Showing papers on "Molecular models of DNA published in 2006"

Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation.

Abstract: A new single-molecule approach is used to examine how a nucleoid-associated protein, H-NS, functions. H-NS sits between the two DNA molecules and is aligned along the helical pitch. H-NS does not act as a barrier to RNA polymerase, and its cooperative binding ensures that H-NS is dynamic enough to accommodate the movement of DNA-associated motor proteins, but stable enough to maintain DNA loops. Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions1. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins2,3. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA–DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS–DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.

YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

Abstract: Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily.

Nanotechnology : science and computation

Abstract: Part 1 DNA Nanotechnology Algorithmic Self-assembly: Scaffolded DNA Origami: From Generalized Multi-crossovers to Polygonal Networks.- A Fresh Look at DNA Nanotechnology.- DNA Nanotechnology: An Evolving Field.- Self-healing Tile Sets.- Compact Error Resilient Computational DNA Tilings.- Forbidding-Enforcing Conditions in DNA Self-assembly of Graphs.- Part 2: Codes for DNA Nanotechnology: Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set.- Selection of Large Independent Sets of DNA Oligonucleotides.- Involution Solid Codes.- Part III: DNA Nanodevices: DNA-Based Motor Work at Bell Laboratories.- Nanoscale Molecular Transport by Synthetic DNA Machines.- Part IV: Electronics, Nanowires and DNA: A Supramolecular Approach to Metal Array Programming Using Artificial DNA.- Multicomponent Assemblies Including Long DNA and Nanoparrticles An Answer for the Integration Problem? Molecular Electronics From Physics to Computing.- Part V: Other Bio-molecules in Self-assembly: Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials.- Adding Functionality to DNA Arrays: The Developments of Semisynthetic DNA-Protein Conjugates.- Bacterial Surface Layer Proteins: A Simple but Versatile Biological Self-assembly System in Nature.- Part VI: Biomolecular Computational Models: Computing with Hairpins and Secondary Structures of DNA.- Bottom-up Approach to Complex Molecular Behaviors.- Aqueous Computing: Writing on Molecules Dissolved in Water.- Part VII: Computations Inspired by Cells: Turing Machines with Cells on the Tape.- Insights into a Biological Computer: Detangling Scrambled Genes of Ciliates.- Modeling Simple Operations for Gene Assembly.-

Functional Materials Derived from DNA

Abstract: DNA has special properties and its unique double-helical structure offers excellent prospects forcreating novel DNA-based materials. In recent years, DNA has been shown to be an ideal molecule in thematerial world. This review is intended to provide an overview of functional materials derived from DNAbased on the double-helical structure. Various DNA-based materials are reviewed according to the basicDNA structural properties, including the electrostatic properties of DNA as a highly charged polyelectrolyte,complementary base pairing, and intercalation and groove binding interaction with small molecules. Finally,attempts to produce biomaterials based on DNA are also summarized.

Modelling the biomechanical properties of DNA using computer simulation

Abstract: Duplex DNA must remain stable when not in use to protect the genetic material. However, the two strands must be separated whenever genes are copied or expressed to expose the coding strand for synthesis of complementary RNA or DNA bases. Therefore, the double stranded structure must be relatively easy to take apart when required. These conflicting biological requirements have important implications for the mechanical properties of duplex DNA. Considerable insight into the forces required to denature DNA has been provided by nanomanipulation experiments, which measure the mechanical properties of single molecules in the laboratory. This paper describes recent computer simulation methods that have been developed to mimic nanomanipulation experiments and which, quite literally, 'destruction test' duplex DNA in silico. The method is verified by comparison with single molecule stretching experiments that measure the force required to unbind the two DNA strands. The model is then extended to investigate the thermodynamics of DNA bending and twisting. This is of biological importance as the DNA must be very tightly packaged to fit within the nucleus, and is therefore usually found in a highly twisted or supercoiled state (in bacteria) or wrapped tightly around histone proteins into a densely compacted structure (in animals). In particular, these simulations highlight the importance of thermal fluctuations and entropy in determining the biomechanical properties of DNA. This has implications for the action of DNA processing molecular motors, and also for nanotechnology. Biological machines are able to manipulate single molecules reliably on an energy scale comparable to that of thermal noise. The hope is that understanding the statistical mechanisms that a cell uses to achieve this will be invaluable for the future design of 'nanoengines' engineered to perform new technological functions at the nanoscale.

On the discrete Peyrard-Bishop model of DNA: stationary solutions and stability.

Abstract: As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite, and homogeneous Peyrard-Bishop DNA model. We find and classify all the stationary solutions of the model, as well as analytic approximations of them, both in the continuum and in the discrete limits. Our results explain the structure of the solutions reported by Theodorakopoulos et al. [Phys. Rev. Lett. 93, 258101 (2004)] and provide a way to proceed to the analysis of the generalized version of the model incorporating the genetic information.

Electronic transport and localization in short and long DNA

Abstract: The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations Here, we review recent theoretical progress by concentrating on quantum chemical, molecular dynamics-based approaches to short DNA strands and physics-motivated tight-binding transport studies of long or even complete DNA sequences In both cases, we observe small, but significant differences between specific DNA sequences such as periodic repetitions and aperiodic sequences of AT bases, λ - DNA, centromeric DNA, and promoter sequences as well as random-ATGC DNA

Single DNA conformations and biological function

Abstract: From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications

DNA Mechanics and Statistical Mechanics

Abstract: The elastic properties of DNA are essential for its biological function. They control its bending and twisting as well as the induction of structural modifications in the molecule. These can affect its interaction with the cell machinery. The response of a single DNA molecule to a mechanical stress can be precisely determined in single-molecule experiments that give access to accurate measurements of the elastic parameters of DNA. Keywords: elasticity of DNA; single molecule manipulations; theoretical models of DNA; structural transitions in DNA

Topological Solitons in a Heterogeneous DNA Molecule 1

Abstract: The dynamics of topological solitons describing the opening of the double helix of a DNA molecule is studied. The estimated actual values of the rigidity parameters of the polynucleotide chains made it possible to develop a more precise DNA model and to show that four types of topological solitons can appear in the DNA double helix. Interactions between solitons are studied, as well as their interaction with the chain heterogene- ities and the stability of solitons with respect to thermal fluctuations. Thermal fluctuations promote propagation of solitons along a heterogeneous base sequence.