No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Computational Screening and Design of DNA-Linked Molecular Nanowires
Abstract
DNA can be used as a structural component in the process of making conductive polymers called nanowires. Accurate molecular models could lead to a better understanding of how to prepare these types of materials. Here we present a computational tool that allows potential DNA-linked polymer designs to be screened and evaluated. The approach involves an iterative procedure that adjusts the positions of DNA-linked monomers in order to obtain reasonable molecular geometry compatible with normal DNA conformations and with the properties of the polymer being formed. This procedure has been used to evaluate designs already reported experimentally, as well as to suggest a new design based on pyrrylene vinylene (PV) monomers.
... Figure 2(a,b) show that a helical structure is obtained for one and two polymer chains in the (16,16) and (17,17) armchair SWNTs, respectively. Whereas in SWNTs (15,15) and (16,16) with smaller diameters the polymer keeps curving or straight pattern for one and two PPYs. If the diameter of the SWNT is smaller enough, the polymer cannot be encapsulated in the nanotube. ...
... Figure 2(a,b) show that a helical structure is obtained for one and two polymer chains in the (16,16) and (17,17) armchair SWNTs, respectively. Whereas in SWNTs (15,15) and (16,16) with smaller diameters the polymer keeps curving or straight pattern for one and two PPYs. If the diameter of the SWNT is smaller enough, the polymer cannot be encapsulated in the nanotube. ...
The polymer possessing with planar structure can be activated and guided to encapsulate the inner space of SWNT and form a helix through van der Waals interaction and the π-π stacking effect between the polymer and the inner surface of SWNT. The SWNT size, the nanostructure and flexibility of polymer chain are all determine the final structures. The basic interaction between the polymer and the nanotubes is investigated, and the condition and mechanism of the helix-forming are explained particularly. Hybrid polymers improve the ability of the helix formation. This study provides scientific basis for fabricating helical polymers encapsulated in SWNTs and eventually on their applications in various areas.
... At a nanoscopic scale, naturally occurring proteins and nucleic acids with a self-assembled helical construction direct the sophisticated functions in living processes. Inspired by the elegance and complexity of biological helices, long-strand polymers are expected to be created with well-defined and functional helicity to design elongated supramolecular architectures [1][2][3][4]. Helicity may further explore new functions of polymers because the aggregation pattern is more direct and important than the chain structure in affecting the properties of polymers [5]. Nevertheless, it remains a fundamental challenge to unambiguously construct helical configurations from artificial supramolecules considering the complicated organic synthesis, though a new and reliable method for unambiguously constructing a polymer helix is urgently needed [6][7][8]. ...
Molecular dynamics simulations demonstrate that several polyacetylene (PA) chains can encapsulate and self-assemble into multi-stranded helical structures in confined inner space of carbon nanotubes (SWCNT). The driving van der Waals force and curvature provided by tube wall enable polymers to bend and spiral to maximize the π-π stacking area with tube wall when filling inside SWCNT. Structural forms and knitting pattern of multiple helices are influenced by the combined effect of tube space, number of PA chains and temperature. The knitting pattern of six-helix is unique and knitted six-helix can exist steadily after remove the SWCNT while two- to five-helix will recover intrinsic straight configurations.
Using a combined approach of molecular dynamics (MD) and density functional theoretical (DFT) calculations, we perform the investigation of structures, energetics and optical properties of Ag12 and Au12 clusters in the presence of single-stranded DNA (ssDNA) scaffold of various nucleobase sequences (i.e. ssdA12, ssdT12, ssdG12 and ssdC12). The individual ssDNA undergoes various conformational changes in the presence of different metal clusters during the course of 1.5 ns MD simulations in aqueous media. We find that ssdG12 interacts strongly with the Ag12 cluster while ssdA12 shows greater binding affinity towards the Au12 cluster. We also find that the two different kinds of binding modes of a nucleobase play a key role in deciding the overall structure and stability of the complex while interacting with metal clusters. The metal clusters form nanocomposites with ssDNA either via π-stacking and/or by the interaction mediated through specific atoms (nitrogen and/or oxygen) present in the nucleobases. The optical response properties of these Ag12/Au12–ssDNA composites together with the bare metal clusters are calculated with the MD simulated structures alone, which are comparable with experimental results. The optical absorption characteristics of metal clusters are little affected by the presence of ssDNA scaffold due to the frontier orbital localization mainly on the metal clusters or ssDNA.
We use molecular dynamics (MD) simulations to show that a DNA-like double helix of two poly(acetylene) (PA) chains can form inside single-walled carbon nanotubes (SWNTs). The computational results indicate that SWNTs can activate and guide the self-assembly of polymer chains, allowing them to adopt a helical configuration in a SWNT through the combined action of the van der Waals potential well and the π-π stacking interaction between the polymer and the inner surface of SWNTs. Meanwhile both the SWNT size and polymer chain stiffness determine the outcome of the nanostructure. Furthermore, we also found that water clusters encourage the self-assembly of PA helical structures in the tube. This molecular model may lead to a better understanding of the formation of a double helix biological molecule inside SWNTs. Alternatively, it could form the basis of a novel nanoscale material by utilizing the 'empty' spaces of SWNTs.
A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method is applied to a molecular dynamics simulation of a liquid of 64 n-butane molecules and compared to a simulation using generalized coordinates. The method should be useful for molecular dynamics calculations on large molecules with internal degrees of freedom.
The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction,
and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their complexes with proteins and
other ligands. The server allows the user to determine a wide variety of conformational parameters in a given structure—such
as the identities and rigid-body parameters of interacting nucleic-acid bases and base-pair steps, the nucleotides comprising
helical fragments, etc. It is also possible to build 3D models of arbitrary nucleotide sequences and helical types, customized
single-stranded and double-helical structures with user-defined base-pair parameters and sequences, and models of DNA ‘decorated’
at user-defined sites with proteins and other molecules. The visualization component offers unique, publication-quality representations
of nucleic-acid structures, such as ‘block’ images of bases and base pairs and stacking diagrams of interacting nucleotides.
The w3DNA web server, located at http://w3dna.rutgers.edu, is free and open to all users with no login requirement.
We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668–1688, 2005
In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable and fail to converge. We present an algorithm developed originally for inverse kinematics applications in robotics. In robotics, an end effector in the form of a robot hand must reach for an object in space by altering adjustable joint angles and arm lengths. In loop prediction, dihedral angles must be adjusted to move the C-terminal residue of a segment to superimpose on a fixed anchor residue in the protein structure. The algorithm, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C-terminal anchor and the corresponding atoms in the fixed C-terminal anchor. The result is an equation in one variable for the proposed change in each dihedral. The algorithm proceeds iteratively through all of the adjustable dihedral angles from the N-terminal to the C-terminal end of the loop. CCD is suitable as a component of loop prediction methods that generate large numbers of trial structures. It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average.
A new method for computing numerical solutions to the inverse
kinematics problem of robotic manipulators is developed. The method is
based on a combination of two nonlinear programming techniques and the
forward recursion formulas, with the joint limitations of the robot
being handled implicitly as simple boundary constraints. This method is
numerically stable since it converges to the correct answer with
virtually any initial approximation, and it is not sensitive to the
singular configuration of the manipulator. In addition, this method is
computationally efficient and can be applied to serial manipulators
having any number of degrees of freedom
An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.
Helical conformations of infinite polymer chains may be described by the helical parameters, d and θ (the translation along the helix axis and the angle of rotation about the axis per repeat unit), pi (the distance of the ith atom from the axis), dij, and dij (the translation along the axis and the angle of rotation, respectively, on passing from the ith atom to the jth). A general method has been worked out for calculating all those helical parameters from the bond lengths, bond angles, and internal-rotation angles. The positions of the main chain and side chain atoms with respect to the axis may also be calculated. All the equations are applicable to any helical polymer chain and are readily programmed for electronic computers. A method is also presented for calculating the partial derivatives of helical parameters with respect to molecular parameters.
Specifically designed conducting polymers were prepared from monomers that are covalently linked to duplex DNA. These materials combine the self-assembly properties of DNA with those of conducting polymers and may be valuable in the development of self-directing molecular nanowires. Single-strand DNA oligomers having 2,5-bis(2-thienyl)pyrroles (SNS monomers) covalently linked at every other nucleobase along one strand form stable duplexes with their complementary strands. The duplex DNA serves as a scaffold that aligns the SNS monomers within its major groove. The reaction of these SNS-containing duplexes with horseradish peroxidase and H2O2 (an oxidant) results in the conversion of the SNS monomers to a conjoined (covalently linked) polymer having the optical properties of a conducting polymer. Examination of radiolabeled oligomers confirms bond formation between SNS monomers, and that conclusion is supported by AFM images. The conjoined polymers have structures that are determined and controlled by the DNA template.
A thienopyrrole oligomer conjoined to DNA was prepared by means of a templated synthesis protocol. The oligomer was formed by reaction, initiated with HRP/H2O2, of thieno[3,2-b]pyrrole monomers attached to cytosine bases. The thienopyrrole oligomer was characterized spectroscopically.
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
The synthesis of DNA/nylon ladder oligomers is described. Three stages of the development are addressed: the synthesis of 2'-beta-substituted phosphoramidites, the deprotection/purification protocols of ODNs modified with both amino and carboxyl groups, and amide bond-forming reactions on the ODNs. The established technology and the novel DNA-based ladder oligomer structure opens a pathway to the synthesis of topological molecular objects and networks templated by DNA through versatile DNA nanotechnology. The DNA-based ladder oligomers may find application in the antisense area.
We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.
Many applications require a method for translating a large list of bond angles and bond lengths to precise atomic Cartesian coordinates. This simple but computationally consuming task occurs ubiquitously in modeling proteins, DNA, and other polymers as well as in many other fields such as robotics. To find an optimal method, algorithms can be compared by a number of operations, speed, intrinsic numerical stability, and parallelization. We discuss five established methods for growing a protein backbone by serial chain extension from bond angles and bond lengths. We introduce the Natural Extension Reference Frame (NeRF) method developed for Rosetta's chain extension subroutine, as well as an improved implementation. In comparison to traditional two-step rotations, vector algebra, or Quaternion product algorithms, the NeRF algorithm is superior for this application: it requires 47% fewer floating point operations, demonstrates the best intrinsic numerical stability, and offers prospects for parallel processor acceleration. The NeRF formalism factors the mathematical operations of chain extension into two independent terms with orthogonal subsets of the dependent variables; the apparent irreducibility of these factors hint that the minimal operation set may have been identified. Benchmarks are made on Intel Pentium and Motorola PowerPC CPUs.
A series of polyaniline (PANI) oligomers was constructed from monomer units covalently linked to duplex DNA through N-(2-aminoethyl) groups bonded through cytosines. DNA oligomers containing the aniline monomers were treated with horseradish peroxidase (HRP) and H2O2 under conditions known to cause polymerization of aniline. No change in the absorption spectrum of the DNA was observed for samples containing fewer than four contiguous aniline groups. However, for oligomers containing four, five, or six aniline units, treatment with HRP and H2O2 led to the appearance of absorption features characteristic of the conducting "proton doped" emeraldine oxidation state of PANI. Molecular modeling shows that the DNA is distorted in the region of the PANI, but flanking regions of the DNA maintain their B-form structure. These findings provide a method to exploit the self-recognition, self-assembly, and sequence programmability of DNA for the formation of conducting polymers.
A new class of materials was prepared from aniline-containing oligomers that are covalently linked to the nucleobases of duplex DNA. Oligomers composed of repeating aniline (PANI) or 4-aminobiphenyl (PAB) units having the properties of conducting polymers conjoined to the DNA were prepared by the reaction of horseradish peroxidase and H2O2 with DNA having the appropriate monomers aligned within the major groove. These oligomers exhibit the spectral and chemical properties typical of para-linked polyanilines. This method of preparation enables utilization of the unique self-recognizing properties and sequence programmability of DNA to create tailored oligomers. This ability was demonstrated experimentally by preparation of PAB oligomers from alternating benzene and aniline monomers. Conjoined conducting polymers carrying the sequence information of DNA may have applicability as nanowires.
The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 degrees C increase in the thermal transition temperature (T(m)) for five linkages) and RNA (around 15 degrees C increase in T(m) for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised T(m) from less to slightly greater than T(m) of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2'-position of ribose and recovery of stability upon linkage of the side chains.