scholarly journals Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

2008 ◽  
Vol 36 (8) ◽  
pp. 2505-2513 ◽  
Author(s):  
Davide Normanno ◽  
Francesco Vanzi ◽  
Francesco Saverio Pavone
Keyword(s):  
Single Molecule ◽  
Lac Repressor ◽  
Dna Looping ◽  
Single Molecule Manipulation

scholarly journals Negative DNA supercoiling tunes protein-mediated looping

2021 ◽  
Author(s):  
Yan Yan ◽  
Wenxuan Xu ◽  
Sandip Kumar ◽  
Alexander Zhang ◽  
Fenfei Leng ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Emergent Behavior ◽  
Dna Looping ◽  
Inherent Feature ◽  
Loop Dynamics ◽  
Negative Supercoiling ◽  
Deterministic Behavior ◽  
Fundamental Mechanism

Protein-mediated DNA looping is a fundamental mechanism of gene regulation. Such loops occur stochastically, and a calibrated response to environmental stimuli would seem to require more deterministic behavior, so experiments were preformed to determine whether additional proteins and/or DNA supercoiling might be definitive. In experiments on DNA looping mediated by the Escherichia coli lac repressor protein, increasing compaction by the nucleoid-associated protein, HU, progressively increased the average looping probability for an ensemble of single molecules. Despite this trend, the looping probabilities associated with individual molecules ranged from 0 to 100 throughout the titration, and observations of a single molecule for an hour or longer were required to observe the statistical looping behavior of the ensemble, ergodicity. Increased negative supercoiling also increased the looping probability for an ensemble of molecules, but the looping probabilities of individual molecules more closely resembled the ensemble average. Furthermore, supercoiling accelerated the loop dynamics such that in as little as twelve minutes of observation most molecules exhibited the looping probability of the ensemble. Notably, this is within the timescale of the doubling time of the bacterium. DNA supercoiling, an inherent feature of genomes across kingdoms, appears to be a fundamental determinant of time-constrained, emergent behavior in otherwise random molecular activity.

Combined single-molecule manipulation and localization for the study of lac Repressor 1D-diffusion along DNA

2013 ◽  
Author(s):  
G. Belcastro ◽  
C. Mónico ◽  
M. Capitanio ◽  
F. Vanzi ◽  
F. S. Pavone
Keyword(s):  
Single Molecule ◽  
Lac Repressor ◽  
Single Molecule Manipulation

scholarly journals In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

2014 ◽  
Vol 10 (2) ◽  
pp. e1003456 ◽  
Author(s):  
Pascal Carrivain ◽  
Maria Barbi ◽  
Jean-Marc Victor
Keyword(s):  
Rigid Body ◽  
Single Molecule ◽  
In Silico ◽  
Rigid Body Dynamics ◽  
Body Dynamics ◽  
Single Molecule Manipulation

scholarly journals New Tool for Single Molecule Manipulation: Optical Pushing

2012 ◽  
Vol 102 (3) ◽  
pp. 385a-386a
Author(s):  
Gerrit Sitters ◽  
Niels Laurens ◽  
Emile J. de Rijk ◽  
Erwin J.G. Peterman ◽  
Gijs J.L. Wuite
Keyword(s):  
Single Molecule ◽  
Single Molecule Manipulation

scholarly journals The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope

2014 ◽  
Vol 5 ◽  
pp. 202-209 ◽  
Author(s):  
Christian Wagner ◽  
Norman Fournier ◽  
F Stefan Tautz ◽  
Ruslan Temirov
Keyword(s):  
Frequency Shift ◽  
Single Molecule ◽  
Oscillation Amplitude ◽  
Surface Corrugation ◽  
Atomic Force ◽  
Data Points ◽  
Atomic Surface ◽  
Tetracarboxylic Dianhydride ◽  
Single Molecule Manipulation

Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule–surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.

scholarly journals Scc2/Nipbl hops between chromosomal cohesin rings after loading

2017 ◽  
Author(s):  
James D.P. Rhodes ◽  
Davide Mazza ◽  
Kim A. Nasmyth ◽  
Stephan Uphoff
Keyword(s):  
Single Molecule ◽  
Sister Chromatid ◽  
Fluorescence Recovery After Photobleaching ◽  
Sister Chromatid Cohesion ◽  
Dna Looping ◽  
Cohesin Complex ◽  
Single Molecule Tracking ◽  
Loading Function ◽  
Stop And Go ◽  
Chromatid Cohesion

AbstractThe cohesin complex mediates DNA-DNA interactions both between (sister chromatid cohesion) and within chromosomes (DNA looping) via a process thought to involve entrapment of DNAs within its tripartite ring. It has been suggested that intra- chromosome loops are generated through processive extrusion of DNAs through the lumen of cohesin’s ring. Scc2 (Nipbl) is essential for loading cohesin onto chromosomes but not for maintaining sister chromatid cohesion following DNA replication. It has therefore been assumed that Scc2 is involved exclusively in the cohesin loading process. However, it is possible that the stimulation of cohesin’s ABC-like ATPase by Scc2 also has a post-loading function, for example driving loop extrusion. Using fluorescence recovery after photobleaching (FRAP) and single-molecule tracking, we show that Scc2 binds dynamically to chromatin, principally through an association with cohesin. Scc2’s movement within chromatin is consistent with a “stop-and-go” or “hopping” motion. We suggest that a low diffusion coefficient, a low stoichiometry relative to cohesin, and a high affinity for chromosomal cohesin enables Scc2 to move rapidly from one chromosomal cohesin complex to another, performing a function distinct from loading.

Sign in / Sign up

Export Citation Format

Share Document