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PubMed1999

Extended circular dichroism measurements using synchrotron radiation show that the assembly of clathrin coats requires no change in secondary structure.

A number of models have been proposed for the assembly of clathrin triskelia into coats. However, little is known of the effects of assembly on triskelion structure. A more detailed knowledge of the way in which assembly affects triskelion structure would be valuable for assessing the relative merits of the proposed models. The development of a vacuum-ultraviolet circular dichroism (CD) instrument that uses synchrotron radiation as a light source has allowed us to extend the range of CD measurements to shorter wavelengths. This has greatly increased signal quality even for highly scattering samples. Also, we have improved CD data analysis to provide standard deviations for calculated secondary structure content. These developments have increased the precision of CD analysis beyond what has been thus far possible. Using these developments, we have determined the secondary structure content of all components of coat protein, under both assembly and dissociating conditions. The assembly of coats does not incur any change in secondary structure content, but a 10% loss of triskelion helical content accompanies assembly in the absence of AP-2. We conclude that coat assembly requires no detectable reorganization of triskelion structure. Our result indicates that AP-2 stabilizes helical structure in the triskelion, and we propose that this increases triskelion rigidity, restricting the range of coat sizes.

Adaptor Proteins, Vesicular Transport↗
PubMedDate not supplied

Alternating bioactivity of polymeric layer-by-layer assemblies: anticoagulation vs procoagulation of human blood.

The layer-by-layer assembly between cationic chitosan and anionic dextran sulfate was analyzed quantitatively by a quartz crystal microbalance technique in the absence and presence of 0.2, 0.5, and 1 M NaCl in the polymer solution. The apparent film thickness increased upon increasing the NaCl concentration. The anti- versus procoagulant activity of these films against whole human blood was studied by the immersion of a substrate into blood for 30 min incubation time at 37 degrees C. The substrate was coated with films of varying NaCl concentrations and assembly step numbers. There was a critical concentration for the alternating activity; above a concentration of 0.5 M NaCl, both anti- and procoagulation could be observed on the dextran sulfate and chitosan surfaces, respectively. The underlying layer of the assembly was necessary for this alternating activity; after a five-step assembly, the activity was realized. The adsorption of a cationic dye (methylene blue) onto the films revealed that the anionic-charge density derived from dextran sulfate on the film surface was linearly increased with increased NaCl concentration. There was a critical charge density of the dextran sulfate for the anticoagulant activity. An assembly was also constructed from a combination of chitosan and heparin, but the activity was different from that of the former system; strong anticoagulant activity was observed even on the chitosan surface. We suggest that the polymer species and/or the assembly conditions are key factors for realizing the alternating bioactivities of films prepared by the layer-by-layer assembly.

Blood Coagulation↗
PubMed2004

Inter-string arrays of bimetallic assemblies with alternative Cu2+-Cl-Cu2+ and Cu-NC-M (M = Co3+, Fe+3, Cr+3) bridges: syntheses, crystal structure, and magnetic properties.

Three bimetallic assemblies with alternate homometallic bridges through chloride ligands and heterometallic bridges through cyanide ligands of formula [(323)(2)Cu(2)(Cl)M(CN)(6)](n).2n(H(2)O), where 323 = N,N'-bis(3-aminopropyl)ethylenediamine and M = Co(3+) for 1, Fe(3+) for 2, and Cr(3+) for 3, were synthesized. They have been characterized structurally, analytically, spectroscopically, and magnetically. All three assemblies crystallize in the monoclinic system in the same space group P2(1)/n, with a = 11.642(2) A, b = 10.285(3) A, c = 13.622(2) A, beta = 95.69(3) degrees, V = 1623.1(6) A(3), and Z = 4 for 1; a = 11.681(4) A, b = 10.315(3) A, c = 13.567(5) A, beta = 95.62(3) degrees, V = 1626.8(9) A(3), Z = 4 for 2, and a = 11.782(4) A, b = 10.386(2) A, c = 13.755(4) A, beta = 95.51(3) degrees, V = 1657.4(8) A(3), Z = 4 for 3. Crystal structure analyses reveal that one-dimensional zigzag chains propagate in two different crystallographic directions (a and b) which are held together during the course of their propagation. All three assemblies have a homometallic Cu-Cl-Cu core in common. Assembly 1 exhibits metamagnetic behavior and shows weak antiferromagnetic interactions between Cu(2+) paramagnetic centers, through the chloride bridges. The Neel temperature, T(N), is 3.5 K, and the critical field is 4 T. In the presence of a magnetic field larger than 4 T, the local spin doublets of Cu(2+) in the assembly 1 remain in parallel arrangements. Assemblies 2 and 3 may be described as an alternative repetition of the antiferromagnetically coupled Cu-Cl-Cu fragment and ferromagnetically coupled Cu-CN-Fe(3+)/Cr(3+)fragment. The overall magnetic character of the strings in assemblies 2 and 3 are antiferromagnetic. Ferromagnetic interaction evidenced by the (Cu-CN-Fe(3+)/Cr(3+)) fragment was masked by the antiferromagnetic interaction between the Cu(2+) centers through the chloride bridge. The magnetic properties agree well with those expected for two [323 Cu(2+)] and a [Fe(CN)](3+) unit with spin-orbit coupling effect of the low-spin iron(III) ions for 2 and for two [323 Cu(2+)] and a [Cr(CN)](3+) unit for 3. In aqueous solution, trinuclear [(323)(2)Cu(2)M(CN)(6)](+) and dinuclear [(323)CuM(CN)(6)](-) species were observed.

Journal Article↗
PubMed2002

Cooperative self-assembly of dendrimers via pseudorotaxane formation from a homotritopic guest molecule and complementary monotopic host dendrons.

Interaction of the homotritopic guest 1,3,5-tris[p-(benzylammoniomethyl)phenyl]benzene tris(hexafluorophosphate) (1a) with dibenzo-24-crown-8 (DB24C8) leads to the sequential self-assembly of [2]-, [3]-, and [4]-pseudorotaxanes 7a, 8a, and 9a, respectively. The self-assembly processes were studied using NMR spectroscopy. In CD(3)CN and CD(3)COCD(3) the individual association constants K(1), K(2), and K(3) for 1:1, 1:2, and 1:3 complexes were determined by several methods. Via Scatchard plots, the three NH(2)(+) sites of 1a were shown to behave independently in binding DB24C8. K values (4.4 x 10(2), 1.4 x 10(2), and 41 M(-)(1), respectively, in CD(3)CN) directly determined from signals for the individual complexes (7a, 8a, and 9a) were somewhat higher than those estimated from the Scatchard plot because of concentration dependence, but the ratios of association constants followed the expected statistical order (K(1):K(2):K(3) = 3:1:(1)/(3)). These are believed to be the first evaluations of association constants leading to a [4]-pseudorotaxane. In the less polar CDCl(3), association constants could not be determined because approximately 90% of the dissolved tritopic guest, which by itself is insoluble, was present as the fully loaded [4]pseudorotaxane 9a! Self-assembly of homotritopic guest 1a with benzyl ether dendrons of the first, second, and third generations functionalized at the "focal point" with DB24C8 moieties (3-5) produces pseudorotaxane dendrimers. The self-assembly processes were studied using (1)H NMR spectroscopy. In CD(3)COCD(3) for all three generations the individual association constants K(1), K(2), and K(3) for [2]-, [3]-, and [4]-pseudorotaxane complexes 7c-e, 8c-e, and 9c-e indicated that the self-assembly was cooperative; that is, the ratios of the individual association constants exceeded the expected statistical ratios. Scatchard plots confirmed this behavior. Self-assembly processes in the less polar CDCl(3) were kinetically slow, requiring ca. 1, 2, and 3 days, respectively, for the first, second, and third generation systems to reach equilibrium with 1a; the slow rate is attributed to the insolubility of the homotritopic guest 1a in this medium and the steric demands of the resulting dendrimers. However, only dendrimers of 1:3 stoichiometry, that is, the nanoscopic [4]pseudorotaxanes 9, were formed! Moreover, it is noteworthy that the extent of dissolution of 1a (reflective of the overall association constant which is too high to measure) increases with generation number, presumably because of the more effective screening of the ionic guest by the larger dendrons and perhaps favorable pi-pi and CH-pi interactions. Such cooperative effects suggest a number of applications that can take advantage of the pH-switchable nature of these self-assembly processes.

Journal Article↗
PubMed2002

Novel spherical assembly of gold nanoparticles mediated by a tetradentate thioether.

The ability to construct three- and two-dimensional architectures via nanoscale engineering is important for emerging applications of nanotechnology in sensors, catalysis, controlled drug delivery, microelectronics, and medical diagnostics. In this paper, we report novel 3D assembly using multidentate molecular building blocks. It is demonstrated that the interparticle linking of gold nanoparticles (3.7 nm core size) by a tetradentate thioether, tetra[(methylthio)methyl]silane, leads to the formation of a spherical assembly. The spherical size (30-80 nm diameter) is dependent on reaction time and relative ratio of the building blocks. The novelty of this approach is the viability of multidentate thioethers to link nanoparticles and produce spherical assemblies that can be readily assembled and disassembled. The spherical assembly can also be partially "melted" depending on the nature of interfacial interactions between the assembly and the substrate. These unusual morphological properties in shape and surface interaction and the intriguing assembling-disassembling capabilities may form the basis of designing and fabricating novel functional nanostructures.

Gold↗
PubMed2003

Nickel-catalyzed highly regio- and stereoselective three-component assembly of allenes, aryl iodides, and alkenylzirconium reagents.

Cyclohexylallene (1a) and alkenylzirconium reagent (n-PrCH=CHZr(Cp)2Cl) undergo three-component assembly with a variety of aromatic iodides (R1-I: R1 = 4-PhOMe, 4-PhCOMe, 4-PhMe, 2-thiophene, 2-PhOMe, 3-PhOMe, and 4-PhCO2Et) in the presence of NiCl2(PPh3)2 and zinc powder in THF at 50 degrees C to afford corresponding three-component assembly products in moderate to good yields with very high regio- and stereoselectivity. In addition to cyclohexylallene, also phenylallene, n-butylallene, cyclopentylallene, and cycloheptylallene underwent the three-component assembling reaction to furnish the corresponding 1,4-diene derivatives in good yields. Several alkenylzirconium reagents (R2CH=CHZr(Cp)2Cl: R2 = Ph (3b), t-Bu, TMS) were also employed for this three-component assembly. The nickel-catalyzed three-component assembly was further extended to vinyl iodides. Thus, 1a reacts with 3b and ethyl (Z)-3-iodoacrylate to produce a highly substituted triene in excellent yield. In all of these three-component assembly reactions, the E isomers were formed predominantly with E/Z ratios between 94/6 and 99/1. A possible mechanism for this highly regio- and stereoselective three-component assembly is proposed.

Journal Article↗
PubMed2005

Mediator-template assembly of nanoparticles.

The ability to construct size- and shape-controllable architectures using nanoparticles as building blocks is essential for the exploration of nanoparticle-structured properties. This paper reports findings of an investigation of a mediator-template strategy for the size-controllable assembly of nanoparticles. This strategy explores multidentate thioether ligands as molecular mediators and tetraalkylammonium-capped gold nanoparticles (5 nm) as templates toward the preparation of size-controllable and monodispersed spherical assemblies ( approximately 20-300-nm diameters). The combination of the mediation force of the multidentate thioether and the hydrophobic force of the tetraalkylammonium template establishes the interparticle linkage and stability. The morphological properties of the spherical assemblies have been characterized using TEM, AFM, and SAXS techniques. The finding of the soft-hard nature of the nanoparticle assemblies and their interactions with contacting substrates could form the basis of a new strategy for manipulating nanoscale linkages between nanoparticle assemblies, soldering nanoelectronics, and constructing nanosensor devices. The intriguing light scattering and optical absorption properties in response to assembly, disassembly, sizing, and interparticle spacing parameters have been characterized by dynamic light scattering and spectrophotometric measurements. The discovery of the controlled disassembly into individual nanoparticles and the size regulation by a third capping component could form the basis for applications in controlled drug delivery. The fundamental basis for the mediator-template strategy as a versatile assembly technique is further discussed in terms of experimental and theoretical correlations of the morphological and optical properties.

Journal Article↗
PubMed2004

Selective 226Ra2+ ionophores provided by self-assembly of guanosine and isoguanosine derivatives.

The self-assembled guanosine (G 1)-based hexadecamers and isoguanosine (isoG 2)-based decamers are excellent 226Ra2+ selective ionophores even in the presence of excess alkali (Na+, K+, Rb+, and Cs+) and alkaline earth (Mg2+, Ca2+, Sr2+, and Ba2+) cations over the pH range 3-11. G 1 requires additional picrate anions to provide a neutral assembly, whereas the isoG 2 assembly extracts 226Ra2+ cations without any such additives. Both G 1-picrate and isoG 2 assemblies show 226Ra2+ extraction even at a 0.35 x 10(6) fold excess of Na+, K+, Rb+, Cs+, Mg2+, or Ca2+ (10(-2) M) to 226Ra2+ (2.9 x 10(-8) M) and at a 100-fold salt to ionophore excess. In the case of the G 1-picrate assembly, more competition was observed from Sr2+ and Ba2+, as extraction of 226Ra2+ ceased at an M2+/226Ra2+ ratio of 10(6) and 10(4), respectively. With the isoG 2 assembly, 226Ra2+ extraction also occurred at a Sr2+/226Ra2+ ratio of 10(6) but ceased at a 10(6) excess of Ba2+. The results clearly demonstrate the power of molecular self-assembly for the construction of highly selective ionophores.

Adenosine↗
PubMed2006

Molecular-level helical stack of a nucleotide-appended oligo(p-phenylenevinylene) directed by supramolecular self-assembly with a complementary oligonucleotide as a template.

The nucleotide-appended oligo(p-phenylenevinylene), {bis[2,5-bis(2-methoxyethoxy)-1,4-phenylene]bis(2,1-ethenediyl-1,4-phenylenemethylene)}bis(2'-deoxy-3'-thymidylic acid) (8), has been synthesized, and self-assembly of the single-component 8 and binary self-assembly of 8 with a complementary single-stranded 20-meric oligodeoxyadenylic acid (9) have been examined in aqueous solutions. Atomic force microscopy (AFM), UV-visible (UV-vis), and circular dichroism (CD) measurements revealed that right-handed helical stacks with 6.4- and 5.1-nm diameters self-assemble from the binary components of 8 and 9 as a template depending on the residual stoichiometry of the two components (thymine (T):adenine (A) = 1:1 and T:A = 2:1, respectively). The concentration of 9 was found to strongly influence the CD spectra of 8 in aqueous solutions. Consequently, we concluded that the one side of the thymine moieties in the stacked assemblies of 8 complexes with a single chain of 9. Complementary T-A base pairs thus formed and induced helical stack of the oligo(p-phenylenevinylene)s in the binary self-assembly. In contrast, self-assembly of the single-component 8 and binary self-assembly of 8 with the noncomplementary 20-meric oligothymidylic acid (10) produced no remarkable formation of fibrous structures like helical stacks.

Circular Dichroism↗
PubMed2002

Kinetic stabilities of double, tetra-, and hexarosette hydrogen-bonded assemblies.

A study of the kinetic stabilities of hydrogen-bonded double, tetra-, and hexarosette assemblies, comprising 36, 72, and 108 hydrogen bonds, respectively, is described. The kinetic stabilities are measured using both chiral amplification and racemization experiments. The chiral amplification studies show that solvent polarity and temperature strongly affect the kinetic stabilities of these hydrogen-bonded assemblies. For example, the activation energy for the dissociation of a tetramelamine from a tetrarosette assembly, a process that involves the breakage of 24 hydrogen bonds, was determined at 98.7 +/- 16.6 kJ mol(-1) in chloroform and 172.8 +/- 11.3 kJ mol(-1) in benzene. Moreover, racemization studies with enantiomerically enriched assemblies reveal a strong dependence of the kinetic stability on the number and strength of the hydrogen bonds involved in assembly formation. The half-lives for double, tetra-, and hexarosette assemblies were found to be 8.4 min, 5.5 h, and 150 h in chloroform at 50 degrees C, respectively. For higher generations of these types of assemblies, the kinetic stabilities become so high that they can no longer measured in a direct manner.

Journal Article↗
PubMed2006

Electrochemically partitioned assembly of organosulfur monolayers and nanoparticles.

Partitionally assembled organosulfur monolayers were prepared by using an electrochemically assisted assembly method on gold films that were preseparated into two regions insulated from each other. Cyclic voltammetry (CV) and X-ray photoelectron spectroscopy (XPS) were employed to characterize the n-dodecanethiol (DDT) and the 11-mercaptoundecanoic acid (MUA) monolayers, which were separately assembled on different substrate regions. CV results indicated that both the DDT- and MUA-coated gold electrodes showed a blocking property toward the negatively charged redox probe Fe(CN)6(3-). However, when positively charged Ru(NH3)6(3+) was used as the redox probe, the MUA- and DDT-modified electrodes showed quasireversible and blocking CV features, respectively. These phenomena were attributed to different interactions between the negatively charged MUA surface and the negatively or positively charged redox probes. XPS spectra obtained on the MUA modified region exhibited an O(1s) peak and a small discrete C(1s) peak, which arose from the oxygen and the carbon atoms in the carboxylic acid groups, respectively. For the DDT-modified region, these two peaks were absent. CV and XPS experimental results provided strong evidence that different SAMs were selectively deposited onto different regions of the preexisting patterns of the substrate by electrochemically partitioned assembly. The partitionally assembled sulfur-based monolayers with different terminal groups were used to form location-selective nanoparticle assemblies. This electrochemically partitioned assembly technique has great potential in controllable constructions of molecular layers and nanostructures on different surface microarchitectures that are closely integrated on one substrate but insulated from each other.

Journal Article↗
PubMed2006

Controlled, simultaneous assembly of polyethylenimine onto nanoparticle silica colloids.

A novel precision-assembly methodology is described on the basis of the controlled, simultaneous assembly (CSA) of a core nanoparticle substrate and polyelectrolyte solutions. The method is capable of assembly rates at least as fast as 10(16) core particles s(-1) L(-1) and affords concentrated suspensions of stable colloids with an adsorbed polyelectrolyte. The resulting dispersions are highly homogeneous, have a low viscosity and narrow particle-size distribution, and are stable colloids, even at solid concentrations of at least 33 wt %. The adsorption isotherm and the saturation adsorption for polyethylenimine (PEI) assemblies onto a 15 nm silica colloid have been evaluated with 1H NMR spectroscopy. The saturation adsorption is highly dependent upon the pH at assembly and is given by the equation PEIa (micromol m(-2)) = 1.73pH - 1.89, R2 = 0.986, where micromoles refers to the concentration of the EI monomer. The saturation concentration increases from 6.8 micromol m(-2) at pH 5.0 to 13.7 micromol m(-2) at pH 9.0. The adsorbed polyelectrolyte may be cross-linked and thereby permanently fixed to the colloid surface to prepare nanoparticle-polyelectrolyte colloidal assemblies having enhanced colloid stability, high homogeneity, and a high fraction (>80%) of permanently adsorbed polyelectrolyte. These assemblies are stable at physiological pH and ionic strength and may represent ideal substrates for bioconjugation and, ultimately, the design of nanocarriers for in vivo applications.

Journal Article↗
PubMed1999

Assembly of the yeast vacuolar proton-translocating ATPase.

The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterized member of the V-ATPase family. Biochemical and genetic screens led to the identification of a large number of genes in yeast, designated VMA, encoding proteins required to assemble a functional V-ATPase. A total of thirteen genes encode subunits of the final enzyme complex. In addition to subunit-encoding genes, we have identified three genes that code for proteins that are not part of the final V-ATPase complex yet required for its assembly. We refer to these nonsubunit Vma proteins as assembly factors, since their function is dedicated to assembling the V-ATPase. The assembly factors, Vma12p, Vma21p, and Vma22p are localized to the endoplasmic reticulum (ER) and aid the assembly of newly synthesized V-ATPase subunits that are translocated into the ER membrane. At least two of these proteins, Vma12p and Vma22p, function together in an assembly complex and interact directly with nascent V-ATPase subunits.

Fungal Proteins↗
PubMed1997

Assembly of deletion mutants of the Rieske iron-sulfur protein into the cytochrome bc1 complex of yeast mitochondria.

The assembly of two deletion mutants of the Rieske iron-sulfur protein into the cytochrome bc1 complex was investigated after import in vitro into mitochondria isolated from a strain of yeast, JPJ1, from which the iron-sulfur protein gene (RIP) had been deleted. The assembly process was investigated by immunoprecipitation of the labeled iron-sulfur protein or the two deletion mutants from detergent-solubilized mitochondria with specific antisera against either the iron-sulfur protein or the bc1 complex (complex III) [Fu and Beattie (1991). J. Biol. Chem. 266, 16212-16218]. The deletion mutants lacking amino acid residues 55-66 or residues 161-180 were imported into mitochondria in vitro and processed to the mature form via an intermediate form. After import in vitro, the protein lacking residues 161-180 was not assembled into the complex, suggesting that the region of the iron-sulfur protein containing these residues may be involved in the assembly of the protein into the bc1 complex; however, the protein lacking residues 55-66 was assembled in vitro into the bc1 complex as effectively as the wild type iron-sulfur protein. Moreover, this mutant protein was present in the mitochondrial membrane fraction obtained from JPJ1 cells transformed with a single-copy plasmid containing the gene for this protein lacking residues 55-66. This deletion mutant protein was also assembled into the bc1 complex in vivo, suggesting that the hydrophobic stretch of amino acids, residues 55-66, is not required for assembly of the iron-sulfur protein into the bc1 complex; however, this association did not lead to enzymatic activity of the bc1 complex, as the Rieske FeS cluster was not epr detectable in these mitochondria.

Electron Transport Complex III↗
PubMed1990

The mitochondrial chaperonin hsp60 is required for its own assembly.

Heatshock protein 60 (hsp60) in the matrix of mitochondria is essential for the folding and assembly of newly imported proteins. Hsp60 belongs to a class of structurally related chaperonins found in organelles of endosymbiotic origin and in the bacterial cytosol. Hsp60 monomers form a complex arranged as two stacked 7-mer rings. This 14-mer complex binds unfolded proteins at its surface, then seems to catalyse their folding in an ATP-dependent process. The question arises as to how such an assembly machinery is itself folded and assembled. Hsp60 subunits are encoded by a nuclear gene and translated in the cytosol as precursors which are translocated into mitochondria and proteolytically processed. In both intact cells and isolated mitochondria of the hsp60-defective yeast mutant mif4, self-assembly of newly imported wild-type subunits is not observed. Functional pre-existing hsp60 complex is required in order to form new, assembled, 14-mer. Subunits imported in vitro are assembled with a surprisingly fast half-time of 5-10 min, indicative of a catalysed reaction. These findings are further evidence that self-assembly may not be the principal mechanism by which proteins attain their functional conformation in the intact cell.

Biological Transport↗
PubMed2000

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules.

Recent work has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by 'sticky' ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of 'Wang' tiles, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations; there is also a logical equivalence between DNA sticky ends and Wang tile edges. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.

Algorithms↗
PubMed2001

Hierarchical self-assembly of metal nanostructures on diblock copolymer scaffolds.

Self-assembly is emerging as an elegant, 'bottom-up' method for fabricating nanostructured materials. This approach becomes particularly powerful when the ease and control offered by the self-assembly of organic components is combined with the electronic, magnetic or photonic properties of inorganic components. Here we demonstrate a versatile hierarchical approach for the assembly of organic-inorganic, copolymer-metal nanostructures in which one level of self-assembly guides the next. In a first step, ultrathin diblock copolymer films form a regular scaffold of highly anisotropic, stripe-like domains. During a second assembly step, differential wetting guides diffusing metal atoms to aggregate selectively along the scaffold, producing highly organized metal nanostructures. We find that, in contrast to the usual requirement of near-equilibrium conditions for ordering, the metal arranged on the copolymer scaffold produces the most highly ordered configurations when the system is far from equilibrium. We delineate two distinct assembly modes of the metal component-chains of separate nanoparticles and continuous wires-each characterized by different ordering kinetics and strikingly different current-voltage characteristics. These results therefore demonstrate the possibility of guided, large-scale assembly of laterally nanostructured systems.

Journal Article↗
PubMed2004

Shotgun sequence assembly and recent segmental duplications within the human genome.

Complex eukaryotic genomes are now being sequenced at an accelerated pace primarily using whole-genome shotgun (WGS) sequence assembly approaches. WGS assembly was initially criticized because of its perceived inability to resolve repeat structures within genomes. Here, we quantify the effect of WGS sequence assembly on large, highly similar repeats by comparison of the segmental duplication content of two different human genome assemblies. Our analysis shows that large (> 15 kilobases) and highly identical (> 97%) duplications are not adequately resolved by WGS assembly. This leads to significant reduction in genome length and the loss of genes embedded within duplications. Comparable analyses of mouse genome assemblies confirm that strict WGS sequence assembly will oversimplify our understanding of mammalian genome structure and evolution; a hybrid strategy using a targeted clone-by-clone approach to resolve duplications is proposed.

Animals↗