19 research outputs found
DNA: From rigid base-pairs to semiflexible polymers
The sequence-dependent elasticity of double-helical DNA on a nm length scale
can be captured by the rigid base-pair model, whose strains are the relative
position and orientation of adjacent base-pairs. Corresponding elastic
potentials have been obtained from all-atom MD simulation and from
high-resolution structural data. On the scale of a hundred nm, DNA is
successfully described by a continuous worm-like chain model with homogeneous
elastic properties characterized by a set of four elastic constants, which have
been directly measured in single-molecule experiments. We present here a theory
that links these experiments on different scales, by systematically
coarse-graining the rigid base-pair model for random sequence DNA to an
effective worm-like chain description. The average helical geometry of the
molecule is exactly taken into account in our approach. We find that the
available microscopic parameters sets predict qualitatively similar mesoscopic
parameters. The thermal bending and twisting persistence lengths computed from
MD data are 42 and 48 nm, respectively. The static persistence lengths are
generally much higher, in agreement with cyclization experiments. All
microscopic parameter sets predict negative twist-stretch coupling. The
variability and anisotropy of bending stiffness in short random chains lead to
non-Gaussian bend angle distributions, but become unimportant after two helical
turns.Comment: 13 pages, 6 figures, 6 table
Sequence-dependent thermodynamics of a coarse-grained DNA model
We introduce a sequence-dependent parametrization for a coarse-grained DNA
model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134,
085101 (2011)] originally designed to reproduce the properties of DNA molecules
with average sequences. The new parametrization introduces sequence-dependent
stacking and base-pairing interaction strengths chosen to reproduce the melting
temperatures of short duplexes. By developing a histogram reweighting
technique, we are able to fit our parameters to the melting temperatures of
thousands of sequences. To demonstrate the flexibility of the model, we study
the effects of sequence on: (a) the heterogeneous stacking transition of single
strands, (b) the tendency of a duplex to fray at its melting point, (c) the
effects of stacking strength in the loop on the melting temperature of
hairpins, (d) the force-extension properties of single strands and (e) the
structure of a kissing-loop complex. Where possible we compare our results with
experimental data and find a good agreement. A simulation code called oxDNA,
implementing our model, is available as free software.Comment: 15 page
The temperature dependence of the helical twist of DNA.
DNA is the carrier of all cellular genetic information and increasingly used in nanotechnology. Quantitative understanding and optimization of its functions requires precise experimental characterization and accurate modeling of DNA properties. A defining feature of DNA is its helicity. DNA unwinds with increasing temperature, even for temperatures well below the melting temperature. However, accurate quanti-tation of DNA unwinding under external forces and a microscopic understanding of the corresponding structural changes are currently lacking. Here we combine single-molecule magnetic tweezers measurements with atomistic molecular dynamics and coarse-grained simulations to obtain a comprehensive view of the temperature dependence of DNA twist. Experimentally, we find that DNA twist changes by Tw(T) = (−11.0 ± 1.2)â—¦/(â—¦C·kbp), independent of applied force, in the range of forces where torque-induced melting is negligible. Our atomistic simulations predict Tw(T) = (−11.1 ± 0.3)â—¦/(â—¦C·kbp), in quantitative agreement with experiments, and suggest that the untwisting of DNA with temperature is predominantly due to changes in DNA structure for defined backbone substates, while the effects of changes in substate populations are minor. Coarse-grained simulations using the oxDNA framework yield a value of Tw(T) = (−6.4 ± 0.2)â—¦/(â—¦C·kbp) in semi-quantitative agreement with experiments
Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations
The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40Â pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5Â pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40Â pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy
Intracellular speciation of gold nanorods alters the conformational dynamics of genomic DNA
Gold nanorods are one of the most widely explored inorganic materials in nanomedicine for diagnostics, therapeutics and sensing1. It has been shown that gold nanorods are not cytotoxic and localize within cytoplasmic vesicles following endocytosis, with no nuclear localization2,3, but other studies have reported alterations in gene expression profiles in cells following exposure to gold nanorods, via unknown mechanisms4. In this work we describe a pathway that can contribute to this phenomenon. By mapping the intracellular chemical speciation process of gold nanorods, we show that the commonly used Au–thiol conjugation, which is important for maintaining the noble (inert) properties of gold nanostructures, is altered following endocytosis, resulting in the formation of Au(i)–thiolates that localize in the nucleus5. Furthermore, we show that nuclear localization of the gold species perturbs the dynamic microenvironment within the nucleus and triggers alteration of gene expression in human cells. We demonstrate this using quantitative visualization of ubiquitous DNA G-quadruplex structures, which are sensitive to ionic imbalances, as an indicator of the formation of structural alterations in genomic DNA