Sun, 27 Jul 2008 07:58:34 BST CiteULike: dna's library [223 articles] http://www.citeulike.org/user/dna/order/to_read CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/dna/article/2402276 <i>Ultramicroscopy, Vol. 97, No. 1-4. ( 2003), pp. 249-255.</i><br /><br />The effect of a surface water layer on DNA strands deposited on a substrate was studied by atomic force microscopy (AFM). DNA molecules were deposited and stretched on chemically modified glass coverslips by a molecular combing method. Lambda bacteriophage DNA molecules were aligned on the organosilane-modified substrate surfaces by chemical and physical adsorption during the molecular combing. The combed DNA molecules were observed in humidity-controlled air and in aqueous solutions by pulsed-force-mode AFM (PFM-AFM). Chemical modification of cantilevers with an Au-coated tip by organothiol compounds was also applied to DNA observation. Mapping adhesive forces in aqueous media was useful to discriminate chemically the DNA strands from the substrate surface. The results suggest that PFM-AFM can be used widely to image the stretched DNA molecules on the silane-modified substrates. Imaging stretched single DNA molecules by pulsed-force-mode atomic force microscopy KJ Kwak H Kudo M Fujihira doi:10.1016/S0304-3991(03)00049-4 Ultramicroscopy, Vol. 97, No. 1-4. ( 2003), pp. 249-255. 2008-02-20T10:10:42-00:00 2003 Ultramicroscopy 97 1-4 249 255 afm mica-dna-afm origami positioning si-substrate http://www.citeulike.org/user/dna/article/2401992 <i>Science, Vol. 297, No. 5578. (5 July 2002), pp. 72-75.</i><br /><br />10.1126/science.1071247 Sequence-Specific Molecular Lithography on Single DNA Molecules Kinneret Keren Michael Krueger Rachel Gilad Gdalyahu Ben-Yoseph Uri Sivan Erez Braun doi:10.1126/science.1071247 Science, Vol. 297, No. 5578. (5 July 2002), pp. 72-75. 2008-02-20T09:28:53-00:00 2002 Science 297 5578 72 75 lithography metallization metallization-ag metallization-au nanogold origami http://www.citeulike.org/user/dna/article/2400632 <i>Trends in Biotechnology, Vol. 20, No. 9. (1 September 2002), pp. 395-401.</i><br /><br />Semisynthetic DNA-protein conjugates, generated by either covalent or non-covalent coupling chemistry, are versatile molecular tools applicable in bioanalytical and synthetic chemical procedures. This article reviews the synthesis and characterization of artificial nucleic acid-protein conjugates, in addition to applications arising in the life sciences and nanobiotechnology, such as the self-assembly of high-affinity reagents for immunological detection assays and biosensors, the fabrication of laterally microstructured biochips, and the biomimetic `bottom-up' synthesis of nanostructured supramolecular devices. The developments of semisynthetic DNA-protein conjugates Christof Niemeyer doi:10.1016/S0167-7799(02)02022-X Trends in Biotechnology, Vol. 20, No. 9. (1 September 2002), pp. 395-401. 2008-02-20T00:05:50-00:00 2002 Trends in Biotechnology 20 9 395 401 addons addons-protein origami review http://www.citeulike.org/user/dna/article/2310032 <i>J. Am. Chem. Soc., Vol. 129, No. 34. (29 August 2007), pp. 10304-10305.</i><br /><br />Abstract: Here we generalize a highly programmable strategy to self-assemble multiprotein nanoarrays with deterministic positional addressability. These protein nanoarrays were templated by aptamer-tagged DNA nanoarchitectures. Arrays of proteins with precisely controlled positions and interprotein spacings offer great potential in proteomics, tissue engineering, and medical diagnostics. Spatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA Nanoarchitectures R Chhabra J Sharma Y Ke Y Liu S Rinker S Lindsay H Yan doi:10.1021/ja072410u J. Am. Chem. Soc., Vol. 129, No. 34. (29 August 2007), pp. 10304-10305. 2008-01-31T09:20:24-00:00 2007 J. Am. Chem. Soc. 129 34 10304 10305 addons addons-protein aptamer origami http://www.citeulike.org/user/dna/article/2309947 <i>Nature, Vol. 451, No. 7178. (31 January 2008), pp. 553-556.</i> DNA-programmable nanoparticle crystallization Sung Park Abigail Lytton-Jean Byeongdu Lee Steven Weigand George Schatz Chad Mirkin doi:10.1038/nature06508 Nature, Vol. 451, No. 7178. (31 January 2008), pp. 553-556. 2008-01-31T08:37:22-00:00 2008 Nature 451 7178 553 556 Nature Publishing Group origami http://www.citeulike.org/user/dna/article/2309940 <i>Nature, Vol. 451, No. 7178. (31 January 2008), pp. 549-552.</i> DNA-guided crystallization of colloidal nanoparticles Dmytro Nykypanchuk Mathew Maye Daniel van der Lelie Oleg Gang doi:10.1038/nature06560 Nature, Vol. 451, No. 7178. (31 January 2008), pp. 549-552. 2008-01-31T08:32:06-00:00 2008 Nature 451 7178 549 552 Nature Publishing Group origami http://www.citeulike.org/user/dna/article/2120164 <i>Scanning Microsc Suppl, Vol. 10 (1996)</i><br /><br />To investigate DNA and DNA-protein assembly, nucleic acids were adsorbed to freshly cleaved mica in the presence of magnesium ions. The efficiency of DNA adhesion and the distribution of the molecules on the mica surface were checked by transmission electron microscopy. In addition, various kinds of DNA-protein interactions including DNA wrapping and DNA supercoiling were analyzed using electron microscopy. In parallel, this Mg2+/mica method can be applied (1) to analyze embedded DNA by scanning tunneling microscopy, (2) to visualize freeze-dried, metal coated DNA-protein complexes by tunneling microscopy, and (3) to image DNA or DNA-protein interaction in air or in liquid by scanning force microscopy. An advantage of such a correlative approach is that parallel imaging can reveal complementary information. The benefit of such a combined approach in analysis of protein-induced DNA bending is discussed. Microscopic analysis of DNA and DNA-protein assembly by transmission electron microscopy, scanning tunneling microscopy and scanning force microscopy. T Müller-Reichert H Gross Scanning Microsc Suppl, Vol. 10 (1996) 2007-12-14T19:49:30-00:00 1996 Scanning Microsc Suppl 0892-953X 10 mica-tem origami http://www.citeulike.org/user/dna/article/1986688 <i>J Nanosci Nanotechnol, Vol. 5, No. 3. (March 2005), pp. 409-415.</i><br /><br />An approach to the design of DNA-based electronics is presented, in which standard microfabrication processes are integrated with lithographic patterning of single-stranded oligonucleotides followed by hybridization to gold-labeled, complementary oligonucleotides and subsequent silver enhancement for signal amplification. The resulting bioinorganic devices demonstrate micron-sized geometric features, very little non-specific silver growth, a distinct silver morphology in the patterned region, and a 10(9)-fold increase in conductivity across an electrode gap when compared with control devices. This approach may prove useful for the fabrication of high fidelity, high-density arrays for DNA-based biosensing applications. Silver growth on micropatterned DNA chips: effect of growth conditions and morphology on I-V behavior. DA Greninger S Pathak AA Talin PM Dentinger J Nanosci Nanotechnol, Vol. 5, No. 3. (March 2005), pp. 409-415. 2007-11-26T14:33:47-00:00 2005 J Nanosci Nanotechnol 1533-4880 5 3 409 415 addons-metal metallization metallization-ag metallization-au origami http://www.citeulike.org/user/dna/article/1744787 <i>(1995)</i> Immunogold-Silver Staining: Principles, Methods, and Applications (1995) 2007-10-09T07:37:44-00:00 1995 CRC Press book origami http://www.citeulike.org/user/dna/article/400084 <i>J Histochem Cytochem, Vol. 48, No. 4. (April 2000), pp. 471-480.</i><br /><br />Recent advances in gold technology have led to probes with improved properties and performance for cell biologists: higher labeling density, better sensitivity, and greater penetration into tissues. Gold clusters, such as the 1.4-nm Nanogold, are gold compounds that can be covalently linked to Fab' antibody fragments, making small and stable probes. Silver enhancement then makes these small gold particles easily visible by EM, LM, and directly by eye. Another advance is the combination of fluorescent and gold probes for correlative microscopy. Chemical crosslinking of gold particles to many biologically active molecules has made possible many novel probes, such as gold-lipids, gold-Ni-NTA, and gold-ATP. New frontiers in gold labeling. JF Hainfeld RD Powell J Histochem Cytochem, Vol. 48, No. 4. (April 2000), pp. 471-480. 2005-11-18T16:08:25-00:00 2000 J Histochem Cytochem 0022-1554 48 4 471 480 addons addons-metal metallization metallization-ag metallization-au nanogold nanogold-procedure origami review http://www.citeulike.org/user/dna/article/1716022 <i>Biochemistry, Vol. 32, No. 13. (1993), pp. 3211-3220.</i> DNA double-crossover molecules Tsu Fu Nadrian Seeman doi:10.1021/bi00064a003 Biochemistry, Vol. 32, No. 13. (1993), pp. 3211-3220. 2007-10-01T15:27:10-00:00 1993 Biochemistry 32 13 3211 3220 background origami http://www.citeulike.org/user/dna/article/1704592 <i>Applied Physics Letters, Vol. 89, No. 3. (2006)</i><br /><br />We report on the electrical conductivity measurement of silver nanowires templated on native -bacteriophage and synthetic double-stranded DNA molecules. After an electroless chemical deposition, the metallized DNA wires have a diameter down to 15  nm and are among the thinnest metallic nanowires available to date. Two-terminal I-V measurements demonstrating various conduction behaviors are presented. DNA templated functional nanowires may, in the near future, be targeted to connect at specific locations on larger-scale circuits and represent a potential breakthrough in the self-assembly of nanometer-scale structures for electronics layout. ©2006 American Institute of Physics Optimized fabrication and electrical analysis of silver nanowires templated on DNA molecules Sung Park Matthew Prior Thomas Labean Gleb Finkelstein doi:10.1063/1.2234282 Applied Physics Letters, Vol. 89, No. 3. (2006) 2007-09-28T10:46:22-00:00 2006 Applied Physics Letters 89 3 AIP metallization metallization-ag nanowires origami http://www.citeulike.org/user/dna/article/1239446 <i>J. Phys.: Conf. Ser., Vol. 61, No. 1. (2007), 458.</i> DNA-scaffolded nanoparticle structures Björn Högberg Håkan Olin doi:10.1088/1742-6596/61/1/092 J. Phys.: Conf. Ser., Vol. 61, No. 1. (2007), 458. 2007-04-20T12:38:58-00:00 2007 J. Phys.: Conf. Ser. 1742-6596 61 1 458 Institute of Physics Publishing addons addons-metal lit-sem-1 nanogold origami http://www.citeulike.org/user/dna/article/1660130 <i>Comput. Appl. Biosci., Vol. 12, No. 1. (1 February 1996), pp. 25-30.</i><br /><br />Using a new set of reduced coordinates developed for describing regular and unusual nucleic acid structures, we have revised our nucleic acid modeling tool NAMOT2. NAMOT2 is general in terms of modeling different nucleic acid structures. A set of modifiable libraries allows users to customize their modeling environment. With this set of libraries, NAMOT2 can be used to model non-canonical structures such as parallel-stranded, triple-stranded and quadruple-stranded nucleic acid molecules. For modeling irregular structures (junctions, hairpin loops, etc.), we introduce a structural recipe approach. The complete procedure using NAMOT2 to construct the structure of a specific molecule is treated as the recipe for that structural motif. The existing recipes can be modified to generate new recipes for different structural motifs. Several examples of nucleic acids with non-canonical structures were modeled using NAMOT2. These examples include a DNA-drug complex, a DNA cube, a six-arm junction and a curved DNA molecule. 10.1093/bioinformatics/12.1.25 NAMOT2--a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures Eugene Carter Chang-Shung Tung doi:10.1093/bioinformatics/12.1.25 Comput. Appl. Biosci., Vol. 12, No. 1. (1 February 1996), pp. 25-30. 2007-09-15T07:48:30-00:00 1996 Comput. Appl. Biosci. 12 1 25 30 origami origami-design http://www.citeulike.org/user/dna/article/1618949 <i>(April 2005)</i><br /><br />Die Arbeit beschäftigt sich mit Goldkolloiden, die durch DNA (Desoxyribonucleinsäure) zu Partikelnetzwerken, den so genannten DNA-Hybrid-Materialien, verbunden werden. Es handelt sich dabei um eine DNA-vermittelte Selbstorganisation. Die Arbeit gliedert sich in zwei Teile. Im ersten Teil steht die DNA als "Werkstoff" Klebstoff im Mittelpunkt. Dabei werden grundsätzliche Aspekte dieser Methode diskutiert. Ein neuer Ansatz wird vorgestellt, der die Verknüpfung von Gold-Nanopartikeln mittels doppelsträngiger DNA einerseits und der Variation der Anzahl verfügbarer Thiolgruppen andererseits untersucht. Ebenso werden die Resultate zur Morphologie der entstandenen Partikelnetzwerke sowie zum Denaturieren der DNA in den DNA-Hybriden präsentiert. Der zweite Teil beschäftigt sich mit den Wechselwirkungen zwischen DNA und Partikel. Hier stehen insbesondere der Einfluß von Kationen und die Frage, inwieweit die elektrostatischen Wechselwirkungen zwischen den Partikeln einen Einfluß auf die Bildung der DNA-Partikel-Hybride haben im Mittelpunkt. Verwendet wurden zum einen Goldkolloide mit einem Durchmesser von 20 nm, 50 nm bzw. 80 nm und zum anderen überwiegend doppelsträngige DNA mit einer Länge von 24 Basenpaaren, die thiolfunktionalisiert war. Die Untersuchungen wurden mittels UV/Vis-Spektroskopie, Transmissionselektronen- und Rasterelektronen-Mikroskopie durchgeführt. Die Verwendung von doppelsträngiger DNA stellt einen Brückenschlag dar, um die gewonnenen Erkenntnisse zu Mechanismen und Wechselwirkungen für eine effizientere Erzeugung von DNA-Hybrid-Materialien nutzen zu können. DNA was used as "glue" for gold nanoparticles, and the specific binding characteristics of DNA have been investigated. DNA-mediated self-assembly leads to the so-called DNA-hybrid-materials. In contrast to previous works, a method based on the use of double-stranded DNA and a variation of available thiol-groups was exploited. Besides the unambiguous evidence for the guidance of the particle network formation by the DNA, the morphology of the hybrid materials as well as the reversibility of the network formation was investigated. The second part of the thesis deals with the interactions between DNA and the particles, in particular with the influence of cations. The role of electrostatic interactions between the particles is also discussed. The investigations were carried out with gold nanoparticles having diameters of 20 nm, 50 nm and 80 nm and with mainly 24mer of double-stranded DNA. The DNA was functionalized with thiol-groups. The hybrid materials were investigated by uv-vis spectroscopy, transmission electron microscopy and scanning electron microscopy. The results thus obtained significantly enhance the understanding of mechanisms and interactions of the DNA-mediated particle linking. This is a prerequisite for the efficient generation of DNA-hybrid-materials. DNA als Klebstoff: Untersuchungen zur Wirkung und Wechselwirkung mit Gold-Nanopartikeln Ulrike Rehn (April 2005) 2007-09-04T11:13:15-00:00 2005 addons addons-metal background metallization origami http://www.citeulike.org/user/dna/article/500248 <i>Nano Lett, Vol. 5, No. 4. (April 2005), pp. 729-733.</i><br /><br />We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimensional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density. Programmable DNA self-assemblies for nanoscale organization of ligands and proteins. SH Park P Yin Y Liu JH Reif TH LaBean H Yan doi:10.1021/nl050175c Nano Lett, Vol. 5, No. 4. (April 2005), pp. 729-733. 2006-02-09T18:35:17-00:00 2005 Nano Lett 1530-6984 5 4 729 733 addons addons-protein origami http://www.citeulike.org/user/dna/article/1282394 <i>(2005), pp. 471-478.</i> Design of DNA origami PWK Rothemund (2005), pp. 471-478. 2007-05-07T21:59:07-00:00 2005 471 478 IEEE Computer Society base origami origami-design http://www.citeulike.org/user/dna/article/1304293 <i>PNAS, Vol. 101, No. 3. (20 January 2004), pp. 717-722.</i><br /><br />DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of approx25 nm and have been observed with lengths up to 20 microm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods. 10.1073/pnas.0305860101 DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires Dage Liu Sung Park John Reif Thomas Labean doi:10.1073/pnas.0305860101 PNAS, Vol. 101, No. 3. (20 January 2004), pp. 717-722. 2007-05-17T21:34:31-00:00 2004 PNAS 101 3 717 722 metallization nanogold nanotubes nanowires origami http://www.citeulike.org/user/dna/article/2813528 <i>Physics Reports, Vol. 288, No. 1-6. (September 1997), pp. 13-60.</i> Biophysics of the DNA molecule Maxim Frank-Kamenetskii doi:10.1016/S0370-1573(97)00020-3 Physics Reports, Vol. 288, No. 1-6. (September 1997), pp. 13-60. 2008-05-19T15:56:18-00:00 1997 Physics Reports 288 1-6 13 60 background dna origami http://www.citeulike.org/user/dna/article/2744347 <i>Angewandte Chemie, Vol. 120, No. 11. (2008), pp. 2165-2168.</i> Hochdurchsatz-Analyse der Selbstorganisation von DNA- Nanostrukturen in Echtzeit mittels FRET-Spektroskopie Barbara Saccà Rebecca Meyer Udo Feldkamp Hendrik Schroeder Christof m doi:10.1002/ange.200704836 Angewandte Chemie, Vol. 120, No. 11. (2008), pp. 2165-2168. 2008-05-02T07:24:00-00:00 2008 Angewandte Chemie 120 11 2165 2168 background fret origami http://www.citeulike.org/user/dna/article/2675586 <i>Current biology : CB, Vol. 15, No. 3. (8 February 2005)</i><br /><br />The crystal structure of human DNA ligase I catches the enzyme just before the last step of ligation and shows that the protein wraps completely around nicked DNA. The elegant structure explains how ligase attains fidelity for the sealing operation. DNA ligase: getting a grip to seal the deal. A Johnson M O'Donnell doi:10.1016/j.cub.2005.01.025 Current biology : CB, Vol. 15, No. 3. (8 February 2005) 2008-04-15T22:44:28-00:00 2005 Current biology : CB 0960-9822 15 3 ligation lit-sem-2 origami http://www.citeulike.org/user/dna/article/2478951 <i>Biophys J, Vol. 81, No. 3. (September 2001), pp. 1580-1587.</i><br /><br />Ag(I) is a strong nucleic acids binder and forms several complexes with DNA such as types I, II, and III. However, the details of the binding mode of silver(I) in the Ag-polynucleotides remains unknown. Therefore, it was of interest to examine the binding of Ag(I) with calf-thymus DNA and bakers yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentration of DNA or RNA and various concentrations of Ag(I). Fourier transform infrared spectroscopy and capillary electrophoresis were used to analyze the Ag(I) binding mode, the binding constant, and the polynucleotides' structural changes in the Ag-DNA and Ag-RNA complexes. The spectroscopic results showed that in the type I complex formed with DNA, Ag(I) binds to guanine N7 at low cation concentration (r = 1/80) and adenine N7 site at higher concentrations (r = 1/20 to 1/10), but not to the backbone phosphate group. At r = 1/2, type II complexes formed with DNA in which Ag(I) binds to the G-C and A-T base pairs. On the other hand, Ag(I) binds to the guanine N7 atom but not to the adenine and the backbone phosphate group in the Ag-RNA complexes. Although a minor alteration of the sugar-phosphate geometry was observed, DNA remained in the B-family structure, whereas RNA retained its A conformation. Scatchard analysis following capillary electrophoresis showed two binding sites for the Ag-DNA complexes with K(1) = 8.3 x 10(4) M(-1) for the guanine and K(2) = 1.5 x 10(4) M(-1) for the adenine bases. On the other hand, Ag-RNA adducts showed one binding site with K = 1.5 x 10(5) M(-1) for the guanine bases. Silver(I) complexes with DNA and RNA studied by Fourier transform infrared spectroscopy and capillary electrophoresis. H Arakawa JF Neault HA Tajmir-Riahi Biophys J, Vol. 81, No. 3. (September 2001), pp. 1580-1587. 2008-03-06T14:27:20-00:00 2001 Biophys J 0006-3495 81 3 1580 1587 background metallization metallization-ag origami silver-stain http://www.citeulike.org/user/dna/article/2466165 <i>Nat. Protocols, Vol. 2, No. 11. (October 2007), pp. 2649-2654.</i> Silver staining DNA in polyacrylamide gels Brant Bassam Peter Gresshoff doi:10.1038/nprot.2007.330 Nat. Protocols, Vol. 2, No. 11. (October 2007), pp. 2649-2654. 2008-03-04T17:24:38-00:00 2007 Nat. Protocols 2 11 2649 2654 Nature Publishing Group origami silver-stain http://www.citeulike.org/user/dna/article/2402364 <i>Langmuir, Vol. 21, No. 9. (26 April 2005), pp. 4180-4184.</i><br /><br />This paper reports a robust and efficient approach to assemble highly aligned DNA strands onto Si chips. The method combines advantages from molecular combing and microcontact printing to realize controlling both the density and direction of DNA strands on the Si chip. In addition, it also can be utilized to prepare stretched DNA structures on solid surfaces. Compared to approaches that use molecular combing directly on silanated surfaces, the stretched single-chain DNA structures are straighter. Furthermore, by exploiting the hydrophobic property of the intrinsic poly(dimethylsiloxane) stamp, this study also describes a simple way to produce straight bundled DNA arrays on Si and other substrates. Assembly of highly aligned DNA strands onto Si chips. J Zhang Y Ma S Stachura H He doi:10.1021/la050129s Langmuir, Vol. 21, No. 9. (26 April 2005), pp. 4180-4184. 2008-02-20T10:15:14-00:00 2005 Langmuir 0743-7463 21 9 4180 4184 origami positioning si-substrate http://www.citeulike.org/user/dna/article/2400637 <i>Angewandte Chemie International Edition, Vol. 37, No. 16. (1998), pp. 2265-2268.</i><br /><br />Supramolecular aggregates of DNA, RNA, streptavidin, immunoglobulin, and nanocrystalline metal clusters can be generated by self-assembly on the basis of oligonucleotide hybridization (shown schematically). Following selective immunosorption on surface-immobilized antigen, the biometallic hybrid is detectable by electron microscopy. Covalent DNA-Streptavidin Conjugates as Building Blocks for Novel Biometallic Nanostructures Christof Niemeyer Wolfgang Bürger Jörg Peplies doi:10.1002/(SICI)1521-3773(19980904)37:16<2265::AID-ANIE2265>3.0.CO;2-F Angewandte Chemie International Edition, Vol. 37, No. 16. (1998), pp. 2265-2268. 2008-02-20T00:07:55-00:00 1998 Angewandte Chemie International Edition 37 16 2265 2268 addons addons-metal addons-protein origami http://www.citeulike.org/user/dna/article/2373555 <i>Journal of Inorganic Biochemistry, Vol. 26, No. 2. (February 1986), pp. 77-91.</i><br /><br />We report simple and rapid procedures for the synthesis of a variety of stable, water-soluble undecagold clusters, and model applications of a thiol-reactive gold cluster for the specific labeling of cysteine residues in proteins. Undecagold clusters for site-specific labeling of biological macromolecules: simplified preparation and model applications Daniel Safer Lizann Bolinger John Leigh doi:10.1016/0162-0134(86)80001-0 Journal of Inorganic Biochemistry, Vol. 26, No. 2. (February 1986), pp. 77-91. 2008-02-14T12:14:24-00:00 1986 Journal of Inorganic Biochemistry 26 2 77 91 addons addons-metal background nanogold nanogold-procedure origami http://www.citeulike.org/user/dna/article/2310072 <i>Photochem Photobiol Sci, Vol. 6, No. 6. (June 2007), pp. 614-618.</i><br /><br />Several authors demonstrated that an oligonucleotide based pH-sensitive construct can act as a switch between an open and a closed state by changing the pH. To validate this process, specially designed fluorescence dye-quencher substituted oligonucleotide constructs were developed to probe the switching between these two states. This paper reports on bulk and single molecule fluorescence investigations of a duplex-triplex pH sensitive oligonucleotide switch. On the bulk level, only a partial quenching of the fluorescence is observed, similarly to what is observed for other published switches and is supposed to be due to intermolecular interactions between oligonucleotide strands. On the single molecule level, each DNA-based nanometric construct shows a complete switching. These observations suggest the tendency of the DNA construct to associate at high concentration. Single molecule fluorescence spectroscopy of pH sensitive oligonucleotide switches. B Kolaric M Sliwa M Brucale RA Vallée G Zuccheri B Samori J Hofkens FC De Schryver doi:10.1039/b618689k Photochem Photobiol Sci, Vol. 6, No. 6. (June 2007), pp. 614-618. 2008-01-31T09:43:16-00:00 2007 Photochem Photobiol Sci 1474-905X 6 6 614 618 origami single-molecule-spectroscopy http://www.citeulike.org/user/dna/article/1987595 <i>Science, Vol. 289, No. 5485. (8 September 2000), pp. 1757-1760.</i><br /><br />A method for analyzing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional flatbed scanner is described here. Labeling oligonucleotide targets with nanoparticle rather than fluorophore probes substantially alters the melting profiles of the targets from an array substrate. This difference permits the discrimination of an oligonucleotide sequence from targets with single nucleotide mismatches with a selectivity that is over three times that observed for fluorophore-labeled targets. In addition, when coupled with a signal amplification method based on nanoparticle-promoted reduction of silver(I), the sensitivity of this scanometric array detection system exceeds that of the analogous fluorophore system by two orders of magnitude. Scanometric DNA Array Detection with Nanoparticle Probes Andrew Taton Chad Mirkin Robert Letsinger doi:10.1126/science.289.5485.1757 Science, Vol. 289, No. 5485. (8 September 2000), pp. 1757-1760. 2007-11-26T17:22:09-00:00 2000 Science 289 5485 1757 1760 addons addons-metal metallization-ag origami http://www.citeulike.org/user/dna/article/1986533 <i>Nano Lett., Vol. 5, No. 12. (14 December 2005), pp. 2399-2402.</i><br /><br />Abstract: Regular 2D arrays of multiple types of nanocomponents were constructed by self-assembly to DNA scaffolding with alternating rows of sequence-encoded hybridization sites. Different-sized Au particles coated with DNA complementary to one of the sites were bound to the scaffolding, producing alternating rows of the two nanocomponents with a 32-nm inter-row spacing. These results demonstrate the potential for using DNA to self-assemble complex arrays of components with nanometer-scale precision. Sequence-Encoded Self-Assembly of Multiple-Nanocomponent Arrays by 2D DNA Scaffolding YY Pinto JD Le NC Seeman K Musier-Forsyth TA Taton RA Kiehl doi:10.1021/nl0515495 Nano Lett., Vol. 5, No. 12. (14 December 2005), pp. 2399-2402. 2007-11-26T14:20:51-00:00 2005 Nano Lett. 5 12 2399 2402 addons-metal lit-sem-1 origami http://www.citeulike.org/user/dna/article/1984496 <i>Nano Lett., Vol. 6, No. 2. (8 February 2006), pp. 248-251.</i><br /><br />Abstract: We report the use of a self-assembled two-dimensional (2D) DNA nanogrid as a template to organize 5-nm gold nanoparticles (Au NPs) into periodic square lattices. Each particle sits on only a single DNA tile. The center-to-center interparticle spacing between neighboring particles is controlled to be ~38 nm. These evenly distributed Au NP arrangements with accurate control of interparticle spacing may find applications in nanoelectronic and nanophotonic devices. Periodic Square-Like Gold Nanoparticle Arrays Templated by Self-Assembled 2D DNA Nanogrids on a Surface J Zhang Y Liu Y Ke H Yan doi:10.1021/nl052210l Nano Lett., Vol. 6, No. 2. (8 February 2006), pp. 248-251. 2007-11-26T10:09:49-00:00 2006 Nano Lett. 6 2 248 251 addons-metal lit-sem-1 origami http://www.citeulike.org/user/dna/article/1984490 <i>Nano Lett., Vol. 4, No. 12. (8 December 2004), pp. 2343-2347.</i><br /><br />Abstract: A method for laying out arrays of components in programmable 2D arrangements with nanometer-scale precision is needed for the manufacture of high density nanoelectronic circuitry. We report programmed self-assembly of gold prototype nanoelectronic components into closely packed rows with precisely defined inter-row spacings by in situ hybridization of DNA-functionalized components to a preassembled 2D DNA scaffolding on a surface. This approach is broadly applicable to the manufacture of nanoscale integrated circuits for logic, memory, sensing, and other applications. DNA-Templated Self-Assembly of Metallic Nanocomponent Arrays on a Surface JD Le Y Pinto NC Seeman K Musier-Forsyth TA Taton RA Kiehl doi:10.1021/nl048635+ Nano Lett., Vol. 4, No. 12. (8 December 2004), pp. 2343-2347. 2007-11-26T10:07:57-00:00 2004 Nano Lett. 4 12 2343 2347 addons-metal lit-sem-1 origami http://www.citeulike.org/user/dna/article/1967597 <i>Nucleic Acids Res, Vol. 19, No. 3. (11 February 1991)</i> A rapid method for the purification of deprotected oligodeoxynucleotides. M Sawadogo MW Van Dyke Nucleic Acids Res, Vol. 19, No. 3. (11 February 1991) 2007-11-23T17:19:03-00:00 1991 Nucleic Acids Res 0305-1048 19 3 oligo-purification origami http://www.citeulike.org/user/dna/article/1745008 <i>J. Histochem. Cytochem., Vol. 40, No. 2. (1 February 1992), pp. 177-184.</i><br /><br />A large gold cluster (Au1.4nm) was covalently coupled to IgG and Fab' fragments. Its gold core is 1.4 nm in diameter and the Fab'-Au1.4nm immunoconjugate is the smallest gold immunoprobe that can be seen directly in the conventional electron microscope. It is useful in high- resolution immunolabeling, providing a resolution of 7.0 nm. The cluster's visibility can be enhanced with silver development for use in EM or light microscopy for histological purposes, or to detect less than or equal to 0.2 pg of antigen in immunoblots. By using a gold compound with covalent attachment, a number of advantages over colloidal gold probes are realized, including better resolution, stability, uniformity, sensitivity, and complete absence of aggregation; its small size should also improve penetration and more quantitative labeling of antigenic sites. A 1.4-nm gold cluster covalently attached to antibodies improves immunolabeling JF Hainfeld FR Furuya J. Histochem. Cytochem., Vol. 40, No. 2. (1 February 1992), pp. 177-184. 2007-10-09T09:12:57-00:00 1992 J. Histochem. Cytochem. 40 2 177 184 background metallization metallization-au origami http://www.citeulike.org/user/dna/article/1705030 <i>Nature, Vol. 415, No. 6868. (10 January 2002), pp. 152-155.</i><br /><br />Increasingly detailed structural and dynamic studies are highlighting the precision with which biomolecules execute often complex tasks at the molecular scale. The efficiency and versatility of these processes have inspired many attempts to mimic or harness them. To date, biomolecules have been used to perform computational operations and actuation, to construct artificial transcriptional loops that behave like simple circuit elements and to direct the assembly of nanocrystals. Further development of these approaches requires new tools for the physical and chemical manipulation of biological systems. Biomolecular activity has been triggered optically through the use of chromophores, but direct electronic control over biomolecular 'machinery' in a specific and fully reversible manner has not yet been achieved. Here we demonstrate remote electronic control over the hybridization behaviour of DNA molecules, by inductive coupling of a radio-frequency magnetic field to a metal nanocrystal covalently linked to DNA. Inductive coupling to the nanocrystal increases the local temperature of the bound DNA, thereby inducing denaturation while leaving surrounding molecules relatively unaffected. Moreover, because dissolved biomolecules dissipate heat in less than 50 picoseconds (ref. 16), the switching is fully reversible. Inductive heating of macroscopic samples is widely used, but the present approach should allow extension of this concept to the control of hybridization and thus of a broad range of biological functions on the molecular scale. Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna Kimberly Hamad-Schifferli John Schwartz Aaron Santos Shuguang Zhang Joseph Jacobson doi:10.1038/415152a Nature, Vol. 415, No. 6868. (10 January 2002), pp. 152-155. 2007-09-28T13:27:56-00:00 2002 Nature 415 6868 152 155 addons addons-metal metallization-au nanogold nanogold-procedure origami http://www.citeulike.org/user/dna/article/1702493 <i>Nature, Vol. 382, No. 6592. (1996), pp. 609-611.</i><br /><br />PATTERNING matter on the nanometre scale is an important objective of current materials chemistry and physics. It is driven by both the need to further miniaturize electronic components and the fact that at the nanometre scale, materials properties are strongly size-dependent and thus can be tuned sensitively1. In nanoscale crystals, quantum size effects and the large number of surface atoms influence the, chemical, electronic, magnetic and optical behaviour2—4. 'Top-down' (for example, lithographic) methods for nanoscale manipulation reach only to the upper end of the nanometre regime5; but whereas 'bottom-up' wet chemical techniques allow for the preparation of mono-disperse, defect-free crystallites just 1–10 nm in size6–10, ways to control the structure of nanocrystal assemblies are scarce. Here we describe a strategy for the synthesis of'nanocrystal molecules', in which discrete numbers of gold nanocrystals are organized into spatially defined structures based on Watson-Crick base-pairing interactions. We attach single-stranded DNA oligonucleotides of defined length and sequence to individual nanocrystals, and these assemble into dimers and trimers on addition of a complementary single-stranded DNA template. We anticipate that this approach should allow the construction of more complex two-and three-dimensional assemblies. Organization of 'nanocrystal molecules' using DNA Paul Alivisatos Kai Johnsson Xiaogang Peng Troy Wilson Colin Loweth Marcel Bruchez Peter Schultz doi:10.1038/382609a0 Nature, Vol. 382, No. 6592. (1996), pp. 609-611. 2007-09-27T18:37:01-00:00 1996 Nature 382 6592 609 611 lit-sem-1 metallization metallization-au nanogold origami tem-dna tem-nanogold http://www.citeulike.org/user/dna/article/1699618 <i>Advanced Materials, Vol. 13, No. 23. (2001), pp. 1793-1797.</i><br /><br />No abstracts. Platinated DNA as Precursors to Templated Chains of Metal Nanoparticles WE Ford O Harnack A Yasuda JM Wessels doi:10.1002/1521-4095(200112)13:23<1793::AID-ADMA1793>3.0.CO;2-V Advanced Materials, Vol. 13, No. 23. (2001), pp. 1793-1797. 2007-09-27T08:39:54-00:00 2001 Advanced Materials 13 23 1793 1797 metallization metallization-pt origami http://www.citeulike.org/user/dna/article/1660162 <i>Nature, Vol. 394, No. 6693. (6 August 1998), pp. 539-544.</i><br /><br />Molecular self-assembly presents a 'bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA molecular structures and intermolecular interactions are particularly amenable to the design and synthesis of complex molecular objects. We report the design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules. Intermolecular interactions between the structural units are programmed by the design of 'sticky ends' that associate according to Watson-Crick complementarity, enabling us to create specific periodic patterns on the nanometre scale. The patterned crystals have been visualized by atomic force microscopy. Design and self-assembly of two-dimensional DNA crystals. E Winfree F Liu LA Wenzler NC Seeman doi:10.1038/28998 Nature, Vol. 394, No. 6693. (6 August 1998), pp. 539-544. 2007-09-15T08:17:49-00:00 1998 Nature 0028-0836 394 6693 539 544 background origami origami-design http://www.citeulike.org/user/dna/article/241724 <i>Nature Reviews Genetics, Vol. 6, No. 7. (01 July 2005), pp. 533-543.</i> Synthetic biology Steven Benner Michael Sismour doi:10.1038/nrg1637 Nature Reviews Genetics, Vol. 6, No. 7. (01 July 2005), pp. 533-543. 2005-07-01T19:29:31-00:00 2005 Nature Reviews Genetics 1471-0056 6 7 533 543 Nature Publishing Group background origami review http://www.citeulike.org/user/dna/article/500253 <i>Science, Vol. 301, No. 5641. (26 September 2003), pp. 1882-1884.</i><br /><br />A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 x 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 x 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires. DNA-templated self-assembly of protein arrays and highly conductive nanowires. H Yan SH Park G Finkelstein JH Reif TH Labean doi:10.1126/science.1089389 Science, Vol. 301, No. 5641. (26 September 2003), pp. 1882-1884. 2006-02-09T18:56:32-00:00 2003 Science 1095-9203 301 5641 1882 1884 addons metallization origami http://www.citeulike.org/user/dna/article/2998378 <i>(1989)</i> Molecular cloning: a laboratory manual Joseph Sambrook Edward Fritsch Thomas Maniatis (1989) 2008-07-14T08:00:41-00:00 1989 Cold Spring Harbor Laboratory Press origami http://www.citeulike.org/user/dna/article/2978070 <i>Applied Physics Letters, Vol. 89, No. 20. (2006)</i><br /><br />View this record in Web of Science Increasing the Q factor in the constant-excitation mode of frequency-modulation atomic force microscopy in liquid D Ebeling H Hölscher B Anczykowski Applied Physics Letters, Vol. 89, No. 20. (2006) 2008-07-09T16:54:10-00:00 2006 Applied Physics Letters 89 20 AIP afm origami q-control http://www.citeulike.org/user/dna/article/2976337 <i>Applied Physics Letters, Vol. 85, No. 15. (2004), pp. 3232-3234.</i><br /><br />View This Record in Scopus Dynamical properties of the [bold Q]-controlled atomic force microscope János Kokavecz Zoltán Horváth ádám Mechler Applied Physics Letters, Vol. 85, No. 15. (2004), pp. 3232-3234. 2008-07-09T11:56:29-00:00 2004 Applied Physics Letters 85 15 3232 3234 AIP afm origami q-control http://www.citeulike.org/user/dna/article/542022 <i>Nucleic Acids Research, Vol. 34, No. 4. (2006), pp. e29-e29.</i> Nucleic acid visualization with UCSF Chimera Gregory Couch Donna Hendrix Thomas Ferrin doi:10.1093/nar/gnj031 Nucleic Acids Research, Vol. 34, No. 4. (2006), pp. e29-e29. 2006-03-09T13:02:20-00:00 2006 Nucleic Acids Research 0305-1048 34 4 e29 e29 Oxford University Press dna origami visualization http://www.citeulike.org/user/dna/article/2853113 <i>Journal of molecular biology, Vol. 39, No. 2. (January 1969), pp. 265-277.</i><br /><br />The single-stranded DNA in the virion has a molar extinction coefficient per phosphate group at 260 mμ of 6750 ± 300. This low value suggests that the DNA is in a base-stacked conformation. Hypochromism, in the 190 to 205 mμ range, of the protein subunits in the virion indicates an -helix content of 80 to 90%. According to criteria for distinguishing the effects of spectral shifts and changes in absorption intensity on difference spectra, the spectrum for intact phage shows significant hyperchromicity centered around 290 mμ relative to the spectra of separated DNA and protein. Conformations of single-stranded DNA and coat protein in fd bacteriophage as revealed by ultraviolet absorption spectroscopy. LA Day Journal of molecular biology, Vol. 39, No. 2. (January 1969), pp. 265-277. 2008-05-31T12:33:23-00:00 1969 Journal of molecular biology 0022-2836 39 2 265 277 background origami http://www.citeulike.org/user/dna/article/620724 <i>Nucleic Acids Res, Vol. 31, No. 17. (1 September 2003), pp. 5108-5121.</i><br /><br />We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. XJ Lu WK Olson Nucleic Acids Res, Vol. 31, No. 17. (1 September 2003), pp. 5108-5121. 2006-05-09T20:53:54-00:00 2003 Nucleic Acids Res 1362-4962 31 17 5108 5121 background origami origami-design visualization http://www.citeulike.org/user/dna/article/2791094 <i>J. Am. Chem. Soc., Vol. 118, No. 26. (3 July 1996), pp. 6131-6140.</i><br /><br />Abstract: Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. We have examined these molecules from the viewpoint of their potential utility in nanoconstruction. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, so these have been characterized in a ligation cyclization assay. In contrast to other molecules that contain branched junctions, we find that these molecules cyclize rarely or not at all. The double crossover molecules cyclize no more readily than the linear molecule containing the same sequence as the ligation domain. We have tested both a conventional DAE molecule and one containing a bulged three-arm branched junction between the crossovers. The conventional DAE molecule appears to be slightly stiffer, but so few cyclic products are obtained in either case that quantitative comparisons are not possible. Thus, it appears that these molecules may be able to serve as the rigid components that are needed to assemble symmetric molecular structures, such as periodic lattices. We suggest that they be combined with DNA triangles and deltahedra in order to accomplish this goal. Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction X Li X Yang J Qi NC Seeman doi:10.1021/ja960162o J. Am. Chem. Soc., Vol. 118, No. 26. (3 July 1996), pp. 6131-6140. 2008-05-12T22:22:35-00:00 1996 J. Am. Chem. Soc. 118 26 6131 6140 origami origami-design http://www.citeulike.org/user/dna/article/2791089 <i>Nanotechnology, Vol. 9 (September 1998), pp. 257-273.</i><br /><br />Not Available New motifs in DNA nanotechnology NC Seeman H Wang X Yang F Liu C Mao W Sun L Wenzler Z Shen R Sha H Yan Hoi Wong P Sa-Ardyen B Liu H Qiu X Li J Qi SM Du Y Zhang JE Mueller TJ Fu Y Wang J Chen Nanotechnology, Vol. 9 (September 1998), pp. 257-273. 2008-05-12T22:20:20-00:00 1998 Nanotechnology 9 257 273 origami review http://www.citeulike.org/user/dna/article/2790756 <i>Science, Vol. 306, No. 5704. (17 December 2004), pp. 2048-2049.</i><br /><br />10.1126/science.1106754 MATERIALS SCIENCE: Nucleic Acid Nanotechnology Hao Yan doi:10.1126/science.1106754 Science, Vol. 306, No. 5704. (17 December 2004), pp. 2048-2049. 2008-05-12T20:11:38-00:00 2004 Science 306 5704 2048 2049 origami origami-alternatives rna http://www.citeulike.org/user/dna/article/4297 <i>Science, Vol. 306, No. 5704. (17 December 2004), pp. 2068-2072.</i><br /><br />One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules. Building programmable jigsaw puzzles with RNA. A Chworos I Severcan AY Koyfman P Weinkam E Oroudjev HG Hansma L Jaeger doi:10.1126/science.1104686 Science, Vol. 306, No. 5704. (17 December 2004), pp. 2068-2072. 2004-12-20T03:27:54-00:00 2004 Science 1095-9203 306 5704 2068 2072 origami origami-alternatives rna http://www.citeulike.org/user/dna/article/2789725 <i>J. Biol. Chem., Vol. 278, No. 50. (12 December 2003), pp. 49663-49666.</i><br /><br />10.1074/jbc.R300033200 Caution! DNA Crossing: Crystal Structures of Holliday Junctions Franklin Hays Jeffrey Watson Shing Ho doi:10.1074/jbc.R300033200 J. Biol. Chem., Vol. 278, No. 50. (12 December 2003), pp. 49663-49666. 2008-05-12T15:19:53-00:00 2003 J. Biol. Chem. 278 50 49663 49666 background origami review