Nanostructured luminescently labeled nucleic acids

Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods

Towards autonomous DNA-based Nanodevices

Molecular recognition, programmability, self-assembling capabilites and biocompatibility are unique features of DNA. The basic approach of DNA nanotechnology is to exploit these properties in order to fabricate novel materials and structures on the nanometer scale. This cumulative dissertation deals with three aspects of this young research area: fast analysis, autonomous control of functional structures, and biocompatible autonomous delivery systems for nanoscale objects. 1. At low temperatures and under favorable buffer conditions, two complementary DNA strands will form a double-helical structure in which the bases of the two strands are paired according to the Watson-Crick rules: adenine bases bind with thymine bases, guanine bases with cytosine bases. The melting temperature TM of a DNA duplex is defined as the temperature at which half of the double strands are separated into single strands. The melting temperature can be calculated for DNA strands of known sequences under standard conditions. However, it has to be determined experimentally for strands of unknown sequences and for applications under extreme buffer conditions. A method for fast and reliable determination of DNA melting temperatures has been developed. Stable gradients of the denaturing agent formamide were generated by means of diffusion in a microfluidic setup. Formamide lowers the melting temperature of DNA and a given formamide concentration can be mapped to a corresponding virtual temperature along the formamide gradient. Differences in the length of complementary sequences of only one nucleotide as well as a single nucleotide mismatch can be detected with this method, which is of great interest for the detection of sequence mutations or variations such as single nucleotide polymorphisms (SNPs). 2. Knowledge of the stability of DNA duplexes is also of great importance for the construction of DNA-based nanostructures and devices. Conformational changes occuring in artificially generated DNA structures can be used to produce motion on the nanometer scale. Usually, DNA devices are driven by the manual addition of fuel molecules or by the periodic variation of buffer conditions. One prominent example of such a conformational change is the formation of the so-called i-motif, which is a folded four-stranded DNA structure characterized by noncanonical hemiprotonated cytosine-cytosine base-pairs. In order to achieve controlled autonomous motion, the oscillating pH-value of a chemical oscillator has been employed to drive the i-motif periodically through its conformational states. The experiments were conducted with the DNA switch in solution and attached to a solid substrate and constitute the first example of DNA-based devices driven autonomously by a chemical non-equilibrium reaction. 3. Finally, a DNA-crosslinked and switchable polyacrylamide hydrogel is introduced, which is used to trap and release fluorescent colloidal quantum dots in response to externally applied programmable DNA signal strands. Trapping and release of the nanoparticles is demonstrated by studying their diffusion properties using single molecule fluorescence microscopy, single particle tracking and fluorescence correlation spectroscopy. Due to the biocompatibility of the polymerized acrylamide and the crosslinking DNA strands, such gels could find application in the context of controlled drug delivery, where the autonomous release of a drug-carrying nanoparticle could be triggered by naturally occurring, potentially disease-related DNA or RNA strands

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5′-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability towards thermocycling, functionalization reproducibility and storage stability. The derivatization process, first developed for glass slides, was then adapted to microfabricated glass channels containing integrated fluidic connections. This implementation resulted in an important reduction of reaction times, consumption of reagents and process automation. Innovative analytical methods for the characterization of attached DNA were developed for assessing the surface immobilized DNA content after amplification. The results obtained showed that the BTA chemistry is compatible and suitable for forming highly dense arrays of DNA colonies with optimal surface coverage of about 10 million colonies/cm(2) from the amplification of initial single-template DNA molecules immobilized. We also demonstrate that the dsDNA colonies generated can be quantitatively processed in situ by restriction enzymes digestion. DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies

Encoding information into polymers

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Self-Healing Tile Sets

Biology provides the synthetic chemist with a tantalizing and frustrating challenge: to create complex objects, defined from the molecular scale up to meters, that construct themselves from elementary components, and perhaps even reproduce themselves. This is the challenge of bottom-up fabrication. The most compelling answer to this challenge was formulated in the early 1980s by Ned Seeman, who realized that the information carried by DNA strands provides a means to program molecular self-assembly, with potential applications including DNA scaffolds for crystallography [19] or for molecular electronic circuits [15]. This insight opened the doors to engineering with the rich set of phenomena available in nucleic acid chemistry [20]

Fluorescent labeling of plasmid DNA and mRNA : gains and losses of current labeling strategies

Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs

Ultrasensitive surface enhanced Raman scattering nanomotors : for location predicable biochemical detection, single-cell bioanalysis, and controllable biochemical release and real-time detection

Localized surface plasmon resonance resulting from the concerted oscillations of conduction-band electrons in noble-metal (Au, Ag) nanostructures greatly induces enhanced electric ([italic E]) fields in confined nanoscale locations, such as on the tips of nanorods or in the junctions of nanodimers. These [italic E]-field enhanced locations are called hot spots. In the vicinity of hot spots, Raman scattering spectra of biochemicals can be substantially amplified with an [italic E]⁴ dependence due to the [italic E]-field enhancement of both the incident light and Raman spectra. This is called surface enhanced Raman scattering (SERS). SERS is known for its high sensitivity in providing fingerprint vibrational information of molecules. It has triggered intense interest because of its potential applications for label-free and multiplex biochemical detection relevant to medical, environmental and defense purposes. However, the tremendous potential of SERS for ultrasensitive detection has still not materialized because of four major obstacles: (1) it is extremely difficult to obtain a large number of hotspots for sensitive and reproducible detection due to the stringent requirement of hot spots of only a few nanometers; (2) it is arduous to achieve ultrasensitivity for the detection of a single/few molecules; (3) it is challenging to assemble the hot-spots at designated positions for location predicable sensing; and (4) it is even more difficult to change the state-of-the-art static/passive sensing schemes into dynamic/robotized schemes and also to incorporate multi-functionality into a single SERS nanostructure. In this research, we addressed the aforementioned problems by rational design, fabrication and robotization of ultrasensitive SERS nanomotor sensors. A nanomotor sensor consists of a tri-layer structure with a three-segment Ag/Ni/Ag nanorod as the core, a thin layer of silica in the center, and uniformly distributed Ag nanoparticles as the outer layer. The inner metallic nanorod core is the key structure in realizing the concept of the robotization of nanosensors, which can be electrically polarized and thus efficiently manipulated by electric tweezers. The presence of the Ni segment in the metallic nanowire core also allows manipulation and assembling by magnetic interactions. The central silica layer provides a supporting substrate for the synthesis of the Ag nanoparticles and separates the Ag nanoparticles from the metallic nanorod core to eliminate the effect of plasmonic quenching. Finally, the outermost layer made of Ag nanoparticles with optimized sizes and junctions provides a large number of hot spots (~1200/μm²) for ultrasensitive SERS detection with single molecule sensitivity and an enhancement factor (EF) of 1.1×10¹⁰. Moreover, two additional SERS enhancement mechanisms were investigated, i.e., the optical management with nanophotonic devices and the near field effect, which can readily increase the EF by 10 and 2 times, respectively, to at least 10¹¹. Finally, three applications of the SERS nanomotor sensors have been demonstrated: (1) the ultrasensitive SERS nanomotors were transported and assembled into a 3×3 array for location predicable sensing of multiplex molecules; (2) ultrasensitive SERS nanomotors were transported to individual living cells amidst many cells for single-cell bioanalysis; and (3) the SERS nanomotor sensors can be controlled to rotate by the electric tweezers for tunable biochemical release and detection. This research, exploring robotized nanosensors by integrating SERS and NEMS, is innovative in both material design and device concept, which could inspire a new device scheme for various bio-relevant applications.Materials Science and Engineerin

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature

Electrically Deflected Nanomechanical Sensors

An electrically-induced deflective amplification sensor as an actively controlled and reconfigureable nanomechanical sensor for the detection and recognition of cehmicals, biomolecules, and gaseous molecules. The electrically-induced deflective amplification sensors use electric fields to control the bending of transducers, have adjustable sensitivites that depend on electric field strength, and reconfigureable operation ranges for the detection of target molecules at ultra-low and ultra-high concentrations. The sensors are highly integrated, sensitive, provide real-time detection ability, and do not require labels. The electrically-induced deflective amplification transducers can be reconfigured to identify molecules in spectroscopy. A new type of electrophoresis is established using nanostructured transducers. These adaptive and reconfigureable sensors have application in the fields of national security, public health and economic development