Showing papers on "Molecular models of DNA published in 2007"

An overview of structural DNA nanotechnology.

Abstract: Structural DNA Nanotechnology uses unusual DNA motifs to build target shapes and arrangements. These unusual motifs are generated by reciprocal exchange of DNA backbones, leading to branched systems with many strands and multiple helical domains. The motifs may be combined by sticky ended cohesion, involving hydrogen bonding or covalent interactions. Other forms of cohesion involve edge-sharing or paranemic interactions of double helices. A large number of individual species have been developed by this approach, including polyhedral catenanes, a variety of single-stranded knots, and Borromean rings. In addition to these static species, DNA-based nanomechanical devices have been produced that are ultimately targeted to lead to nanorobotics. Many of the key goals of structural DNA nanotechnology entail the use of periodic arrays. A variety of 2D DNA arrays have been produced with tunable features, such as patterns and cavities. DNA molecules have be used successfully in DNA-based computation as molecular representations of Wang tiles, whose self-assembly can be programmed to perform a calculation. About 4 years ago, on the fiftieth anniversary of the double helix, the area appeared to be at the cusp of a truly exciting explosion of applications; this was a correct assessment, and much progress has been made in the intervening period.

Addressing Single Molecules on DNA Nanostructures

Abstract: The synthesis of devices and materials from molecular components is a major goal of nanotechnology. Although many such molecular components have been demonstrated previously,1–3 the ability to combine these components into designed architectures containing significant complexity remains a challenge. By using the hybridization properties of DNA and Watson–Crick base pairing, it has been possible to create well-defined DNA architectures of increasing complexity.4 The structure of an assembled DNA complex is directly and uniquely determined by the sequence of the DNA bases, which can be designed and manipulated. These methods provide a versatile and programmable way to control the structure and architecture of DNA nanostructures.

Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases

Abstract: We performed numerical simulations of DNA chains to understand how local geometry of juxtaposed segments in knotted DNA molecules can guide type II DNA topoisomerases to perform very efficient relaxation of DNA knots. We investigated how the various parameters defining the geometry of inter-segmental juxtapositions at sites of inter-segmental passage reactions mediated by type II DNA topoisomerases can affect the topological consequences of these reactions. We confirmed the hypothesis that by recognizing specific geometry of juxtaposed DNA segments in knotted DNA molecules, type II DNA topoisomerases can maintain the steady-state knotting level below the topological equilibrium. In addition, we revealed that a preference for a particular geometry of juxtaposed segments as sites of strand-passage reaction enables type II DNA topoisomerases to select the most efficient pathway of relaxation of complex DNA knots. The analysis of the best selection criteria for efficient relaxation of complex knots revealed that local structures in random configurations of a given knot type statistically behave as analogous local structures in ideal geometric configurations of the corresponding knot type.

Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling.

Abstract: Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. Currently, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, solving the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains similar contacts with DNA as those observed in the homologous Dri-DNA complex.

Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes

Abstract: This paper presents a parametric model to estimate the DNA-protein binding time using the DNA and protein structures and details of the binding site. To understand the stochastic behavior of biological systems, we propose an "in silico" stochastic event based simulation that determines the temporal dynamics of different molecules. This paper presents a parametric model to determine the execution time of one biological function (i.e. simulation event): protein-DNA binding by abstracting the function as a stochastic process of microlevel biological events using probability measure. This probability is coarse grained to estimate the stochastic behavior of the biological function. Our model considers the structural configurations of the DNA, proteins and the actual binding mechanism. We use a collision theory based approach to transform the thermal and concentration gradients of this biological process into the probability measure of DNA-protein binding event. This information theoretic approach significantly removes the complexity of the classical protein sliding along the DNA model, improves the speed of computation and can bypass the speed-stability paradox. This model can produce acceptable estimates of DNA-protein binding time to be used by our event-based stochastic system simulator where the higher order (more than second order statistics) uncertainties can be ignored. The results show good correspondence with available experimental estimates. The model depends very little on experimentally generated rate constants

Solitary excitations in B-Z DNA transition: a theoretical and numerical study.

Abstract: The molecular mechanism of B-Z DNA transition remains elusive since the elucidation of the left-handed Z-DNA structure using atomic resolution crystallographic study. Numerous proposals for the molecular mechanism have been advanced, but none has provided a satisfactory explanation for the process. A nonlinear DNA model is proposed which enables one to derive various hypothesized molecular mechanisms, namely the Harvey model, Zang and Olson model, and the stretched intermediate model, by imposing certain constraints and conditions on the model. These constraints raise the need to reevaluate experimental investigations on B-Z DNA transition.

Topology in molecular biology : DNA and Proteins

Abstract: Topology in Biology: From DNA Mechanics to Enzymology.- Monte Carlo Simulation of DNA Topological Properties.- Dynamics of DNA Supercoiling.- From Tangle Fractions to DNA.- Linear Behavior of the Writhe Versus the Number of Crossings in Rational Knots and Links.- Combinatories and Topology of the ?-Sandwich and ?-Barrel Proteins.- The Structure of Collagen.- Euler Characteristic, Dehn-Sommerville Characteristics, and Their Applications.- Hopf Fibration and Its Applications.- Multi-Valued Functionals, One-Forms and Deformed de Rham Complex.- The Spectral Geometry of Riemann Surfaces.

DNA Computer Principle,Advances and Difficulties (III):The Structure and Character of “Data” in DNA Computing

Abstract: Biomolecular computing,including DNA computing,RNA computing and protein computing,is a kind of computing mode of information processing whose “data” is biomolecule.In addition,the biomolecular computing mode using PNA molecule as “data” was presented.This paper does not discuss PNA computing,RNA computing and protein computing because their research results are less.Clearly,it is a foundation problem to know well the structure and character of the “data”(that is DNA molecules)in DNA computing.So,this paper mainly discusses the structure and characters of several type of DNA molecule.We usually adopt different DNA molecule for different problem or models.Now,the main kinds of DNA molecules used in DNA computing are single,double and sticker terminal DNA molecules.Secondly,the DNA molecules used in DNA computing have also hairpin DNA molecules and plasmid DNA molecule.Especially,the relationship between the “data”(DNA molecule)and corresponding biomolecular model is disscuss.

Design and implementation of an anomaly-based network intrusion detection system utilizing the DNA model

Abstract: The genetic material that encodes the unique characteristics of each individual such as gender, eye color, and other human features is the well-known DNA. In this work, we introduce an anomaly intrusion detection system, built on the notion of a DNA sequence or gene, which is responsible for the normal network traffic patterns. Subsequently, the system detects suspicious activities by searching the "normal behavior DNA sequence" through string matching. On the other hand, string matching is a computationally intensive task and can be converted into a potential bottleneck without high-speed processing. Furthermore, conventional software-implemented string matching algorithms have not kept pace with the ever increasing network speeds. As a result, we adopt a monitoring phase that is hardware-implemented with the intention that DNA pattern matching is performed at wire-speed. Finally, we provide the details of our FPGA implementation of the bioinformatics-based string matching technique.

Towards a robust biocomputing solution of intractable problems

Abstract: An incremental approach to construction of biomolecular algorithms solving intractable problems is presented. The core idea is to build gradually the space of candidate solutions and remove invalid solutions as soon as possible. We demonstrate two examples of this strategy: a P system with replication and inhibitors for solving the Maximum Clique Problem for a graph, and an incremental DNA algorithm for the same problem inspired by the membrane solution. The DNA implementation is based on the parallel filtering DNA model featuring error-resistance of the employed operations. The algorithm is compared with two standard papers that addressed the same problem and its DNA implementation in the past. The comparison is carried out on the basis of a series of computational and physical parameters. The incremental algorithm features a dramatically lower cost in terms of time, the number and size of DNA strands, together with a high error-resistance. A probabilistic analysis shows that physical parameters (volume of the DNA pool, concentration of the solution-encoding strands) and error-resistance of the algorithm should allow to process in vitro instances of graphs with hundreds to thousands of vertices.

Topological Differences in the Interaction of Human DNA Topoisomerase I with DNA–Histone Complexes Modified by cis - and trans -DDP

Abstract: We show that the trefoil, figure-eight knot, and mini circular closed DNA are formed by the reaction of cis-DDP-modified φX174DNA–histoneLNCaP complexes as a new nucleosome model with human DNA topoisomease I. The yields from cis-DDP-modified complexes were far higher than that of trans-DDP. The topologically-distinct invariant DNA such as the trefoil and figure-eight knot are not produced in the reaction of DNA topo I with φX174DNA–histoneLNCaP complexes that are not modified by platinum. Therefore, the anti-cancer activity of cis-DDP may be related to the production of the trefoil, figure-eight knot, and mini circular closed DNA forms in the living cell. We subsequently demonstrate that the yield mechanism and identification of the topologically-distinct invariant DNA can be explained by the topological method using a Jones polynomial and recombination through the topo I path intra-twisted looped DNA model. These results suggest that the distinguishing of anti-neoplastic activity of cis- and trans-DDP can be partially explained by the distinct topologies of DNA, trefoil, figure-eight knot, and mini circular closed DNA that they produce.

Ab initio and Molecular Dynamics Study of the Nanomechanical Properties of DNA Oligomers

Abstract: Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic level Since this area of work is relatively new, this paper reports the results of computer simulation of elongation and compression of B-DNA structures providing new insights into high- energy forms of DNA implicated in these processes