Induce DNA Compaction Research Articles

Urea effect on Cu 2+-induced DNA structural transitions in solution

Cu 2+ ion interaction with DNA in aqueous solutions containing urea (0–5 M) was studied by IR spectroscopy. It was shown that upon the Cu 2+ ion binding DNA transition into a compact form occurs. This transition is of positive cooperativity. We suppose that the mechanism of Cu 2+-induced DNA compaction in solutions containing urea is not completely electrostatic. Urea addition to the DNA solution decreases the Cu 2+ ion concentration required to induce DNA compaction. As the urea content in solution rises, the binding constant of Cu 2+ ions interacting with DNA increases, going through the maximum in the case of 2 M solution; further increase of the urea content in solutions leads to decrease of the binding constant. DNA transition into the compact form under the Cu 2+ ion action is determined not only by the effects of the solution dielectric permeability but by the solvation effects; when changes of the dielectric permeability are small the solvation effects may prevail. Urea addition to the DNA solution also decreases cooperativity of the DNA compaction process. Perhaps, cooperativity of the DNA transition into the compact state depends on the ordered spatial structure of water adjacent to the macromolecule and decreases on the structure destruction.

Real-Time Detection of Single-Molecule DNA Compaction by Condensin I

Background: Condensin is thought to contribute to large-scale DNA compaction during mitotic chromosome assembly. It remains unknown, however, how the complex reconfigures DNA structure at a mechanistic level.Results: We have performed single-molecule DNA nanomanipulation experiments to directly measure in real-time DNA compaction by the Xenopus laevis condensin I complex. Condensin can bind to the nanomanipulated DNA in the absence of ATP, but it compacts the DNA only in the presence of hydrolyzable ATP. Linear compaction is evidenced by a reduction in the end-to-end extension of nanomanipulated DNA. The reaction results in total compaction of the DNA (i.e., zero end-to-end extension). Discrete and reversible DNA compaction events are observed in the presence of competitor DNA when the DNA is subjected to weak stretching forces (F = 0.4 picoNewton [pN]). The distribution of step sizes is broad and displays a peak at ∼60 nm (∼180 bp) as well as a long tail. This distribution is essentially unaffected by the topological state of the DNA substrate. Increasing the force to F = 10 pN drives the system toward step-wise reversal of compaction. The distribution of step sizes observed upon disruption of condensin-DNA interactions displays a sharp peak at ∼30 nm (∼90 bp) as well as a long tail stretching out to hundreds of nanometers.Conclusions: The DNA nanomanipulation assay allows us to demonstrate for the first time that condensin physically compacts DNA in an ATP-hydrolysis-dependent manner. Our results suggest that the condensin complex may induce DNA compaction by dynamically and reversibly introducing loops along the DNA.

On the Role of H-NS in the Organization of Bacterial Chromatin: From Bulk to Single Molecules and Back…

The chromosomal DNA in the bacterium Escherichia coli is thought to be organized and compacted at least in part as a consequence of the interaction with so-called histone-like or nucleoid-associated proteins. The groups of Stavans and Oppenheim have recently embarked on an ambitious project which aims to quantify the compactive effects of the various members of this group of proteins using magnetic tweezers (Ali et al., 2001). Eventually this could lead to a better understanding of how these proteins work together in the formation of a compact nucleoid.

Surface histidine residue of archaeal histone affects DNA compaction and thermostability

Archaeal histone, which possesses only the core domain part of eukaryal histone, induced DNA compaction by binding to DNA. Based on structural modeling, tetramer formation by dimer–dimer interaction is considered to require two intermolecular ion pairs formed between histidine and aspartate. To examine the role of the ion pairs on DNA compaction, mutant histones were constructed and analyzed using HpkB from Thermococcus kodakaraensis KOD1 as a model protein. The mutant histones, HpkB-H50A, HpkB-H50V, and HpkB-H50G were constructed by replacing conserved surface His50 with Ala, Val, and Gly, respectively. Circular dichroism analysis indicated no significant difference between wild-type and mutants in their structures. Gel mobility shift assays showed that all mutants possessed DNA binding ability, like wild-type HpkB, however all mutants compacted DNA less efficiently than the wild-type. Moreover, all mutants could not maintain the nucleosome-like structure (compacted form of DNA) above 80°C. These results suggest that surface ion pairs between His and Asp play an important role in maintenance of nucleosome structure and DNA stabilization at high temperature.