Facilitating target search in polymer networks: Effects of target size and mixed one-dimensional and three-dimensional diffusion

2021 ◽  
Vol 103 (3) ◽  
Author(s):  
Xiao Xu ◽  
Won Kyu Kim ◽  
Joachim Dzubiella
Keyword(s):  
Polymer Networks ◽  
Three Dimensional ◽  
Target Size ◽  
Target Search ◽  
One Dimensional ◽  
Dimensional Diffusion

scholarly journals Nonspecific interactions between SpCas9 and dsDNA sites located downstream of the PAM mediate facilitated diffusion to accelerate target search

2021 ◽  
Vol 12 (38) ◽  
pp. 12776-12784
Author(s):  
Mengyi Yang ◽  
Ruirui Sun ◽  
Pujuan Deng ◽  
Yuzhuo Yang ◽  
Wenjuan Wang ◽  
...  
Keyword(s):  
Facilitated Diffusion ◽  
Target Search ◽  
One Dimensional ◽  
Dimensional Diffusion ◽  
Nonspecific Interactions

Nonspecific interactions between DNA ∼8 bp downstream of the PAM and lysines within residues 1151–1156 of Cas9 mediate one-dimensional diffusion and cause asymmetric target search regions flanking the PAM.

scholarly journals PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1

2017 ◽  
Vol 45 (22) ◽  
pp. 12834-12847 ◽  
Author(s):  
Lili Liu ◽  
Muwen Kong ◽  
Natalie R. Gassman ◽  
Bret D. Freudenthal ◽  
Rajendra Prasad ◽  
...  
Keyword(s):  
Dna Damage ◽  
Three Dimensional ◽  
One Dimensional ◽  
Dimensional Diffusion

scholarly journals Streptococcus pyogenes Cas9 displays biased one-dimensional diffusion on dsDNA to search for a target

2019 ◽  
Author(s):  
Mengyi Yang ◽  
Lijingyao Zhang ◽  
Ruirui Sun ◽  
Weixiong Zhong ◽  
Yuzhuo Yang ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Single Molecule ◽  
Diffusion Length ◽  
Three Dimensional ◽  
Ionic Concentration ◽  
One Dimensional ◽  
Dimensional Diffusion ◽  
Target Strand

AbstractThe RNA-guided Streptococcus pyogenes Cas9 (spCas9) is a sequence-specific DNA endonuclease that works as one of the most powerful genetic editing tools. However, how the Cas9 locates its target among huge amounts of dsDNAs remains controversial. Here, combining biochemical and single-molecule assays, we revealed that Cas9 uses both three-dimensional and one-dimensional diffusion to find its target. We further observed a surprising biased one-dimensional diffusion of Cas9 from 3’ to 5’ end of the non-target strand under physiological salt condition, whereas low ionic concentration or mutations on PAM recognition residues induce unbiased one-dimensional diffusion of Cas9 along dsDNA. We quantified the diffusion length of 27 bp, which accelerates the target search efficiency of Cas9 by ∼ 10 folds. Our results reveal a unique searching mechanism of Cas9 at physiological salt conditions, and provide important guidance for both in-vitro and in-vivo applications of Cas9.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Exploring the Multidimensional Facets of Authoritarianism: Authoritarian Aggression and Social Dominance Orientation

2008 ◽  
Vol 67 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Stefano Passini
Keyword(s):  
Social Dominance ◽  
Factor Model ◽  
Three Dimensional ◽  
Social Dominance Orientation ◽  
Model Fit ◽  
Regression Analyses ◽  
One Dimensional ◽  
Confirmatory Factor ◽  
The One ◽  
Better Than

The relation between authoritarianism and social dominance orientation was analyzed, with authoritarianism measured using a three-dimensional scale. The implicit multidimensional structure (authoritarian submission, conventionalism, authoritarian aggression) of Altemeyer’s (1981, 1988) conceptualization of authoritarianism is inconsistent with its one-dimensional methodological operationalization. The dimensionality of authoritarianism was investigated using confirmatory factor analysis in a sample of 713 university students. As hypothesized, the three-factor model fit the data significantly better than the one-factor model. Regression analyses revealed that only authoritarian aggression was related to social dominance orientation. That is, only intolerance of deviance was related to high social dominance, whereas submissiveness was not.

Sign in / Sign up

Export Citation Format

Share Document