scholarly journals Role of the ribosomal protein L27 revealed by single-molecule FRET study

2012 ◽  
Vol 21 (11) ◽  
pp. 1696-1704 ◽  
Author(s):  
Yuhong Wang ◽  
Ming Xiao
Keyword(s):  
Ribosomal Protein ◽  
Single Molecule ◽  
Single Molecule Fret

scholarly journals Single Molecule FRET Studies of RNA Tertiary Folding: Elucidating the Thermodynamic and Kinetic Role of Na+ Cations

2010 ◽  
Vol 98 (3) ◽  
pp. 471a
Author(s):  
Erik D. Holmstrom ◽  
Julie L. Fiore ◽  
David Nesbitt
Keyword(s):  
Single Molecule ◽  
Single Molecule Fret ◽  
Tertiary Folding

scholarly journals Role of the primer activation signal in tRNA annealing onto the HIV-1 genome studied by single-molecule FRET microscopy

RNA ◽  
2013 ◽  
Vol 19 (4) ◽  
pp. 517-526 ◽  
Author(s):  
N. Beerens ◽  
M. D. E. Jepsen ◽  
V. Nechyporuk-Zloy ◽  
A. C. Kruger ◽  
J.-L. Darlix ◽  
...  
Keyword(s):  
Single Molecule ◽  
Single Molecule Fret ◽  
Hiv 1

scholarly journals ATAD5 promotes replication restart by regulating RAD51 and PCNA in response to replication stress

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Su Hyung Park ◽  
Nalae Kang ◽  
Eunho Song ◽  
Minwoo Wie ◽  
Eun A. Lee ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Interactions ◽  
Cultured Cells ◽  
Replication Stress ◽  
Dependent Manner ◽  
Dna Breaks ◽  
Single Molecule Fret ◽  
Hydroxyurea Treatment ◽  
Fork Regression

AbstractMaintaining stability of replication forks is important for genomic integrity. However, it is not clear how replisome proteins contribute to fork stability under replication stress. Here, we report that ATAD5, a PCNA unloader, plays multiple functions at stalled forks including promoting its restart. ATAD5 depletion increases genomic instability upon hydroxyurea treatment in cultured cells and mice. ATAD5 recruits RAD51 to stalled forks in an ATR kinase-dependent manner by hydroxyurea-enhanced protein-protein interactions and timely removes PCNA from stalled forks for RAD51 recruitment. Consistent with the role of RAD51 in fork regression, ATAD5 depletion inhibits slowdown of fork progression and native 5-bromo-2ʹ-deoxyuridine signal induced by hydroxyurea. Single-molecule FRET showed that PCNA itself acts as a mechanical barrier to fork regression. Consequently, DNA breaks required for fork restart are reduced by ATAD5 depletion. Collectively, our results suggest an important role of ATAD5 in maintaining genome integrity during replication stress.

scholarly journals Real-time observation of flexible domain movements in Cas9

2017 ◽  
Author(s):  
Saki Osuka ◽  
Kazushi Isomura ◽  
Shohei Kajimoto ◽  
Tomotaka Komori ◽  
Hiroshi Nishimasu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Cleavage ◽  
Potential Role ◽  
Domain Architecture ◽  
Guide Rna ◽  
Single Molecule Fret ◽  
Target Dna ◽  
Time Observation ◽  
Real Time Observation

ABSTRACTThe CRISPR-associated protein Cas9 is a widely used genome editing tool that recognizes and cleaves target DNA through the assistance of a single-guide RNA (sgRNA). Structural studies have demonstrated the multi-domain architecture of Cas9 and sequential domain movements upon binding to the sgRNA and the target DNA. These studies also hinted at the flexibility between domains, but whether these flexible movements occur in solution is unclear. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single-molecule FRET. The flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures. Importantly, the HNH nuclease domain in Cas9 only accessed the DNA cleavage position during such flexible movements, suggesting the importance of this flexibility in the DNA cleavage process. Our FRET data also revealed the conformational flexibility of apo-Cas9, which may play a role in the assembly with the sgRNA. Collectively, our results highlight the potential role of domain fluctuations in driving Cas9-catalyzed DNA cleavage.

scholarly journals Decoupling the bridge helix of Cas12a results in a reduced trimming activity and impaired conformational transitions

2021 ◽  
Author(s):  
Elisabeth Wörle ◽  
Leonhard Jakob ◽  
Andreas Schmidbauer ◽  
Gabriel Zinner ◽  
Dina Grohmann
Keyword(s):  
Single Molecule ◽  
Conformational Transitions ◽  
Structural Element ◽  
Francisella Novicida ◽  
Closed State ◽  
Single Molecule Fret ◽  
Type V ◽  
Single Effector ◽  
Cas Proteins

AbstractThe widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by a central structural element, the so-called bridge helix (BH). We generated BH mutants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility of Francisella novicida Cas12a. We demonstrate that the BH impacts the trimming activity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. Single-molecule FRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH mutants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH mutants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.

The localized electron: magnetic properties

2018 ◽  
Author(s):  
Jean-Pierre Launay ◽  
Michel Verdaguer
Keyword(s):  
Single Molecule ◽  
Model Systems ◽  
Ferromagnetic Coupling ◽  
Single Chain ◽  
Single Molecule Magnets ◽  
Magnetic Systems ◽  
Orbital Interactions ◽  
Prussian Blue Analogues ◽  
Mononuclear Complexes

After preliminaries about electron properties, and definitions in magnetism, one treats the magnetism of mononuclear complexes, in particular spin cross-over, showing the role of cooperativity and the sensitivity to external perturbations. Orbital interactions and exchange interaction are explained in binuclear model systems, using orbital overlap and orthogonality concepts to explain antiferromagnetic or ferromagnetic coupling. The phenomenologically useful Spin Hamiltonian is defined. The concepts are then applied to extended molecular magnetic systems, leading to molecular magnetic materials of various dimensionalities exhibiting bulk ferro- or ferrimagnetism. An illustration is provided by Prussian Blue analogues. Magnetic anisotropy is introduced. It is shown that in some cases, a slow relaxation of magnetization arises and gives rise to appealing single-ion magnets, single-molecule magnets or single-chain magnets, a route to store information at the molecular level.

scholarly journals Encoding Multiple Virtual Signals in DNA Barcodes with Single-Molecule FRET

Nano Letters ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1694-1701 ◽  
Author(s):  
Sung Hyun Kim ◽  
Hyunwoo Kim ◽  
Hawoong Jeong ◽  
Tae-Young Yoon
Keyword(s):  
Single Molecule ◽  
Dna Barcodes ◽  
Single Molecule Fret

Single-Molecule FRET-Based Dynamic DNA Sensor

ACS Sensors ◽  
2021 ◽  
Author(s):  
Anoja Megalathan ◽  
Kalani M. Wijesinghe ◽  
Soma Dhakal
Keyword(s):  
Single Molecule ◽  
Dna Sensor ◽  
Single Molecule Fret
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