Spatial confinement induces hairpins in nicked circular DNA
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Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...
We have implemented the super-resolution method of direct stochastic optical reconstruction microscopy (dSTORM) to image nuclear and mitochondrial DNA in living cells. We also demonstrate time-lapse imaging, all using a dye that associates directly with ce ...
This thesis explores different aspects of DNA topology through experimental and numerical techniques. Topology is a vast mathematical field, that deals with the spatial properties of objects undergoing continuous deformations, but here it is restricted to ...
The aim of this thesis was to explore the topoisomerase-DNA interactions using atomic force microscopy (AFM) in a liquid environment. Firstly, we present a programmable microcontroller-driven injection system for the exchange of an imaging medium while usi ...
Chromosomal and plasmid DNA molecules in bacterial cells are maintained under torsional tension and are therefore supercoiled. With the exception of extreme thermophiles, supercoiling has a negative sign, which means that the torsional tension diminishes t ...
The isolation of high quality DNA from environmental samples such as soil is essential for use in downstream applications. Two common issues often encountered with the purification of DNA from soil are the ability to fully lyse microbial organisms in the s ...
In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are c ...
Using numerical simulations, we compare properties of knotted DNA molecules that are either torsionally relaxed or supercoiled. We observe that DNA supercoiling tightens knotted portions of DNA molecules and accentuates the difference in curvature between ...
The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as a ...
The commercial application of biosensors has had a significant impact in a number of areas, particularly in the field of medical diagnostics. But in spite of the great number of publications, only a few systems are commercially available in food analysis. ...