Related papers: What do we know about DNA mechanics so far?
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Neural networks based on soft and biological matter constitute an interesting potential alternative to traditional implementations based on electric circuits. DNA is a particularly promising system in this context due its natural ability to…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
Does quantum dynamics play a role in DNA replication? What type of tests would reveal that? Some statistical checks that distinguish classical and quantum dynamics in DNA replication are proposed.
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
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 present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…