Related papers: DNA Dynamics in A Water Drop
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
Molecular dynamics in pure water and aqueous salt solutions remain incompletely understood, partly due to the apparent contradictions between results from different spectroscopic techniques. In this work, we demonstrate, by detailed…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
The effect of magnesium ion Mg2+ on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy in the 100 Hz-100 MHz frequency range. De Gennes-Pfeuty-Dobrynin semidilute solution…
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular…
We determine the phase diagram of DNA with inter- and intra-strand native-pair interactions that mimic the compaction of DNA. We show that DNA takes an overall sheet-like structure in the region where an incipient transition to a compact…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is widely used for gene delivery. It is considered here in terms of discrete charges of DNA. We concentrate on the worst scenario case when in the…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
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…
We investigate electrostatic stability of charged droplets, modeled as permeable, charged spheres, and their encapsidation in thin, arbitrarily charged nano-shells, immersed in a neutralizing asymmetric electrolyte background. The latter…
The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
In order to detect the effect of the surface charge discreteness on the properties at the solid-liquid interface, molecular dynamics simulation model taking consideration of the vibration of wall atoms was used to investigate the ion and…