Related papers: Electron Attachment to DNA: The Protective Role of…
We have studied the effect of zwitterionic form of the amino acid on the electron attachment to DNA using thymine glycine as a model system. The electron attachment to thymine in the presence of glycine takes place through a "doorway…
We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently…
We report a benchmark theoretical investigation of both adiabatic and vertical electron affinities of five DNA and RNA nucleobases: adenine, guanine, cytosine, thymine and uracil using state-of-the-art equation of motion coupled cluster…
We present an EOM-CCSD based QM/MM study on the electron attachment process to cytosine, solvated in water. The microhydration studies cannot capture the effect of bulk water environment on the electron attachment process and one need to…
The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
We have analyzed the low-energy electron attachment to wobble base pairs using the equation motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs,…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
Homeodomain containing proteins are a broad class of DNA binding proteins that are believed to primarily function as transcription factors. Electrostatics interactions have been demonstrated to be critical for the binding of the homeodomain…
Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single…
We studied the electronic and the structural properties of amino acids (alanine, glycine, and histidine) attached to graphene oxide (GO) by peptide bonding, via plane wave pseudopotential total-energy calculations within the local spin…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
Although the immobilization of oligonucleotides (nucleic acid) on mineral surfaces is at the basis of different biotechnological applications, an atomistic understanding of the interaction of the nucleic acid components with the titanium…
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists…
Electrostatics plays a key role in biomolecular assembly. Oppositely charged biomolecules, for instance, can co-assembled into functional units, such as DNA and histone proteins into nucleosomes and actin-binding protein complexes into…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a…
In this work, the effect of amino acid environment on the nucleobase-centered anion radical shape resonances is investigated by employing uracil as a model system for pyrimidine base in RNA. Anionic uracil-glycine complexes have been used…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
We model the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. Crucial parameters in our model are…