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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 …
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
However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack of convenient experimental tools to probe these phenomena. Here, we report a novel high-throughput single-molecule assay for re …
However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack o …
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.
RecA filament maintains structural integrity using ATP-driven internal dynamics.
Kim SH, Ahn T, Cui TJ, Chauhan S, Sung J, Joo C, Kim D. Kim SH, et al. Among authors: joo c, kim d. Sci Adv. 2017 Sep 6;3(9):e1700676. doi: 10.1126/sciadv.1700676. eCollection 2017 Sep. Sci Adv. 2017. PMID: 28913424 Free PMC article.
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 structur …
This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster g …
CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly.
Kim SH, Vlijm R, van der Torre J, Dalal Y, Dekker C. Kim SH, et al. Among authors: dekker c. PLoS One. 2016 Nov 7;11(11):e0165078. doi: 10.1371/journal.pone.0165078. eCollection 2016. PLoS One. 2016. PMID: 27820823 Free PMC article.
Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequences, to varying amounts of applied force by using single-molecule magnetic tweezers. We monitor individual disassembly events of …
Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequence …
Dynamic growth and shrinkage govern the pH dependence of RecA filament stability.
Kim SH, Park J, Joo C, Kim D, Ha T. Kim SH, et al. Among authors: joo c, kim d. PLoS One. 2015 Jan 21;10(1):e0115611. doi: 10.1371/journal.pone.0115611. eCollection 2015. PLoS One. 2015. PMID: 25608006 Free PMC article.
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 …
RecA proteins form a long stable filament on a single-stranded DNA and catalyze strand exchange reaction. The stability of RecA filam …
Molecular mechanism of sequence-dependent stability of RecA filament.
Kim SH, Joo C, Ha T, Kim D. Kim SH, et al. Among authors: joo c, kim d. Nucleic Acids Res. 2013 Sep;41(16):7738-44. doi: 10.1093/nar/gkt570. Epub 2013 Jun 26. Nucleic Acids Res. 2013. PMID: 23804763 Free PMC article.
RecA 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 patter …
RecA is a DNA-dependent ATPase and mediates homologous recombination by first forming a filament on a single-stranded (ss) DNA. RecA …
Cooperative conformational transitions keep RecA filament active during ATPase cycle.
Kim SH, Ragunathan K, Park J, Joo C, Kim D, Ha T. Kim SH, et al. Among authors: joo c, kim d. J Am Chem Soc. 2014 Oct 22;136(42):14796-800. doi: 10.1021/ja506363y. Epub 2014 Oct 7. J Am Chem Soc. 2014. PMID: 25252114 Free PMC article.
The active, stretched conformation of the RecA filament bound to single-stranded DNA is required for homologous recombination. During this process, the RecA filament mediates the homology search and base pair exchange with a complementary sequence. ...Little is known about …
The active, stretched conformation of the RecA filament bound to single-stranded DNA is required for homologous recombination. During …
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 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 …
While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet estab …
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 F
Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only
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