Related papers: Structuring of counterions around dna double helix…
Ionic behaviors, including ion distributions and hydration characteristics at solid-liquid interfaces, are important research interests in many important applications, such as electric double-layer capacitors and water lubrication. Here, we…
Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, of diameter 4.4 nm with four different background electrolyte concentrations, to extract the mean force acting between the…
The alkali metal ions in aqueous electrolyte solutions have strong influence on the surrounding network structure of water formed through hydrogen bonds. The extent of ionic perturbation to the structure of water depends on the nature of…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms,…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of…
The microhydration of rock salt (NaCl) molecules was investigated using high-resolution Penning ionization electron spectroscopy (PIES) in helium nanodroplets. Although model calculations predict that NaCl molecules are fully submerged…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
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…
We report on a detailed characterization of complex dielectric response of Na-DNA aqueous solutions by means of low-frequency dielectric spectroscopy (40 Hz - 110 MHz). Results reveal two broad relaxation modes of strength…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
Transfection of an anionic polynucleotide through a negatively charged membrane is an important problem in genetic engineering. The direct association of cationic surfactant to DNA decreases the effective negative charge of the nucleic…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT)…
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…