Association Of DNA Molecules Research Articles

Sequence‐dependent clustering properties of nucleotides fragments in an ionic solution

AbstractThe chemical nature of the DNA bases is an important factor in sequence‐mediated association of DNA molecules. Nucleotides are the fundamental DNA elements and the base identity impacts the molecular properties of nucleotide fragments. It is interesting to study the fundamental nature of nucleotides in DNA, on the basis of base‐specific interactions, association, and modes of standard atomic or molecular interactions. With all‐atom molecular dynamics simulations of model dinucleotide and tetranucleotide systems having single‐stranded dinucleotide or tetranucleotide fragments of varying sequences, we show how the base identity and interactions between the different bases as well as water may affect the clustering properties of nucleotides fragments in an ionic solution. Sequence‐dependent differential interactions between the nucleotide fragments, ionic concentration, and elevated temperature are found to influence the clustering properties and dynamics of association. Well‐known epigenetic modification of DNA, that is, cytosine methylation also promotes dinucleotide clustering in solution. These observations point to one possible chemical nature of the DNA bases, as well as the importance of the base pairing, base stacking, and ionic interactions in DNA structure formation, and DNA sequence‐mediated association. Sequence‐ and the ionic environment‐mediated self‐association properties of the dinucleotides indicate its great potential to develop biological nanomaterials for desired applications.

DNA adsorption on synthetic and natural allophanes

The adsorption of DNA on natural and synthetic samples of allophane, which is a primary clay mineral of andosols, was investigated with respect to the DNA concentration, pH, ionic strength in the sample solution, and competition between DNA molecules and phosphate ions for adsorption to understand the behavior of extracellular DNA molecules in andosols. The relationships between DNA adsorption and the final concentrations were significantly fitted to a simple linear Langmuir equation. DNA adsorption decreased considerably with increasing suspension pH in the range between 3 and 9. The adsorption was less affected by the ionic strength of the suspension from 0.1 to 0.5 mol L − 1 . Under the same experimental conditions, DNA adsorption on allophanes was relatively higher than that on montmorillonite and silica but relatively lower than that on gibbsite and goethite. DNA adsorption on allophanes decreased on the addition of phosphate, indicating that there was a competition between DNA molecules and phosphate ions for adsorption on the minerals. These results suggested that DNA adsorption on allophanes occurred via two mechanisms: direct bonding of the phosphate group at the end of the DNA molecule to the OH groups of the Al-oxide layer on allophane, and the association of DNA molecules with the surface of negatively charged allophane via a bridging of inorganic cations. ► DNA adsorption by allophanes decreased considerably with increasing suspension pH. ► The adsorption was less affected by ionic strength of suspension (0.1 – 0.5 mol L –1 ). ► DNA adsorption on allophanes was higher than silica but lower than gibbsite and goethite. ► There was a competition between DNA molecules and phosphate ions for adsorption.

The Control of Dna Structure and Topology: An Overview

ABSTRACTThe control of structure on the nanoscale relies on intermolecular interactions whose specificity and geometry can be treated on a predictive basis. DNA fulfills this criterion, and provides an extremely convenient construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of double helical DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct in solution a covalently closed DNA molecule whose helix axes have the connectivity of a cube: The molecule has twelve double helical edges; every edge is two helical turns in length, resulting in a hexacatenane, each of whose strands corresponds to a face of the object. We have developed a solid-support-based synthetic methodology that is more effective than solution synthesis. The key features of the technique are control over the formation of each edge of the object, and the topological closure of each intermediate. The isolation of individual objects on the surface of the support eliminates cross-reactions between growing products. The solid-support-based methodology has been used to construct a molecule whose helix axes have the connectivity of a truncated octahedron. This figure has 14 faces, of which six are square and eight are hexagonal; this Archimedean polyhedron contains 24 vertices and 36 edges, and is built from a 14-catenane of DNA. Knotted molecules appear to be the route for cloning DNA objects. It is possible to construct three knotted topologies, as well as a simple cyclic molecule from a single precursor, by control of solution conditions. Control of both branching and braiding topology is strong in this system, but control of 3-D structure remains elusive. Our key aim is the formation of prespecified 2-D and 3-D periodic structures for use in diffraction experiments. Another application envisioned is scaffolding for the assembly of molecular electronic devices.

Chemical Synthesis of Nanostructures

ABSTRACTThe control of structure on the nanoscale relies on intermolecular interactions whose specificity and geometry can be treated on a predictive basis. With this criterion in mind, DNA is an extremely favorable construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of double helical DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct a covalently closed DNA molecule whose helix axes have the connectivity of a cube. The molecule has twelve double helical edges; each edge is two helical turns in length, resulting in a hexacatenane, each of whose strands corresponds to a face of the object. The cube has been fabricated in solution, which is inefficient. We have developed a solid-support-based synthetic methodology that is much more effective. The key features of the technique are control over the formation of each edge of the object, and the topological closure of each intermediate. Each edge results from the restriction of two hairpins, which are then ligated together. The isolation of individual objects on the surface of the support permits one to use both symmetric and asymmetric sites in the formation of edges that close polygons. We have used solid-support-based methodology to construct a molecule whose helix axes have the connectivity of a truncated octahedron. This figure has 14 faces, of which six are ideally square and eight are hexagonal; this Archimedean polyhedron contains 24 vertices and 36 edges. Control of topology is strong in this system, but control of 3-D structure remains elusive. Topological control is enhanced by the use of topological protection techniques. Our key aim is the formation of prespecified 2-D and 3-D periodic structures with defined topologies. Applications envisioned include nanomanipulators and scaffolding for molecular electronic devices.