相关论文: Femtonewton Forces Can Control Protein-Meditated D…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and much debated. One of the major open questions in this field…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
We discuss how a balance can be established between the force acting to eject DNA from viral capsids and the force resisting its entry into a colloidal suspension which mimics the host cell cytoplasm. The ejection force arises from the…
The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the…
The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes…
We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…
Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1)…
The conformational vibrations of Z-DNA with counterions are studied in framework of phenomenological model developed. The structure of left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is…
We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids,which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this…
We study the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage lambda. Past work has demonstrated that bacteriophage DNA is highly pressurized; this pressure has been hypothesized to help drive DNA…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…