Enhanced single strand breaks of supercoiled DNA in a matrix of gold nanotubes under X-ray irradiation.

Single-strand-breaks (SSBs) of supercoiled DNA (scDNA) molecules were used to probe the enhancement of X-ray radiation effect on scDNA mixed with gold nanotubes (AuNTs) in water. The amounts of measured enhancements using SSBs were significantly lower than the expected increase in energy deposition in water by AuNTs under hard X-ray irradiation. Three factors were identified to negatively affect the enhancement: (1) Attenuation of kinetic energies carried by electrons escaped from AuNTs, (2) Scavenging of OH radicals (˙OH) by the surface of bare AuNTs, and (3) Steric effect due to soluble scDNA molecules away from the surface of AuNTs. Benefits and limits of using gold nanomaterials as radiation enhancers and contrast agents are discussed.

Coupling strategies for the synthesis of Peptide-oligonucleotide conjugates for patterned synthetic biomineralization.

This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl)-4-methyl-morpholinium chloride), and two in dimethylformamide (DMF), PyBOP ((Benzotriazol-1-yloxy) tripyrrolidinophosphonium hexafluorophosphate) and HBTU (O-benzotriazole-N,N,N',N'-tetramethyluronium hexafluorophosphate), while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5' amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95%) and solid-phase strategies (24%), while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability.

Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

Weave tile architecture construction strategy for DNA nanotechnology.

Architectural designs for DNA nanostructures typically fall within one of two broad categories: tile-based designs (assembled from chemically synthesized oligonucleotides) and origami designs (woven structures employing a biological scaffold strand and synthetic staple strands). Both previous designs typically contain many Holliday-type multi-arm junctions. Here we describe the design, implementation, and testing of a unique architectural strategy incorporating some aspects of each of the two previous design categories but without multi-arm junction motifs. Goals for the new design were to use only chemically synthesized DNA, to minimize the number of component strands, and to mimic the back-and-forth, woven strand routing of the origami architectures. The resulting architectural strategy employs "weave tiles" formed from only two oligonucleotides as basic building blocks, thus decreasing the burden of matching multiple strand stoichiometries compared to previous tile-based architectures and resulting in a structurally flexible tile. As an example application, we have shown that the four-helix weave tile can be used to increase the anticoagulant activity of thrombin-binding aptamers in vitro.

Recognition of melting of nanoparticle catalysts with cubically shaped Co3O4 nanoparticles.

Cubically shaped cobalt oxide nanoparticle catalysts were used for the first time to investigate the melting of the nanoparticle catalysts responsible for the synthesis of silica nanocoils at 1050 degrees C and straight nanowires at 1100 degrees C. Cobalt nanoparticles remained morphologically highly anisotropic after the growth of nanocoils at 1050 degrees C, whereas they became predominately spherical after straight nanowires were made at 1100 degrees C. These results strongly indicated that cobalt nanoparticles responsible for the synthesis of straight nanowires were completely molten and that melting occurred to these nanoparticles between 1050 and 1100 degrees C.

Nanoscale energy deposition by X-ray absorbing nanostructures.

Here we wish to demonstrate a unique property of nanomaterials: energy deposition with nanometer precision from low-energy electrons released from these nanostructures interacting with hard X-ray radiation in aqueous solution. Three effects combine to cause this phenomenon: (1) localized absorption of X-rays by nanostructures, (2) effective release of low-energy electrons from small nanostructures, and (3) efficient deposition of energy in water in the form of radicals and electrons. This combination creates localized X-ray absorption and localized energy deposition of nanometer precision. We confirmed the theoretically predicted nanoscale energy deposition distribution by measuring hydroxyl radical-induced DNA strand breaks, and observed enhanced damage to a 5600-bp DNA molecule from approximately 10 chemically conjugated small gold nanoparticles under X-ray radiation. These results provide a general guidance to applications of this new concept in many fields including radiation chemistry, radiology, radiation oncology, biochemistry, biology, and nanotechnology.

Damage of supercoiled DNA by an ultrafast laser-driven electron x-ray source.

Using magnetic fields to differentiate the effects of electrons and x-rays, it was discovered that single strand breaks in supercoiled DNA were mainly caused by the energetic ultrafast electrons rather than the ultrafast x-ray photons emitted from the same table-top ultrafast x-ray source. At constant pulse energy of the driving laser pulses, shorter laser pulses produced more strand breaks than longer ones. This was attributed to the increased flux of electrons produced with the shorter laser pulses. Other factors contributing to the DNA damage were investigated and discussed.

Synthesis of tubular gold and silver nanoshells using silica nanowire core templates.

We report the synthesis of tubular gold and silver nanoshells on silica nanowire core templates in solution. Silica nanowires were synthesized and characterized with optical and NMR methods. Gold nanoparticle seeds (2 to 3 nm) with weak repulsive surfactants such as tetrakis-hydroxymethyl-phosphonium chloride (THPC) were conjugated to the surface of these nanowires. A regrowth process was initiated from these nanoparticles on the surface of the silica nanowires dispersed in gold or silver stock solutions in the presence of reducing agents. Micrometers-long gold and silver tubular nanoshells (80-150 nm o.d.) were made, fully covering the silica nanowires.

Silica nanocoils.

We report here the results of nanoparticle-catalyzed synthesis of a variety of silica nanocoils (SiNCs) under similar growth conditions to those of making regular straight silica/silicon nanowires (SiNWs). Synthesis of individual SiNCs with alternating coiled and straight segments was achieved with cobalt nanoparticle catalysts at alternating temperatures. In addition, a variety of SiNCs, including multiple SiNCs sharing the same nanoparticle catalyst, SiNC double helices, and individual SiNCs with varying pitches and diameters were made.

Enhanced relaxation of nanoparticle-bound supercoiled DNA in X-ray radiation.

A therapeutic methodology was developed based on the large X-ray absorption cross-section of gold nanoparticles at high photon energies (>81 keV). Experimental results showed that the amounts of the relaxed circular supercoiled DNA (scDNA) for gold nanoparticle-bound scDNA were more than doubled compared to that for free scDNA under otherwise identical radiation conditions.

Silicon-based nanowires from silicon wafers catalyzed by cobalt nanoparticles in a hydrogen environment.

We present here the synthesis of silicon-based nanowires directly from silicon wafers at high temperatures and in the presence of cobalt nanoparticles and hydrogen gas. All three ingredients were critical to the growth of Si-based nanowires, which were between 5-60 nm in diameter and microm-mm long. Both heavily coiled and straight Si-based nanowires were made. Experimental evidence suggested that the sources of silicon for the nanowires growth were in the gas phase.

Determination of CoSi2 self-aligned nanostructures with grazing incidence X-ray absorption spectroscopy.

Self-aligned nanostructures (SAN) made by reacting Co nanoparticles with crystalline Si substrates at high temperatures were studied with grazing incidence X-ray absorption spectroscopy (GI-XAS). The results from extended X-ray absorption fine structure (EXAFS) analysis and X-ray absorption near-edge spectroscopy (XANES) were used to identify SAN as crystalline CoSi2. Theoretical calculations of EXAFS and XANES spectra of several crystalline cobalt silicides were performed with the FEFF8 package. On the basis of these studies, the SAN samples were determined to contain nearly pure CoSi2.