CiteULike: dna's library [205 articles]

High sensitivity multianalyte immunoassay using covalent DNA-labeled antibodies and polymerase chain reaction.

ER Hendrickson — 2008-05-11T08:05:35-00:00

Nucleic acids research, Vol. 23, No. 3. (11 February 1995), pp. 522-529.

A multianalyte immunoassay for simultaneous detection of three analytes (hTSH, hCG and beta-Gal) has been demonstrated using DNA-labeled antibodies and polymerase chain reaction (PCR) for amplification of assay response. The labeled antibodies were prepared by covalently coupling uniquely designed DNA oligonucleotides to each of the analyte-specific monoclonal antibodies. Each of the DNA oligonucleotide labels contained the same primer sequences to facilitate co-amplification by a single primer pair. Assays were performed using a two-antibody sandwich assay format and a mixture of the three DNA-labeled antibodies. Dose-response relationships for each analyte were demonstrated. Analytes were detected at sensitivities exceeding those of conventional enzyme immunoassays by approximately three orders of magnitude. Detection limits for hTSH, beta-Gal and hCG were respectively 1 x 10(-19), 1 x 10(-17) and 1 x 10(-17) mol. Given the enormous amplification afforded by PCR and the existing capability to differentiate DNA based on size or sequence differences, the use of DNA-labeled antibodies could provide the basis for the simultaneous detection of many analytes at sensitivities greater than those of existing antigen detection systems. These findings in concert with previous reports suggest this hybrid technology could provide a new generation of ultra-sensitive multianalyte immunoassays.

Analyte detection with DNA-labeled antibodies and polymerase chain reaction.

RD Joerger — 2008-05-11T07:43:43-00:00

Clinical chemistry, Vol. 41, No. 9. (September 1995), pp. 1371-1377.

We demonstrate immuno-polymerase chain reaction (PCR) assays for two clinical analytes--human thyroid-stimulating hormone and chorionic gonadotropin (hTSH, hCG)--using DNA-labeled antibodies and PCR for amplification of assay response. DNA-antibody conjugates were synthesized by using heterobifunctional cross-linker chemistries to covalently attach single- or double-stranded DNA labels through amine or sulfhydryl groups on the analyte antibodies. These approaches yielded molecular chimeras possessing both analyte-specific antibody binding and nucleic acid amplification functionalities. Dose-response relationships were demonstrated for immuno-PCR assays of both analytes in a microtiter plate-based, two-antibody sandwich assay format. Detection limits for hTSH (1 x 10(-19) mol, < 1.4 mIU/L) and hCG (5 x 10(-18) mol, 0.025 IU/L) exceeded those of conventional enzyme immunoassays by 2-3 orders of magnitude. We also evaluated various DNA design factors influencing label amplification and assay performance, such as primer sequence, strand number, and DNA length. Our findings, in concert with previous reports, suggest that this hybrid technology could provide the basis for a new generation of ultra-sensitive immunoassays offering multianalyte capabilities.

Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates.

T Sano — 2006-09-27T13:02:27-00:00

Science, Vol. 258, No. 5079. (2 October 1992), pp. 120-122.

An antigen detection system, termed immuno-polymerase chain reaction (immuno-PCR), was developed in which a specific DNA molecule is used as the marker. A streptavidin-protein A chimera that possesses tight and specific binding affinity both for biotin and immunoglobulin G was used to attach a biotinylated DNA specifically to antigen-monoclonal antibody complexes that had been immobilized on microtiter plate wells. Then, a segment of the attached DNA was amplified by PCR. Analysis of the PCR products by agarose gel electrophoresis after staining with ethidium bromide allowed as few as 580 antigen molecules (9.6 x 10(-22) moles) to be readily and reproducibly detected. Direct comparison with enzyme-linked immunosorbent assay with the use of a chimera-alkaline phosphatase conjugate demonstrates that enhancement (approximately x 10(5)) in detection sensitivity was obtained with the use of immuno-PCR. Given the enormous amplification capability and specificity of PCR, this immuno-PCR technology has a sensitivity greater than any existing antigen detection system and, in principle, could be applied to the detection of single antigen molecules.

Algorithmic self-assembly of DNA Sierpinski triangles.

PW Rothemund — 2005-05-02T18:13:02-00:00

PLoS Biol, Vol. 2, No. 12. (December 2004)

Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern--a Sierpinski triangle--as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100-200 correct tiles. Error rates during assembly appear to range from 1% to 10%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks.

Cell adhesion and motility depend on nanoscale RGD clustering.

G Maheshwari — 2008-05-09T14:24:20-00:00

Journal of cell science, Vol. 113 ( Pt 10) (May 2000), pp. 1677-1686.

Integrin adhesion receptors play a crucial role in regulating interactions between cells and extracellular matrix (ECM). Integrin activation initiates multiple intracellular signaling pathways and results in regulation of cell functions such as motility, proliferation and differentiation. Two key observations regarding the biophysical nature of integrin-mediated cell-matrix interactions motivated the present study: (1) cell motility can be regulated by modulating the magnitude of cell-substratum adhesion, by varying cell integrin expression level, integrin-ECM binding affinity or substratum ECM surface density; and (2) integrin clustering enables assembly of multiple cytoplasmic regulatory and structural proteins at sites of aggregated integrin cytoplasmic domains, activating certain intracellular signalling pathways. Here, using a minimal integrin adhesion ligand, YGRGD, we test the hypothesis that ligand clustering can affect cell migration in a manner related to its modulation of cell-substratum adhesion. We employ a synthetic polymer-linking method, which allows us to independently and systematically vary both the average surface density and the local (approx. 50 nm scale) spatial distribution of the YGRGD peptide, against a background otherwise inert with respect to cell adhesion. In this system, the ligand was presented in three alternative spatial distributions: singly, in clusters with an average of five ligands per cluster, or in clusters with an average of nine ligands per cluster; for each of these spatial distributions, a range of average ligand densities (1,000-200,000 ligands/micrometer(2)) were examined. Cluster spacing was adjusted in order to present equivalent average ligand densities independently of cluster size. The murine NR6 fibroblast cell line was used as a model because its migration behavior on ECM in the presence and absence of growth factors has been well-characterized and it expresses integrins known to interact with the YGRGD peptide. Using time-lapse videomicroscopy and analysis of individual cell movement paths, we find that NR6 cells can migrate on substrata where adhesion is mediated solely by the YGRGD peptide. As previously observed for migration of NR6 cells on fibronectin, migration speed on YGRGD is a function of the average surface ligand density. Strikingly, clustering of ligand significantly reduced the average ligand density required to support cell migration. In fact, non-clustered integrin ligands support cell attachment but neither full spreading nor haptokinetic or chemokinetic motility. In addition, by quantifying the strength of cell-substratum adhesion, we find that the variation of cell speed with spatial presentation of YGRGD is mediated via its effect on cell adhesion. These effects on motility and adhesion are also observed in the presence of epidermal growth factor (EGF), a known motility-regulating growth factor. Variation in YGRGD presentation also affects the organization of actin filaments within the cell, with a greater number of cells exhibiting stress fibers at higher cluster sizes of YGRGD. Our observations demonstrate that cell motility may be regulated by varying ligand spatial presentation at the nanoscale level, and suggest that integrin clustering is required to support cell locomotion.

Full activation of the T cell receptor requires both clustering and conformational changes at CD3.

S Minguet — 2008-05-09T14:17:21-00:00

Immunity, Vol. 26, No. 1. (January 2007), pp. 43-54.

T cell receptor (TCR-CD3) triggering involves both receptor clustering and conformational changes at the cytoplasmic tails of the CD3 subunits. The mechanism by which TCRalphabeta ligand binding confers conformational changes to CD3 is unknown. By using well-defined ligands, we showed that induction of the conformational change requires both multivalent engagement and the mobility restriction of the TCR-CD3 imposed by the plasma membrane. The conformational change is elicited by cooperative rearrangements of two TCR-CD3 complexes and does not require accompanying changes in the structure of the TCRalphabeta ectodomains. This conformational change at CD3 reverts upon ligand dissociation and is required for T cell activation. Thus, our permissive geometry model provides a molecular mechanism that rationalizes how the information of ligand binding to TCRalphabeta is transmitted to the CD3 subunits and to the intracellular signaling machinery.

Native protein nanolithography that can write, read and erase

Ali Tinazli — 2008-05-09T11:32:45-00:00

Nat Nano, Vol. 2, No. 4. (April 2007), pp. 220-225.

Activation of integrin function by nanopatterned adhesive interfaces.

M Arnold — 2008-05-09T11:12:14-00:00

Chemphyschem : a European journal of chemical physics and physical chemistry, Vol. 5, No. 3. (19 March 2004), pp. 383-388.

To study the function behind the molecular arrangement of single integrins in cell adhesion, we designed a hexagonally close-packed rigid template of cell-adhesive gold nanodots coated with cyclic RGDfK peptide by using block-copolymer micelle nanolithography. The diameter of the adhesive dots is < 8 nm, which allows the binding of one integrin per dot. These dots are positioned with high precision at 28, 58, 73, and 85 nm spacing at interfaces. A separation of > or = 73 nm between the adhesive dots results in limited cell attachment and spreading, and dramatically reduces the formation of focal adhesion and actin stress fibers. We attribute these cellular responses to restricted integrin clustering rather than insufficient number of ligand molecules in the cell-matrix interface since "micro-nanopatterned" substrates consisting of alternating fields with dense and no nanodots do support cell adhesion. We propose that the range between 58-73 nm is a universal length scale for integrin clustering and activation, since these properties are shared by a variety of cultured cells.

Cell adhesion molecule DM-GRASP presented as nanopatterns to neurons regulates attachment and neurite growth

Karsten Thelen — 2008-05-09T10:59:04-00:00

Soft Matter, Vol. 3 (2007), pp. 1486-1491.

Adhesion and neurite formation of neurons and neuroblastoma cells critically depends on the lateral spacing of the cell adhesion molecule DM-GRASP offered as nanostructured substrate.

Designed DNA molecules: principles and applications of molecular nanotechnology

Anne Condon — 2006-06-20T12:05:51-00:00

Nature Reviews Genetics, Vol. 7, No. 7. (13 June 2006), pp. 565-575.

Anisotropically DNA-functionalized nanoparticle dimers

B Högberg — 2008-05-06T20:26:42-00:00

European Physical Journal D, Vol. 43 (July 2007), pp. 299-302.

Self-assembly of complex, non-periodic nanostructures can only be achieved by using anisotropic building-blocks. The building blocks need to have at least four bonds pointing in separate directions [J. Comput. Theor. Nanosci. 3, 391 (2006)]. We have previously presented a method for the synthesis of such building-blocks using DNA-functionalized gold nanoparticles. Here, we report on the progress in the experimental realization of this scheme. The first goal, in a process to make programmable self-assembly building-blocks using nanoparticles, is the production of dimers with different DNA-functions on the two component particles. We report on the fabrication of anisotropically functionalized dimers of nanoparticles of two different sizes. As a result of their anisotropy, these demonstrator building blocks can be made to assemble into spherical structures.

Principles of nanostructure design with protein building blocks.

Chung-Jung Tsai — 2007-05-25T02:23:33-00:00

Proteins, Vol. 68, No. 1. (3 April 2007), pp. 1-12.

Currently there is increasing interest in nanostructures and their design. Nanostructure design involves the ability to predictably manipulate the properties of the self-assembly of autonomous units. Autonomous units have preferred conformational states. The units can be synthetic material science-based or derived from functional biological macromolecules. Autonomous biological building blocks with available structures provide an extremely rich and useful resource for design. For proteins, the structural databases contain large libraries of protein molecules and their building blocks with a range of shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these can expand the available chemical space and enhance the desired properties. Here we focus on the principles of nanostructure design with protein building blocks. Proteins 2007. (c) 2007 Wiley-Liss, Inc.

Nanometer-Sized Amino Acids for the Synthesis of Nanometer-Scale Water-Soluble Molecular Rods of Precise Length

CM Gothard — 2008-05-06T20:20:45-00:00

J. Am. Chem. Soc., Vol. 129, No. 23. (13 June 2007), pp. 7272-7273.

Abstract: This paper introduces the unnatural amino acid Abc2K as a nanometer-length building block for the creation of water-soluble molecular rods of exceptional size. Abc2K is a water-soluble variant of the unnatural amino acid 4'-amino-[1,1'-biphenyl]-4-carboxylic acid (Abc) with lysinelike propyloxyammonium side chains at the 2- and 5-positions. The protected building block Fmoc-Abc2K(Boc)-OH (1) can be used in standard Fmoc-based solid-phase peptide synthesis to create water-soluble rodlike peptides in nanometer unit lengths up to at least ten nanometers. Oligomers up to and including the decamer were easily prepared on a Rink amide resin. These peptides are easy to purify and characterize by standard reverse-phase HPLC, 1H NMR, and ESI-MS techniques. The Abc2K amino acid can be combined with various standard amino acids to provide well behaved hybrid and biologically relevant peptides. Building block 1 is efficiently prepared on a multigram scale from commercially available starting materials by way of the Suzuki cross-coupling reaction. Molecular modeling studies of Abc2K oligomers show only minor effects from torsional and bending motions and support a model in which the oligomers are relatively straight and rigid. Fluorescence resonance energy transfer (FRET) studies are consistent with a model in which the Abc2K oligomers behave as rigid rods with a length of 1.0 nm per monomer unit.

Design and chance in the self-assembly of macromolecules.

JA Worrall — 2007-06-25T20:58:46-00:00

Biochem Soc Trans, Vol. 35, No. Pt 3. (June 2007), pp. 502-507.

The principles of self-assembly are described for naturally occurring macromolecules and for complex assemblies formed from simple synthetic constituents. Many biological molecules owe their function and specificity to their three-dimensional folds, and, in many cases, these folds are specified entirely by the sequence of the constituent amino acids or nucleic acids, and without the requirement for additional machinery to guide the formation of the structure. Thus sequence may often be sufficient to guide the assembly process, starting from denatured components having little or no folds, to the completion state with the stable, equilibrium fold that encompasses functional activity. Self-assembly of homopolymeric structures does not necessarily preserve symmetry, and some polymeric assemblies are organized so that their chemically identical subunits pack stably in geometrically non-equivalent ways. Self-assembly can also involve scaffolds that lack structure, as seen in the multi-enzyme assembly, the degradosome. The stable self-assembly of lipids into dynamic membraneous sheets is also described, and an example is shown in which a synthetic detergent can assemble into membrane layers.

Cation-dependent switching of DNA nanostructures.

Y He — 2008-05-06T18:13:00-00:00

Macromolecular bioscience, Vol. 7, No. 8. (7 August 2007), pp. 1060-1064.

DNA is a versatile building material for nanoconstruction because of its remarkable molecular-recognition capability and well-predicted duplex conformation. A number of DNA motifs have been engineered, which can assemble into well-defined nanostructures in Mg(2+)-containing buffer solution. XRD studies reveal that the DNA conformation is slightly influenced by divalent cations (such as Mg(2+) or Ca(2+)). This phenomenon can be utilized in DNA self-assembly for regulating self-assembled DNA nanostructures. As an initial step, a symmetric cross motif forms flat, periodic, 2D lattices in Mg(2+)-containing solutions, but long nanofibers in Ca(2+)-containing solutions. The obtained DNA fibers can serve as templates to fabricate CaCO(3) nanotubes and nanowires.

Sequence-Dependent Fluorescence of DNA-Hosted Silver Nanoclusters

Elisabeth Gwinn — 2008-05-06T18:01:21-00:00

Advanced Materials, Vol. 20 (2008), pp. 279-283.

Nanoscale structure and dynamics of DNA.

MA Berg — 2008-05-06T17:47:19-00:00

Physical chemistry chemical physics : PCCP, Vol. 10, No. 9. (7 March 2008), pp. 1229-1242.

DNA is depicted in elementary chemistry and biology texts as a perfect double helix; but local structural variations and nanoscale motions within the double helix are critical for its ability to be packaged, recognized, and transcribed. DNA is becoming a favored nanoscale assembly tool due to the precise pairing of complementary strands that in principle can bring nanoscale objects within a well-defined distance of each other. However, future nanotechnology applications of DNA need to take into account its variable nanoscale structural and dynamic properties, especially in terms of its solvent shell and counterions. This article highlights efforts of the authors to (1) interrogate nanoscale structures of DNA using nanoparticles and (2) measure the dynamic nature of DNA over six orders of magnitude in time, using a fluorescent reporter in the base stack.

An autonomous polymerization motor powered by DNA hybridization

Suvir Venkataraman — 2008-03-19T23:43:07-00:00

Nat Nano, Vol. 2, No. 8. (2007), pp. 490-494.

Autonomous programmable biomolecular devices using self-assembled DNA nanostructures

John Reif — 2008-05-06T17:11:18-00:00

Commun. ACM, Vol. 50, No. 9. (September 2007), pp. 46-53.

Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization.

H Li — 2008-05-06T16:59:48-00:00

Organic & biomolecular chemistry, Vol. 4, No. 18. (21 September 2006), pp. 3420-3426.

Complex DNA nanostructures have been developed as structural components for the construction of nanoscale objects. Recent advances have enabled self-assembly of organized DNA nanolattices and their use in patterning functional bio-macromolecules and other nanomaterials. Adapter molecules that bind specifically to both DNA lattices and nanomaterials would be useful components in a molecular construction kit for patterned nanodevices. Herein we describe the selection from phage display libraries of single-chain antibodies (scFv) for binding to a specific DNA aptamer and their development as adapter molecules for nanoscale construction. We demonstrate the decoration of various DNA tile structures with aptamers and show binding of the selected single-chain antibody as well as the self-assembly of mixed DNA-protein biomolecular lattices.

DNA-templated self-assembly of two-dimensional and periodical gold nanoparticle arrays.

J Sharma — 2008-05-06T16:38:20-00:00

Angewandte Chemie (International ed. in English), Vol. 45, No. 5. (23 January 2006), pp. 730-735.

Molecular scale architecture: engineered three- and four-way junctions.

S Wilkinson — 2008-05-06T11:41:27-00:00

Bioconjugate chemistry, Vol. 19, No. 2. (February 2008), pp. 470-475.

Biomolecular self-assembly provides a basis for the bottom-up construction of useful and diverse nanoscale architectures. DNA is commonly used to create these assemblies and is often exploited as a lattice or an array. Although geometrically rigid and highly predictable, these sheets of repetitive constructs often lack the ability to be enzymatically manipulated or elongated by standard biochemical techniques. Here, we describe two approaches for the construction of position-controlled, molecular-scale, discrete, three- and four-way DNA junctions. The first approach for constructing these junctions relies on the use of nonmigrating cruciforms generated from synthetic oligonucleotides to which large, biologically generated, double-stranded DNA segments are enzymatically ligated. The second approach utilitizes the DNA methyltransferase-based SMILing (sequence-specific methyltransferase-induced labeling of DNA) method to site-specifically incorporate a biotin within biologically derived DNA. Streptavidin is then used to form junctions between unique DNA strands. The resultant assemblies have precise and predetermined connections with lengths that can be varied by enzymatic or hybridization techniques, or geometrically controlled with standard DNA functionalization methods. These junctions are positioned with single nucleotide resolution on large, micrometer-length templates. Both approaches generate DNA assemblies which are fully compatible with standard recombinant methods and thus provide a novel basis for nanoengineering applications.

From DNA to transistors

E Braun — 2008-05-06T11:33:46-00:00

Advances in Physics, Vol. 53 (June 2004), pp. 441-496.

The rapid advance in molecular biology and nanotechnology opens up the possibility to explore the interface between biology and electronics at the single-molecule level. We focus on the organization of molecular electronic circuits. Interconnecting an immense number of molecular devices into a functional circuit and constructing a framework for integrated molecular electronics requires new concepts. A promising avenue relies on bottom-up assembly where the information for the circuit connectivity and functionality is embedded in the molecular building blocks. Biology can provide concepts and mechanisms for advancing this approach, but there is no straightforward way to apply them to electronics since biological molecules are essentially electrically insulating. Bridging the chasm between biology and electronics therefore presents great challenges. Circuit organization on the molecular scale is considered and contrasted with the levels of organization presented by the living world. The discussion then focuses on our proposal to harness DNA and molecular biology to construct the scaffold for integrated molecular electronics. DNA metallization is used to convert the DNA scaffold into a conductive one. We present the framework of sequence-specific molecular lithography based on the biological mechanism of homologous genetic recombination and carried out by the bacterial protein RecA. Molecular lithography enables us to use the information encoded in the scaffold DNA molecules for directing the construction of an electronic circuit. We show that it can lead all the way from DNA molecules to working transistors in a test-tube. Carbon nanotubes are incorporated as the active electronic components in the DNA-templated transistors. Our approach can, in principle, be applied to the fabrication of larger-scale electronic circuits. The realization of complex DNA-based circuits will, however, require new concepts and additional biological machinery allowing, for example, feedback from the electronic functionality to direct the assembly process and adaptation mechanisms.

A single-molecule Förster resonance energy transfer analysis of fluorescent DNA-protein conjugates for nanobiotechnology.

F Kukolka — 2008-05-06T10:32:18-00:00

Small (Weinheim an der Bergstrasse, Germany), Vol. 2, No. 8-9. (August 2006), pp. 1083-1089.

The development of nanobiotechnological devices requires the ability to build various components with nanometer accuracy. DNA is a well-established nanoscale building block that self assembles due to specific interactions that are encoded in its sequence. Recently, it has become possible to couple proteins to DNA, thereby expanding the capabilities of DNA for use with molecular photonics and bioelectronics. Here, we present the design and characterization of a supramolecular Förster resonance energy transfer (FRET) system by using a fluorescent protein bound to single-stranded DNA (ssDNA), a fluorophore attached to a second ssDNA molecule, and a complementary strand for hybridizing the two fluorophores together. The FRET efficiency was studied by using both ensemble and single-pair FRET measurements. The distance between the two fluorophores was determined from the single-pair FRET efficiency and could be described by a simple cylindrical model for the DNA. Hence, DNA can be used as a scaffold for positioning fluorescent proteins, as well as traditional fluorophores, with nanometer accuracy and shows great potential for use in the future of nanobiotechnology.

Architecture with GIDEON, a program for design in structural DNA nanotechnology.

JJ Birac — 2007-10-22T12:57:40-00:00

J Mol Graph Model, Vol. 25, No. 4. (December 2006), pp. 470-480.

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON-a graphical integrated development environment for oligonucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without detailed energetic considerations, can be used to explain certain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction misalignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.

The design of a biochip: a self-assembling molecular-scale memory device

Bruce Robinson — 2008-05-05T17:58:27-00:00

Protein Eng., Vol. 1, No. 4. (1 August 1987), pp. 295-300.

A design for a biochip memory device based on known materials and existing principles is presented. The fabrication of this memory system relies on the self-assembly of the nucleic acid junction system, which acts as the scaffolding for a molecular wire consisting of polyacetylene-like units. A molecular switch to control current is described which is based on the formation of a charge - transfer complex. A molecular-scale bit is presented which is based on oxidation - reduction potentials of metal atoms or clusters. The readable bit' which can be made of these components has a volume of 3x107 A3 and should operate at electronic speeds over short distances. 10.1093/protein/1.4.295

Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks

Paul Rothemund — 2008-05-05T16:22:13-00:00

Nanotechnology: Science and Computation (2006), pp. 3-21.

DNA engineering and its application to nanotechnology.

NC Seeman — 2008-05-05T16:17:32-00:00

Trends in biotechnology, Vol. 17, No. 11. (November 1999), pp. 437-443.

The combination of branched DNA molecules and 'sticky' ends creates a powerful molecular assembly kit for structural DNA nanotechnology. Polyhedra, complex topological objects, a nanomechanical device and two-dimensional arrays with programmable surface features have already been produced in this way. Future applications range from macromolecular crystallography and new materials to molecular electronics and DNA-based computation.

Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy

C Mao — 2008-05-05T16:15:19-00:00

J. Am. Chem. Soc., Vol. 121, No. 23. (16 June 1999), pp. 5437-5443.

Abstract: A two-dimensional DNA crystal has been designed and constructed from Holliday junction analogues that contain two helical domains twisted relative to each other. The Holliday junction is not an inherently rigid system, but it can be made less flexible if it is combined into a larger construct. We have fused four junctions into a rhombus-like molecule consisting of four six-turn helices, two on an upper layer and two on a lower layer; the branch points, which define vertices, are separated by four double helical turns each. Ligation of the rhombus-like motifs produces no cyclic species, when assayed by ligation-closure experiments. Self-assembly of the rhombuses in one dimension leads to a linear pattern. The rhombuses can be directed to self-assemble by hydrogen bonding into a two-dimensional periodic array, whose spacing is six turns in each direction. The expected spacing is seen when the array is observed by atomic force microscopy (AFM). Variation of the dimensions of the repeat unit from six turns × six turns to six turns × eight turns results in the expected increase in unit cell dimensions. Hence, it is possible to assemble periodic arrays with tunable cavities using these components. This system also provides the opportunity to measure directly the angles or torsion angles between the arms of branched junctions; here we measure the torsion angle between the helical domains of the Holliday junction analogue. We find by AFM that the torsion angle between helices is 63.5, in good agreement with previous estimates.

CHEMISTRY: DNA Assembles Materials From the Ground Up

Robert Service — 2008-05-05T14:58:25-00:00

Science, Vol. 319, No. 5863. (1 February 2008), pp. 558a-559.

10.1126/science.319.5863.558a

Virus-Based Toolkit for the Directed Synthesis of Magnetic and Semiconducting Nanowires

Chuanbin Mao — 2005-09-26T19:56:51-00:00

Science, Vol. 303, No. 5655. (09 January 2004), pp. 213-217.

We report a virus-based scaffold for the synthesis of single-crystal ZnS, CdS, and freestanding chemically ordered CoPt and FePt nanowires, with the means of modifying substrate specificity through standard biological methods. Peptides (selected through an evolutionary screening process) that exhibit control of composition, size, and phase during nanoparticle nucleation have been expressed on the highly ordered filamentous capsid of the M13 bacteriophage. The incorporation of specific, nucleating peptides into the generic scaffold of the M13 coat structure provides a viable template for the directed synthesis of semiconducting and magnetic materials. Removal of the viral template by means of annealing promoted oriented aggregation-based crystal growth, forming individual crystalline nanowires. The unique ability to interchange substrate-specific peptides into the linear self-assembled filamentous construct of the M13 virus introduces a material tunability that has not been seen in previous synthetic routes. Therefore, this system provides a genetic toolkit for growing and organizing nanowires from semiconducting and magnetic materials.

Ordering of quantum dots using genetically engineered viruses.

SW Lee — 2008-05-03T12:35:48-00:00

Science (New York, N.Y.), Vol. 296, No. 5569. (3 May 2002), pp. 892-895.

A liquid crystal system was used for the fabrication of a highly ordered composite material from genetically engineered M13 bacteriophage and zinc sulfide (ZnS) nanocrystals. The bacteriophage, which formed the basis of the self-ordering system, were selected to have a specific recognition moiety for ZnS crystal surfaces. The bacteriophage were coupled with ZnS solution precursors and spontaneously evolved a self-supporting hybrid film material that was ordered at the nanoscale and at the micrometer scale into approximately 72-micrometer domains, which were continuous over a centimeter length scale. In addition, suspensions were prepared in which the lyotropic liquid crystalline phase behavior of the hybrid material was controlled by solvent concentration and by the use of a magnetic field.

Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly.

SR Whaley — 2008-05-03T12:33:54-00:00

Nature, Vol. 405, No. 6787. (8 June 2000), pp. 665-668.

In biological systems, organic molecules exert a remarkable level of control over the nucleation and mineral phase of inorganic materials such as calcium carbonate and silica, and over the assembly of crystallites and other nanoscale building blocks into complex structures required for biological function. This ability to direct the assembly of nanoscale components into controlled and sophisticated structures has motivated intense efforts to develop assembly methods that mimic or exploit the recognition capabilities and interactions found in biological systems. Of particular value would be methods that could be applied to materials with interesting electronic or optical properties, but natural evolution has not selected for interactions between biomolecules and such materials. However, peptides with limited selectivity for binding to metal surfaces and metal oxide surfaces have been successfully selected. Here we extend this approach and show that combinatorial phage-display libraries can be used to evolve peptides that bind to a range of semiconductor surfaces with high specificity, depending on the crystallographic orientation and composition of the structurally similar materials we have used. As electronic devices contain structurally related materials in close proximity, such peptides may find use for the controlled placement and assembly of a variety of practically important materials, thus broadening the scope for 'bottom-up' fabrication approaches.

DNA-Directed Assembly of Gold Nanowires on Complementary Surfaces

JKN Mbindyo — 2008-05-03T12:28:01-00:00

Advanced Materials, Vol. 13, No. 4. (2000), pp. 249-254.

Here, we report the DNA-directed assembly of Au nanowires 0.2 lm in diameter and up to 6 lm in length. Oligonucleotides were adsorbed as monolayer coatings on these wires through Au-thiol linkages, and the amount of DNA bound was quantified by absorption and fluorescence spectroscopy. Duplexes formed between strands on the nanowires and on Au coated glass slides bound the two surfaces together. We also show that nanowires can be modified with ssDNA exclusively at the tips or at any desired length on the ends, with the rest of the wire covered by passivating monolayers, thus opening the possibility of site-specific DNA directed assembly.

Approaching the limit: can one DNA oligonucleotide assemble into large nanostructures?

H Liu — 2008-05-02T16:15:30-00:00

Angewandte Chemie (International ed. in English), Vol. 45, No. 12. (13 March 2006), pp. 1942-1945.

Functional DNA nanotube arrays: bottom-up meets top-down.

C Lin — 2008-05-02T16:11:09-00:00

Angewandte Chemie (International ed. in English), Vol. 46, No. 32. (2007), pp. 6089-6092.

Design of Minimally Strained Nucleic Acid Nanotubes

William Sherman — 2008-05-02T16:06:10-00:00

Biophys. J., Vol. 90, No. 12. (15 June 2006), pp. 4546-4557.

A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double-helical domain is connected to each of its neighbors via two or more Holliday-junctionlike reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a five-parameter characterization of the segmented double-helical structure. Once the constraint equations have been derived, the primary design problem for a minimally strained N-domain structure is reduced to solving three simultaneous equations in 2N+2 variables. Symmetry analysis and tube merging then allow for the design of a wide variety of tubes, which can be tailored to satisfy requirements such as specific inner and outer radii, or multiple lobed structures. The general form of the equations allows similar techniques to be applied to various nucleic acid helices: B-DNA, A-DNA, RNA, DNA-PNA, or others. Possible applications for such tubes include nanoscale scaffolding as well as custom-shaped enclosures for other nano-objects. 10.1529/biophysj.105.080390

Emulating biology: building nanostructures from the bottom up.

NC Seeman — 2006-02-13T18:37:29-00:00

Proc Natl Acad Sci U S A, Vol. 99 Suppl 2 (30 April 2002), pp. 6451-6455.

The biological approach to nanotechnology has produced self-assembled objects, arrays and devices; likewise, it has achieved the recognition of inorganic systems and the control of their growth. Can these approaches now be integrated to produce useful systems?

Gold nanoparticle decoration of DNA on silicon.

G Braun — 2008-05-02T15:49:24-00:00

Langmuir : the ACS journal of surfaces and colloids, Vol. 21, No. 23. (8 November 2005), pp. 10699-10701.

Electrostatic assembly of cationic nanoparticles onto the negatively charged backbone of double-stranded DNA has been shown to produce one-dimensional chains with potential use as nanoelectronic components. In this paper, micron long DNA templates stretched on aminosilane- and hexamethyldisilazane-modified silicon surfaces are used to assemble 3.5 nm gold nanoparticles passivated with cationic thiocholine. Atomic force microscopy is used to analyze the density and defects along the approximately 5 nm high structures, with comparison between positively charged and neutral surfaces. Low background adsorption of nanoparticles is facilitated by both these surface chemistries, while the neutral surface yields a more densely packed assembly.

Reconfigurable, braced, three-dimensional DNA nanostructures

Russell Goodman — 2008-02-07T20:41:18-00:00

Nat Nano, Vol. 3, No. 2. (February 2008), pp. 93-96.

DNA-Nanostrukturen durch Self-assembly von Trisoligonucleotidylen

Axel Dorenbeck — 2008-05-02T08:02:08-00:00

(December 2000)

Unter Trisoligonucleotidylen versteht man drei lineare, einzelsträngige Oligonucleotide, die über einen Linker an ihren 3‘-Enden miteinander verknüpft sind. Zum Aufbau von DNA- Nanostrukturen durch reines self-assembly werden Trisoligonucleotidyle mit verschiedenen Strängen benötigt, im Falle der in dieser Arbeit dargestellten tetraedischen Nanostruktur sind es 4 Trisoligonucleotidyle mit jeweils 3 unterschiedlichen Armen. Durch Verwendung von 2 orthogonalen Schutzgruppen (die säurelabile Dimethoxytriphenylmethyl-Schutzgruppe (DMT) sowie die palladiumlabile Allyloxycarbonyl-Schutzgruppe (AOC)) innerhalb des Linkeramidites und mehrfachem Koppeln desselben, war es möglich, die Trisoligonucleotidyle mittels Phosphoamiditchemie an einem DNA-Synthesizer zu synthetisieren. Es wurden Trisoligonucleotidyle mit einer Stranglänge von je 9 bzw. 15 Basen synthetisiert, über präperative PAGE gereinigt und mittels HPLC und MALDI-TOF-Spektroskopie charakterisiert. Trisoligonucleotidyle mit einer Stranglänge von mehr als 15 Basen sind über die herkömmliche DNA-Synthese, bedingt durch die zunehmende Füllung der Festphasenporen, nicht zugänglich, einzig ein ligativer Ansatz konnte dieses Problem lösen. Die Ausbildung von DNA-Nanostrukturen ist abhängig von der jeweiligen Stranglänge der Trisoligonucleotidyle. Trisoligonucleotidyle mit einer Stranglänge von je 15 Basen bilden eine tetraedische Struktur, wohingegen Trisoligonucleotidyle mit 9 Basen je Strang ausschließlich polymere Netzwerke bilden. Die im ersteren Fall gebildete tetraedrische Struktur konnte zum einen durch Verdau mit Mung Bean Exonuclease I hinsichtlich ihrer Duplexstruktur, und zum anderen mittels Fluoreszenz-Resonanz-Energie-Transfer-Messungen hinsichtlich ihrer Form bewiesen werden. Neben der tetraedischen Struktur gelang auch der Aufbau einer pyramidalen DNA- Nanostruktur durch Verwendung eines Tetraoligonucleotidyls. Die Duplexstruktur konnte auch hier durch einen Verdau mit Mung Bean Exonuclease I bewiesen werden. Neben den oben erwähnten DNA-Nanostrukturen wurden erste Ansätze zu einer gerichteten „Nicht-kovalenten Synthese“ von DNA-Netzstrukturen bzw. komplexeren DNA- Nanostrukturen aufgezeigt.

Hochdurchsatz-Analyse der Selbstorganisation von DNA- Nanostrukturen in Echtzeit mittels FRET-Spektroskopie

Barbara Saccà — 2008-05-02T07:24:00-00:00

Angewandte Chemie, Vol. 120, No. 11. (2008), pp. 2165-2168.

A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron.

WM Shih — 2006-04-12T11:17:01-00:00

Nature, Vol. 427, No. 6975. (12 February 2004), pp. 618-621.

Molecular self-assembly offers a means of spontaneously forming complex and well-defined structures from simple components. The specific bonding between DNA base pairs has been used in this way to create DNA-based nanostructures and to direct the assembly of material on the subnanometre to micrometre scale. In principle, large-scale clonal production of suitable DNA sequences and the directed evolution of sequence lineages towards optimized behaviour can be realized through exponential DNA amplification by polymerases. But known examples of three-dimensional geometric DNA objects are not amenable to cloning because they contain topologies that prevent copying by polymerases. Here we report the design and synthesis of a 1,669-nucleotide, single-stranded DNA molecule that is readily amplified by polymerases and that, in the presence of five 40-mer synthetic oligodeoxynucleotides, folds into an octahedron structure by a simple denaturation-renaturation procedure. We use cryo-electron microscopy to show that the DNA strands fold successfully, with 12 struts or edges joined at six four-way junctions to form hollow octahedra approximately 22 nanometres in diameter. Because the base-pair sequence of individual struts is not repeated in a given octahedron, each strut is uniquely addressable by the appropriate sequence-specific DNA binder.

Synthesis from DNA of a molecule with the connectivity of a cube.

JH Chen — 2006-02-13T17:13:22-00:00

Nature, Vol. 350, No. 6319. (18 April 1991), pp. 631-633.

A principal goal of biotechnology is the assembly of novel biomaterials for analytical, industrial and therapeutic purposes. The advent of stable immobile nucleic acid branched junctions makes DNA a good candidate for building frameworks to which proteins or other functional molecules can be attached and thereby juxtaposed. The addition of single-stranded 'sticky' ends to branched DNA molecules converts them into macromolecular valence clusters that can be ligated together. The edges of these frameworks are double-helical DNA, and the vertices correspond to the branch points of junctions. Here, we report the construction from DNA of a covalently closed cube-like molecular complex containing twelve equal-length double-helical edges arranged about eight vertices. Each of the six 'faces' of the object is a single-stranded cyclic molecule, doubly catenated to four neighbouring strands, and each vertex is connected by an edge to three others. Each edge contains a unique restriction site for analytical purposes. This is the first construction of a closed polyhedral object from DNA.

A robust DNA mechanical device controlled by hybridization topology.

H Yan — 2007-10-23T12:58:34-00:00

Nature, Vol. 415, No. 6867. (3 January 2002), pp. 62-65.

Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems-catenanes and rotaxanes, chiroptical molecular switches, molecular ratchets and DNA-by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby 'fuelling' conformational changes in a DNA machine. Here we improve upon the initial prototype system that uses this mechanism but generates by-products, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180 degrees. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.

Varieties of imaging with scanning probe microscopes

Helen Hansma — 2008-04-25T12:26:26-00:00

Proceedings of the National Academy of Sciences, Vol. 96, No. 26. (21 December 1999), pp. 14678-14680.

10.1073/pnas.96.26.14678

Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes.

PJ Rothwell — 2008-04-05T14:40:04-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 4. (18 February 2003), pp. 1655-1660.

By using single-molecule multiparameter fluorescence detection, fluorescence resonance energy transfer experiments, and newly developed data analysis methods, this study demonstrates directly the existence of three structurally distinct forms of reverse transcriptase (RT):nucleic acid complexes in solution. Single-molecule multiparameter fluorescence detection also provides first information on the structure of a complex not observed by x-ray crystallography. This species did not incorporate nucleotides and is structurally distinct from the other two observed species. We determined that the nucleic acid substrate is bound at a site far removed from the nucleic acid-binding tract observed by crystallography. In contrast, the other two states are identified as being similar to the x-ray crystal structure and represent distinct enzymatically productive stages in DNA polymerization. These species differ by only a 5-A shift in the position of the nucleic acid. Addition of nucleoside triphosphate or of inorganic pyrophosphate allowed us to assign them as the educt and product state in the polymerization reaction cycle; i.e., the educt state is a complex in which the nucleic acid is positioned to allow nucleotide incorporation. The second RT:nucleic acid complex is the product state, which is formed immediately after nucleotide incorporation, but before RT translates to the next nucleotide.

Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: Corrections due to nonideal transfer

Chandran Sabanayagam — 2008-04-21T14:55:34-00:00

The Journal of Chemical Physics, Vol. 122, No. 6. (2005)

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Intensification of labelings of the immunogold silver staining method by gold toning.

R Arai — 2008-04-19T17:04:17-00:00

Brain research bulletin, Vol. 28, No. 2. (February 1992), pp. 343-345.

We evaluated the applicability of the gold toning procedure to the immunogold silver staining method using monoclonal antibody against dopamine. Immunolabeling was examined in the rat substantia nigra at light and electron microscopic levels. Vibratome sections of fixed midbrains were incubated with anti-dopamine antiserum and then with 5 nm colloidal gold bound to goat anti-mouse immunoglobulin. Silver staining of these sections produced a light brown immunolabeling. After the sections were processed by gold toning, the labeling became intense black. At a light microscopic level, these high contrast signals were retained after the sections were osmicated and embedded in Epon. At an electron microscopic level, signal-to-noise ratio was high, and the positive staining could easily be verified at a low-power magnification. The technique described here, the gold-toned immunogold silver staining method, provides high contrast signals and is much more sensitive than immunogold silver staining alone. This method, therefore, has great potential for use in immunohistochemical analysis of the central nervous system.

Electron Microscopical Autometallography: Immunogold-Silver Staining (IGSS) and Heavy-Metal Histochemistry

Gerhard Hacker — 2008-04-19T11:32:15-00:00

Methods, Vol. 10, No. 2. (October 1996), pp. 257-269.

Immunogold-silver staining (IGSS) utilizes a histochemical method called autometallography (AMG) to amplify tiny gold particles to sizes easily visible both in light and electron microscopy. In both applications it is advisable to use the smallest possible gold diameters (1-6 nm) to obtain the highest sensitivity, thus, allowing minute amounts of the target substance to be demonstrated. Gold labels smaller than 10 nm in diameter have been clearly shown to give the highest labeling densities of antigen-antibody binding sites. AMG can be used for the detection of catalytic crystal lattices of metallic gold and silver, and sulfides or selenides of mercury, silver, copper, bismuth, and zinc. The method has its roots in "physical development" technique, transplanted from photography to histology by Liesegang at the beginning of this century. In 1981, a series of papers were published by one of us with the purpose of introducing a reliable and easy-to-handle technique for light microscopical and ultrastructural studies. AMG has a multitude of applications apart from its use in detecting tissue metals. These include the highly sensitive and efficientin situcolloidal gold tracing of peptides, proteins, and amines by immunocytochemistry using the IGSS method, of carbohydrates by lectin IGSS, and of nucleic acids by IGSSin situhybridization, IGSSin situpolymerase chain reaction, and IGSSin situself-sustained sequence replication-based amplification (in situ3SR) techniques, the last two even performing with single-copy sensitivity. Applications of pre- and postembedding AMG for semithin and ultrathin tissue sections are described.