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In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
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…
Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins,…
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
DNA-mediated multivalent interactions between colloidal particles have been extensively applied for their ability to program bulk phase behaviour and dynamic processes. Exploiting the competition between different types of DNA-DNA bonds,…
We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains…
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…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…