Showing papers on "Molecular models of DNA published in 1998"
TL;DR: The design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules that create specific periodic patterns on the nanometre scale are reported.
Abstract: Molecular self-assembly presents a `bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA
molecular structures and intermolecular interactions are particularly
amenable to the design and synthesis of complex molecular objects. We
report the design and observation of two-dimensional crystalline forms
of DNA that self-assemble from synthetic DNA double-crossover
molecules. Intermolecular interactions between the structural units are
programmed by the design of `sticky ends' that associate according to
Watson-Crick complementarity, enabling us to create specific periodic
patterns on the nanometre scale. The patterned crystals have been
visualized by atomic force microscopy.
2,713 citations
TL;DR: It appears that novel DNA motifs may be of use in the new field of DNA-based computing, particularly in periodic arrays, with the objects of both crystal facilitation and memory-device construction.
Abstract: DNA nanotechnology entails the construction of specific geometrical and topological targets from DNA. The goals include the use of DNA molecules to scaffold the assembly of other molecules, particularly in periodic arrays, with the objects of both crystal facilitation and memory-device construction. Many of these products are based on branched DNA motifs. DNA molecules with the connectivities of a cube and a truncated octahedron have been prepared. A solid-support methodology has been developed to construct DNA targets. DNA trefoil and figure-8 knots have been made, predicated on the relationship between a topological crossing and a half-turn of B-DNA or Z-DNA. The same basis has been used to construct Borromean rings from DNA. An RNA knot has been used to demonstrate an RNA topoisomerase activity. The desire to construct periodic matter held together by DNA sticky ends has resulted in a search for stiff components; DNA double crossover molecules appear to be the best candidates. It appears that novel DNA motifs may be of use in the new field of DNA-based computing.
388 citations
TL;DR: It is found that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules.
104 citations
TL;DR: It is discovered that DNA double crossover molecules can provide this capability, and these components are incorporated in DNA assemblies that use this rigidity to achieve control on the geometrical level, as well as on the topological level.
Abstract: Recently, we have invested a great deal of effort to construct molecular building blocks from unusual DNA motifs. 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 B-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, and a second molecule, whose helix axes have the connectivity of a truncated octahedron. In addition to branching topology, DNA also yields control of linking topology, because double helical half-turns of B-DNA or Z-DNA can be equated, respectively, with negative or positive crossings in topological objects. Consequently, we have been able to use DNA to make trefoil knots of both signs and figure of 8 knots. By making RNA knots, we have discovered the existence of an RNA topoisomerase. DNA-based topological control has also led to the construction of Borromean rings, which could be used in DNA-based computing applications. The key feature previously lacking in DNA construction has been a rigid molecule. We have discovered that DNA double crossover molecules can provide this capability. We have incorporated these components in DNA assemblies that use this rigidity to achieve control on the geometrical level, as well as on the topological level. Some of these involve double crossover molecules, and others involve double crossovers associated with geometrical figures, such as triangles and deltahedra.
82 citations
TL;DR: The particular complexes described in this review contain linear DNA forming a new ‘hybrid’ phase of matter; that is, the DNA chains form a finite size two dimensional smectic coupled to the three dimensional Smectic phase of membranes.
Abstract: Atomic force microscopy studies of DNA attached to rigid surfaces were initially motivated by the development-of methods which would stretch DNA for the purposes of rapid sequencing. Currently there is much interest in studies of multilayers of DNA chains self-assembled on membranes which form spontaneously when DNA adsorbs onto oppositely charged cationic liposomes (CLs). A major motivation for elucidating the structures and interactions in these CL-DNA complexes arises for two reasons. The first is that they are known to mimic certain characteristics of viruses by being efficient chemical carriers of genes (DNA sections) for delivery in cells. The second is that they are models of studies of DNA condensation phases in two dimensions. DNA-membrane interactions should also provide clues for the relevant molecular forces in the condensation of DNA in chromosomes and viral capsids. The particular complexes described in this review contain linear DNA forming a new ‘hybrid’ phase of matter; that is, the DNA chains form a finite size two dimensional smectic coupled to the three dimensional smectic phase of membranes.
40 citations
TL;DR: Analysis of local and sublocal curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature, and differential curvature and flexibility at the 5' and 3'junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K- DNA fragment.
Abstract: DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X- ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X- ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable ...
2 citations
Posted Content•
TL;DR: In this paper, numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with realistic parameters obtained from experiments.
Abstract: Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with realistic parameters obtained from experiments. Furthermore, collective coordinate method is used to explain a previously observed numerical evidence that breathers placed far from defects are difficult to trap, and the motional effect of RNA-polymerase is investigated.
1 citations
01 Jan 1998
TL;DR: In this article, the authors studied the site juxtaposition process in supercoiled DNA and showed that the site alignment is a slow process, and that the times of juxtaposition are in the range of ms even for highly supercoiling DNA, about two orders of magnitude higher than the relaxation times of writhe and radius of gyration for the same molecules.
Abstract: Thermal motions in supercoiled DNA are studied by Brownian dynamics (BD) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the BD approach is capable of describing actual times of large-scale DNA motion. The bead model of DNA used here accounts for bending and torsional elasticity as well as the electrostatic repulsion among DNA segments. The hydrodynamic interaction among the beads of the model chain and the aqueous solution is incorporated through the Rotne-Prager tensor. All simulations were performed for the sodium ion concentration of 0.01 M. We first showed, to test our BD procedure, that the same distributions of equilibrium conformational properties are obtained as by Monte Carlo simulations for the corresponding DNA model. The BD simulations also predict with accuracy published experimental values of the diffusion coefficients of supercoiled DNA. To describe the rate of conformational changes, we also calculated the autocorrelation functions for the writhe and radius of gyration for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules. By inspecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient mechanism to accomplish site juxtaposition, at least for conditions of low salt concentration. Instead, transient distortions of the interwound superhelix, followed by continuous reshaping of the molecule, contribute more significantly to site juxtaposition kinetics. # 1998 Academic Press