Related papers: Introducing a model of pairing based on Base pair …
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We introduce a simple spherical model whose structural properties are similar to the ones generated by models with directional interactions, by employing a binary mixture of large and small hard spheres, with a square-well attraction acting…