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The location of nucleosomes in DNA and their structural stability are critical in regulating DNA compaction, site accessibility, and epigenetic gene regulation. Here, we combine the nanopore platform-based fast and label-free single-molecule detection technique with a voltage-dependent force rupture assay to detect distinct structures on nucleosoma...
The CRISPR-associated protein 9 (Cas9) system has proven to be a powerful technology for genome editing in a wide variety of in vivo and in vitro applications. CRISPR–Cas9, when loaded with the guide RNA, cleaves the DNA at the target position as recognized by the guide RNA sequence. For successful application of this technology, it is important to...
DNA conformation, in particular it's supercoiling, plays an important structural and functional role in gene accessibility as well as in DNA condensation. Enzyme driven changes of DNA plasmids between its linear, circular and supercoiled conformations control the level of condensation and DNA distal-site interactions. Many efforts have been made to...
Using joint Shannon entropy, we propose an inequality for a four-level system, which is satisfied in a noncontextual realist hidden variable model. We show that this entropic inequality is violated by quantum mechanics for a range of entangled, as well as product states. Our inequality can be experimentally tested using the existing technology.
It requires about 5.3 kcal/mol (or 8 kBT) of energy to break one phoshodiester bond of DNA. How do these enzymes cut the DNA only by using thermal energy and not ATP? I am only considering the ATP-independent restriction enzymes (Type II). How do these enzymes manage to generate the necessary energy? I couldn't find the exact mechanism with energetics of restriction enzymes cleaving DNA. Please provide me any relevant references.
During AFM imaging, the tip does the raster scanning in xy-axes and deflects in z-axis due to the topographical changes on the surface being imaged. The height adjustments made by the piezo at every point on the surface during the scanning is recorded to reconstruct a 3D topographical image. How does the laser beam remain on the tip while the tip moves all over the surface? Isn't the optics static inside the scanner that is responsible for directing the laser beam onto the cantilever or does it move in sync with the tip? How is it that only the z-signal is affected due to the topography but the xy-signal of the QPD not affected by the movement of the tip?
or in other words, why is the QPD signal affected only due to the bending and twisting of the cantilever and not due to its translation?
Does the DNA remain stable or degrade at this temperature? Would there be any difference in thermal stability between supercoiled and linear forms of say, 3 kb plasmid.