216 research outputs found
Sturdier DNA nanotubes via ligation
DNA nanotubes are crystalline self-assemblies of DNA tiles ~10 nm in diameter that readily grow tens of micrometers in length. Easy assembly,
programmability, and stiffness make them interesting for many applications, but DNA nanotubes begin to melt at temperatures below 40 °C,
break open when deposited on mica or scanned by AFM, and disintegrate in deionized water. These weaknesses can be traced to the presence
of discontinuities in the phosphate backbone, called nicks. The nanotubes studied here have five nicks, one in the core of a tile and one at
each corner. We report the successful ligation of all four corner nicks by T4 DNA ligase. Although ligation does not change the nanotubes’
stiffness, ligated nanotubes withstand temperatures over 70 °C, resist breaking during AFM, and are stable in pure water for over a month.
Ligated DNA nanotubes are thus physically and chemically sturdy enough to withstand the manipulations necessary for many technological
applications
Design and characterization of programmable DNA nanotubes
DNA self-assembly provides a programmable bottom-up approach for the synthesis of complex structures from nanoscale components. Although nanotubes are a fundamental form encountered in tile-based DNA self-assembly, the factors governing tube structure remain poorly understood. Here we report and characterize a new type of nanotube made from DNA double-crossover molecules (DAE-E tiles). Unmodified tubes range from 7 to 20 nm in diameter (4 to 10 tiles in circumference), grow as long as 50 μm with a persistence length of ~4 μm, and can be programmed to display a variety of patterns. A survey of modifications (1) confirms the importance of sticky-end stacking, (2) confirms the identity of the inside and outside faces of the tubes, and (3) identifies features of the tiles that profoundly affect the size and morphology of the tubes. Supported by these results, nanotube structure is explained by a simple model based on the geometry and energetics of B-form DNA
Islands of conformational stability for Filopodia
Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work
Morphology of axisymmetric vesicles with encapsulated filaments and impurities
The shape deformation of a three-dimensional axisymmetric vesicle with
encapsulated filaments or impurities is analyzed by integrating a dissipation
dynamics. This method can incorporate systematically the constraint of a fixed
surface area and/or a fixed volume. The filament encapsulated in a vesicle is
assumed to take a form of a rod or a ring so as to imitate cytoskeletons. In
both cases, results of the shape transition of the vesicle are summarized in
phase diagrams in the phase space of the vesicular volume and a rod length or a
ring radius.
We also study the dynamics of a vesicle with impurities coupled to the
membrane curvature. The phase separation and the associated shape deformation
in the early stage of the dynamical evolution can well be explained by the
linear stability analysis. Long runs of simulation demonstrate the nonlinear
coarsening of the wavy deformation of the vesicle in the late stage.Comment: 9 pages, 9 figure
Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion
We study the effects of thermal flucutations on thin elastic filaments with
spontaneous curvature and torsion. We derive analytical expressions for the
orientational correlation functions and for the persistence length of helices,
and find that this length varies non-monotonically with the strength of thermal
fluctuations. In the weak fluctuation regime, the persistence length of a
spontaneously twisted helix has three resonance peaks as a function of the
twist rate. In the limit of strong fluctuations, all memory of the helical
shape is lost.Comment: 1 figur
Fluctuating Filaments I: Statistical Mechanics of Helices
We examine the effects of thermal fluctuations on thin elastic filaments with
non-circular cross-section and arbitrary spontaneous curvature and torsion.
Analytical expressions for orientational correlation functions and for the
persistence length of helices are derived, and it is found that this length
varies non-monotonically with the strength of thermal fluctuations. In the weak
fluctuation regime, the local helical structure is preserved and the
statistical properties are dominated by long wavelength bending and torsion
modes. As the amplitude of fluctuations is increased, the helix ``melts'' and
all memory of intrinsic helical structure is lost. Spontaneous twist of the
cross--section leads to resonant dependence of the persistence length on the
twist rate.Comment: 5 figure
Non-equilibrium self-assembly of a filament coupled to ATP/GTP hydrolysis
We study the stochastic dynamics of growth and shrinkage of single actin
filaments or microtubules taking into account insertion, removal, and ATP/GTP
hydrolysis of subunits. The resulting phase diagram contains three different
phases: a rapidly growing phase, an intermediate phase and a bound phase. We
analyze all these phases, with an emphasis on the bound phase. We also discuss
how hydrolysis affects force-velocity curves. The bound phase shows features of
dynamic instability, which we characterize in terms of the time needed for the
ATP/GTP cap to disappear as well as the time needed for the filament to reach a
length of zero, i.e., (to collapse) for the first time. We obtain exact
expressions for all these quantities, which we test using Monte Carlo
simulations.Comment: 34 page
Collective and single cell behavior in epithelial contact inhibition
Control of cell proliferation is a fundamental aspect of tissue physiology
central to morphogenesis, wound healing and cancer. Although many of the
molecular genetic factors are now known, the system level regulation of growth
is still poorly understood. A simple form of inhibition of cell proliferation
is encountered in vitro in normally differentiating epithelial cell cultures
and is known as "contact inhibition". The study presented here provides a
quantitative characterization of contact inhibition dynamics on tissue-wide and
single cell levels. Using long-term tracking of cultured MDCK cells we
demonstrate that inhibition of cell division in a confluent monolayer follows
inhibition of cell motility and sets in when mechanical constraint on local
expansion causes divisions to reduce cell area. We quantify cell motility and
cell cycle statistics in the low density confluent regime and their change
across the transition to epithelial morphology which occurs with increasing
cell density. We then study the dynamics of cell area distribution arising
through reductive division, determine the average mitotic rate as a function of
cell size and demonstrate that complete arrest of mitosis occurs when cell area
falls below a critical value. We also present a simple computational model of
growth mechanics which captures all aspects of the observed behavior. Our
measurements and analysis show that contact inhibition is a consequence of
mechanical interaction and constraint rather than interfacial contact alone,
and define quantitative phenotypes that can guide future studies of molecular
mechanisms underlying contact inhibition
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