83 research outputs found
Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
Single T4-DNA molecules were confined in rectangular-shaped channels with a
depth of 300 nm and a width in the range 150-300 nm casted in a
poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules
were measured with fluorescence microscopy as a function of the ionic strength
and composition of the buffer as well as the DNA intercalation level by the
YOYO-1 dye. The data were interpreted with scaling theory for a wormlike
polymer in good solvent, including the effects of confinement, charge, and
self-avoidance. It was found that the elongation of the DNA molecules with
decreasing ionic strength can be interpreted in terms of an increase of the
persistence length. Self-avoidance effects on the extension are moderate, due
to the small correlation length imposed by the channel cross-sectional
diameter. Intercalation of the dye results in an increase of the DNA contour
length and a partial neutralization of the DNA charge, but besides effects of
electrostatic origin it has no significant effect on the bare bending rigidity.
In the presence of divalent cations, the DNA molecules were observed to
contract, but they do not collapse into a condensed structure. It is proposed
that this contraction results from a divalent counterion mediated attractive
force between the segments of the DNA molecule.Comment: 38 pages, 10 figures, accepted for publication in The Journal of
Chemical Physic
Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides
Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation.Singapore. National Research Foundation (Singapore Centre on Environmental Life Sciences Engineering (SCELSE))Nanyang Technological UniversityNational University of Singapore (Research Centre of Excellence Program)Singapore-MIT Alliance for Research and Technology (BioSystems and Micromechanics Program
Molecular dynamics simulation of multivalent ion mediated DNA attraction
All atom molecular dynamics simulations with explicit water were done to
study the interaction between two parallel double-stranded DNA molecules in the
presence of the multivalent counterions putrescine (2+), spermidine (3+),
spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is
obtained with the umbrella sampling technique. The attractive force is
rationalized in terms of the formation of ion bridges, i.e. multivalent ions
which are simultaneously bound to the two opposing DNA molecules. The lifetime
of the ion bridges is short on the order of a few nanoseconds.Comment: 4 pages, 5 figures, to be published in Physical Review Letter
Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace
10.1039/c3sm51214bSoft Matter9409593-960
Novel Protein-Protein Interactions Inferred from Literature Context
We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature. This method outperforms previously developed PPI prediction algorithms that rely on the conjunction of two protein names in MEDLINE abstracts. We show significant increases in coverage (76% versus 32%) and sensitivity (66% versus 41% at a specificity of 95%) for the prediction of PPIs currently archived in 6 PPI databases. A retrospective analysis shows that PPIs can efficiently be predicted before they enter PPI databases and before their interaction is explicitly described in the literature. The practical value of the method for discovery of novel PPIs is illustrated by the experimental confirmation of the inferred physical interaction between CAPN3 and PARVB, which was based on frequent co-occurrence of both proteins with concepts like Z-disc, dysferlin, and alpha-actinin. The relationships between proteins predicted by our method are broader than PPIs, and include proteins in the same complex or pathway. Dependent on the type of relationships deemed useful, the precision of our method can be as high as 90%. The full set of predicted interactions is available in a downloadable matrix and through the webtool Nermal, which lists the most likely interaction partners for a given protein. Our framework can be used for prioritizing potential interaction partners, hitherto undiscovered, for follow-up studies and to aid the generation of accurate protein interaction maps
Compaction of Plasmid DNA by Macromolecular Crowding
With
a view to understand compaction of DNA in crowded conditions,
we have measured the radius of gyration of pHSG298 plasmid (2675 bp)
in its supercoiled and linear forms and in the presence of dextran
nanoparticles with light scattering. It was observed that the supercoil
initially expands and subsequently compacts with increasing volume
fraction of the crowder. The extent of the expansion depends on the
size of the nanoparticle, with the smallest particles exhibiting the
largest effect. In the case of the linear plasmid, monotonous compaction
and no apex in the radius of gyration were observed. The plasmid does
not collapse into a condensed state. In crowded conditions, the size
of the supercoiled molecule exceeds the one of its linear variant.
Supercoiling hence restrains rather than facilitates compaction of
crowded DNA. Our results show two different, but closely related,
aspects of the crowding phenomenon. First, the supercoil expands through
a modification of its geometrical properties by the depletion induced
attraction between the two opposing duplexes of the superhelix. Second,
the molecule gets compressed due to the depletion of nanoparticles
in the interior of the coil with concomitant imbalance in osmotic
pressure between the coil and surrounding medium. The antagonistic
nature of these two aspects of crowding results in a much more pronounced
and richer effect on the dimensions of supercoiled plasmid than the
effect of variation in ionic strength. The change in DNA dimensions
as a response to crowding may have implications in biology as well
as biotechnology
Liquid crystal formation in supercoiled DNA solutions.
The critical concentrations pertaining to the liquid crystal formation of pUC18 plasmid in saline solutions were obtained from (31)P nuclear magnetic resonance, polarized light microscopy, and phase equilibrium experiments. The transition is strongly first order with a broad gap between the isotropic and anisotropic phase. The critical boundaries are strongly and reversibly dependent on temperature and weakly dependent on ionic strength. With polarized light microscopy on magnetically oriented samples, the liquid crystalline phase is assigned cholesteric with a pitch on the order of 4 microm. Preliminary results show that at higher concentrations a true crystal is formed. The isotropic-cholesteric transition is interpreted with lyotropic liquid crystal theory including the effects of charge, orientation entropy, and excluded volume effects. It was found that the molecular free energy associated with the topology of the superhelix is of paramount importance in controlling the width of the phase gap. The theoretical results compare favorably with the critical boundary pertaining to the disappearance of the isotropic phase, but they fail to predict the low concentration at which the anisotropic phase first appears
High throughput fabrication of disposable nanofluidic lab-on-chip devices for single molecule studies
10.1063/1.4740231Biomicrofluidics63
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