36 research outputs found
Force Induced DNA Melting
When pulled along the axis, double-strand DNA undergoes a large
conformational change and elongates roughly twice its initial contour length at
a pulling force about 70 pN. The transition to this highly overstretched form
of DNA is very cooperative. Applying force perpendicular to the DNA axis
(unzipping), double-strand DNA can also be separated into two single-stranded
DNA which is a fundamental process in DNA replication. We study the DNA
overstretching and unzipping transition using fully atomistic molecular
dynamics (MD) simulations and argue that the conformational changes of double
strand DNA associated with either of the above mentioned processes can be
viewed as force induced DNA melting. As the force at one end of the DNA is
increased the DNA start melting abruptly/smoothly after a critical force
depending on the pulling direction. The critical force fm, at which DNA melts
completely decreases as the temperature of the system is increased. The melting
force in case of unzipping is smaller compared to the melting force when the
DNA is pulled along the helical axis. In the cases of melting through
unzipping, the double-strand separation has jumps which correspond to the
different energy minima arising due to different base pair sequence. The
fraction of Watson-Crick base pair hydrogen bond breaking as a function of
force does not show smooth and continuous behavior and consists of plateaus
followed by sharp jumps.Comment: 23 pages, 9 figures, accepted for publication in J. Phys.: Condens.
Matte
Translocation and encapsulation of siRNA inside carbon nanotubes
We report spontaneous translocation of small interfering RNA (siRNA) inside
carbon nanotubes (CNTs) of various diameters and chirality using all atom
molecular dynamics (MD) simulations with explicit solvent. We use Umbrella
sampling method to calculate the free energy landscape of the siRNA entry and
translocation event. Free energy profiles shows that siRNA gains free energy
while translocating inside CNT and barrier for siRNA exit from CNT ranges from
40 to 110 kcal/mol depending on CNT chirality and salt concentration. The
translocation time \tau decreases with the increase of CNT diameter with a
critical diameter of 24 \AA for the translocation. In contrast, double strand
DNA (dsDNA) of the same sequence does not translocate inside CNT due to large
free energy barrier for the translocation. This study helps in understanding
the nucleic acid transport through nanopores at microscopic level and may help
designing carbon nanotube based sensor for siRNA.Comment: Accepted for the Journal of Chemical Physics; 24 pages, 6 figures and
1 tabl
Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA
We report a structural polymorphism of the S-DNA when a canonical B-DNA is
stretched under different pulling protocols and provide a fundamental molecular
understanding of the DNA stretching mechanism. Extensive all atom molecular
dynamics simulations reveal a clear formation of S-DNA when the B-DNA is
stretched along the 3' directions of the opposite strands (OS3) and is
characterized by the changes in the number of H-bonds, entropy and free energy.
Stretching along 5' directions of the opposite strands (OS5) leads to force
induced melting form of the DNA. Interestingly, stretching along the opposite
ends of the same strand (SS) leads to a coexistence of both the S- and melted
M-DNA structures. We also do the structural characterization of the S-DNA by
calculating various helical parameters. We find that S-DNA has a twist of ~10
degrees which corresponds to helical repeat length of ~ 36 base pairs in close
agreement with the previous experimental results. Moreover, we find that the
free energy barrier between the canonical and overstretched states of DNA is
higher for the same termini (SE) pulling protocol in comparison to all other
protocols considered in this work. Overall, our observations not only reconcile
with the available experimental results qualitatively but also enhance the
understanding of different overstretched DNA structures.Comment: To be published in the The Journal of Chemical Physics (AIP
Elasticity of DNA and the effect of Dendrimer Binding
Negatively charged DNA can be compacted by positively charged dendrimers and
the degree of compaction is a delicate balance between the strength of the
electrostatic interaction and the elasticity of DNA. We report various elastic
properties of short double stranded DNA (dsDNA) and the effect of dendrimer
binding using fully atomistic molecular dynamics and numerical simulations. In
equilibrium at room temperature, the contour length distribution P(L) and
end-to-end distance distribution P(R) are nearly Gaussian, the former gives an
estimate of the stretch modulus {\gamma}_1 of dsDNA in quantitative agreement
with the literature value. The bend angle distribution P({\theta}) of the dsDNA
also has a Gaussian form and allows to extract a persistence length, L_p of 43
nm. When the dsDNA is compacted by positively charged dendrimer, the stretch
modulus stays invariant but the effective bending rigidity estimated from the
end-to-end distance distribution decreases dramatically due to backbone charge
neutralization of dsDNA by dendrimer. We support our observations with
numerical solutions of the worm-like-chain (WLC) model as well as using
non-equilibrium dsDNA stretching simulations. These results are helpful in
understanding the dsDNA elasticity at short length scales as well as how the
elasticity is modulated when dsDNA binds to a charged object such as a
dendrimer or protein.Comment: 21 pages, 5 figure
Modeling Interlayer Interactions and Phonon Thermal Transport in Silicene Bilayer
We develop an accurate interlayer pairwise potential derived from the
\textit{ab-initio} calculations and investigate the thermal transport of
silicene bilayers within the framework of equilibrium molecular dynamics
simulations. The electronic properties are found to be sensitive to the
temperature with the opening of the band gap in the M
direction. The calculated phonon thermal conductivity of bilayer silicene is
surprisingly higher than that of monolayer silicene, contrary to the trends
reported for other classes of 2D materials like graphene and hBN bilayers. This
counterintuitive behavior of the bilayer silicene is attributed to the
interlayer interaction effects and inherent buckling, which lead to a higher
group velocity in the LA/LA phonon modes. The thermal conductivity of
both the mono- and bilayer silicene decreases with temperature as because of the strong correlations between the characteristic
timescales of heat current autocorrelation function and temperature (). The mechanisms underlying phonon thermal transport in silicene
bilayers are further established by analyzing the temperature induced changes
in acoustic group velocity.Comment: To appear in Phys. Rev.
Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3′end1–3′end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5′end1–5′end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3′end1–3′end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break
Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension
In order to interpret recent experimental studies of the dependence of
conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which
find a sharp conductance jump for a very short (4.5 %) stretching length, we
carried out multiscale modeling, to predict the conductance of dsDNA as it is
mechanically stretched to promote various structural polymorphisms. We
calculate the current along the stretched DNA using a combination of molecular
dynamics simulations, non-equilibrium pulling simulations, quantum mechanics
calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2
attachments we find an abrupt jump in the current within a very short
stretching length (6 or 17 %) leading to a melted DNA state. In
contrast, for 3'end1-3'end2 pulling it takes almost 32 (84 %) of
stretching to cause a similar jump in the current. Thus, we demonstrate that
charge transport in DNA can occur over stretching lengths of several
nanometers. We find that this unexpected behaviour in the B to S conformational
DNA transition arises from highly inclined base pair geometries that result
from this pulling protocol. We find that the dramatically different conductance
behaviors for two different pulling protocols arise from the nature of how
hydrogen bonds of DNA base pairs break
Unzipping and binding of small interfering RNA with single walled Carbon Nanotube: a platform for small interfering RNA delivery
In an effort to design efficient platform for siRNA delivery, we combine all
atom classical and quantum simulations to study the binding of small
interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our
results show that siRNA strongly binds to SWCNT surface via unzipping its
base-pairs and the propensity of unzipping increases with the increase in the
diameter of the SWCNTs. The unzipping and subsequent wrapping events are
initiated and driven by van der Waals interactions between the aromatic rings
of siRNA nucleobases and the SWCNT surface. However, MD simulations of double
strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less
unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This
interesting difference is due to smaller interaction energy of thymidine of
dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by
dispersion corrected density functional theory (DFT) methods. After the optimal
binding of siRNA to SWCNT, the complex is very stable which serves as one of
the major mechanisms of siRNA delivery for biomedical applications. Since siRNA
has to undergo unwinding process with the effect of RNA- induced silencing
complex, our proposed delivery mechanism by SWCNT possesses potential
advantages in achieving RNA interference (RNAi).Comment: 28 pages, 7 figures, 4 table