Spatial confinement induces hairpins in nicked circular DNA

Abstract

In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent–tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.

Confinement‐Induced Ordering and Self‐Folding of Cellulose Nanofibrils

“…Alignment was observed and quantified. us to suggest that a weak confinement experiment offers more information on the fibril characteristics, by bringing into observation kinks or weak regions that were not noticeable in the unconfined state, much like in the case of the circular DNA studied by Japaridze et al [32] In addition, a monotonic decrease in average kink angle as a function the increasing number of kinks, k k n θ 〈 〉 was observed. Simulations showed that this effect could not be solely explained by a specific selectivity of the slits for pre-existing fibril populations, but rather confinement itself induces the conformational change.…”

“…Confinement was chosen as it has been extensively studied both theoretically [26][27][28] and, in recent years, experimentally. [29,32,34] A noteworthy example of this was observed by Japaridze et al [32] in the case of circular DNA, where they observed hairpins at the nicked regions of the DNA plasmids when under strong confinement. [29,32,34] A noteworthy example of this was observed by Japaridze et al [32] in the case of circular DNA, where they observed hairpins at the nicked regions of the DNA plasmids when under strong confinement.…”

“…Fibril ConformationIt has been reported that confinement can influence the conformation of the confined elements [29,32,34,41]. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.advancedscience.com2.2.…”

AFM images of open and collapsed states of yeast condensin suggest a scrunching model for DNA loop extrusion

“…Next to the population that showed this linear correlation, a second smaller population (blue data in Figure 5B; and S10D) showed no dependence of the DNA neck width on condensin size. From studying the individual images ( Figure S10), we conclude that the small DNA-neck width of these molecules is caused by interwound structures within the DNA, that likely are induced upon depositing the DNA onto the polylysine-treated mica surface (Japaridze et al, 2017a). Overall, the data suggest that conformational changes of the condensin complex appear to be associated with changes in the width of the stem of the DNA loop that is extruded by condensin.…”

Interplay between Confinement and Drag Forces Determine the Fate of Amyloid Fibrils

“…Initially, studies were carried out using fluorescence microscopy [17][18][19]. However, by taking setups applicable to atomic force microscopy (AFM), it is possible to obtain higher resolution images of polymers under confinement [20,21] or extension [22], thus leading to detailed statistical characterization at the single-molecule level.…”