule fluorescence experiments allow monitoring of the structural change and dynamics of a single biomolecule in real time using dye molecules attached to the molecule. ...This trend was also followed in the uncertainties of the single-molecule …
Single-molecule fluorescence experiments allow monitoring of the structural change and dynamics of a single biomolecule in rea …
iMAX FRET (Information Maximized FRET) for Multipoint Single-Molecule Structural Analysis.
Joshi BS, de Lannoy C, Howarth MR, Kim SH, Joo C. Joshi BS, et al. Among authors: joo c, kim sh. Nano Lett. 2024 Jul 17;24(28):8487-8494. doi: 10.1021/acs.nanolett.4c00447. Epub 2024 Jul 8. Nano Lett. 2024. PMID: 38975639 Free PMC article.
Understanding the structure of biomolecules is vital for deciphering their roles in biological systems. Single-molecule techniques have emerged as alternatives to conventional ensemble structure analysis methods for uncovering new biology in molecular dynamics and i …
Understanding the structure of biomolecules is vital for deciphering their roles in biological systems. Single-molecule techni …
FRETboard: Semisupervised classification of FRET traces.
de Lannoy CV, Filius M, Kim SH, Joo C, de Ridder D. de Lannoy CV, et al. Among authors: joo c, kim sh. Biophys J. 2021 Aug 17;120(16):3253-3260. doi: 10.1016/j.bpj.2021.06.030. Epub 2021 Jul 6. Biophys J. 2021. PMID: 34237288 Free PMC article.
We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule scenarios and correctly estimate parameters for up to 11 states. On in vitro data, we retrieve parameters identical to those obtained by …
We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule …
Intercalation-Based Single-Molecule Fluorescence Assay To Study DNA Supercoil Dynamics.
Ganji M, Kim SH, van der Torre J, Abbondanzieri E, Dekker C. Ganji M, et al. Among authors: dekker c, kim sh. Nano Lett. 2016 Jul 13;16(7):4699-707. doi: 10.1021/acs.nanolett.6b02213. Epub 2016 Jul 1. Nano Lett. 2016. PMID: 27356180
Here, we report a novel high-throughput single-molecule assay for real-time visualization of supercoiled DNA molecules, named ISD (Intercalation-induced Supercoiling of DNA). ...
Here, we report a novel high-throughput single-molecule assay for real-time visualization of supercoiled DNA molecules, named …
High-Resolution Single-Molecule FRET via DNA eXchange (FRET X).
Filius M, Kim SH, Severins I, Joo C. Filius M, et al. Among authors: joo c, kim sh. Nano Lett. 2021 Apr 14;21(7):3295-3301. doi: 10.1021/acs.nanolett.1c00725. Epub 2021 Mar 19. Nano Lett. 2021. PMID: 33739111 Free PMC article.
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 …
Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only …
DNA sequence encodes the position of DNA supercoils.
Kim SH, Ganji M, Kim E, van der Torre J, Abbondanzieri E, Dekker C. Kim SH, et al. Among authors: dekker c. Elife. 2018 Dec 7;7:e36557. doi: 10.7554/eLife.36557. Elife. 2018. PMID: 30523779 Free PMC article.
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