Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases
Graph Chatbot
Chat with Graph Search
Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.
DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.
In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and tran ...
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 ...
Enforcing a specific symmetry group on a curve, knotted or not, is not trivial using standard interpolations such as polygons or splines. For a prescribed symmetry group we present a symmetrization process based on a Fourier description of a knot. The pres ...
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 ...
We investigate numerical simulations and visualizations of the problem of tying a knot in a piece of rope. The goal is to use the least possible rope of a fixed, prescribed radius to tie a particular knot, e.g. a trefoil, a figure eight, and so on. The rop ...
The main subject of the present thesis is the experimental study of the scaling properties of DNA knots of different complexities by tapping mode atomic force microscopy (AFM) in air. Homo- or heterogeneous mixture of DNA knot types were deposited onto mic ...
Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and ...
The design, synthesis, and base-pairing properties of bicyclo[3.2.1]amide-DNA (bca-DNA), a novel phosphodiester-based DNA analog, are reported. This analog consists of a conformationally constrained backbone entity, which emulates a B-DNA geometry, to whic ...
Real-time simulation of knot-tying with visual and force feedback is essential to VR surgery training. We present a physics-based simulator that enables realistic knot tying at haptic speed. The virtual thread obeys Newton's laws and behaves naturally. The ...
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the thr ...
