Related papers: Statics and Dynamics of Condensed DNA within Phage…
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…
Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
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…
A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly \textit{in vitro}, where after triggering with the cellular receptor the…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
The curvature stress of DNA packed inside a phage is balanced against its electrostatic self-interaction. The DNA density is supposed nonuniform and as a result the Donnan effect is also inhomogeneous. The coarse-grained DNA density is a…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and…
The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…
We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and lambda) using the smotic-suppression technique. Our data are analyzed by revisiting the current theories of DNA packaging in…
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…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…