Photografting and patterning of oligonucleotides on benzophenone-modified boron-doped diamond

Irradiation of a patterned benzophenone-terminated boron-doped diamond (BDD) surface with UV light (lambda = 350 nm) in the presence of a 15(mer) oligonucleotide resulted in the covalent linking of the DNA strand to the BDD interface.     

Controlled electrophoretic patterning of polyaniline from a colloidal suspension

We present a method for controlled deposition of polyaniline from colloidal suspensions. Stable suspensions of polyaniline colloids (approximately 115 nm in diameter) were formed by dispersing polyaniline/formic acid solution into acetonitrile. It was demonstrated that the positively charged polyaniline colloids can be electrophoretically deposited onto various substrate materials such as platinum and ITO, forming continuous ultrathin films. We examined the film morphology, as well as the effects of process parameters, such as deposition time, colloid concentration, and applied voltage, on the deposition efficiency. Furthermore, the efficacy of the technique was illustrated by electrophoretically patterning polyaniline thin films onto selected individual micrometer-scale sensing elements within a microfabricated sensor array, and by further demonstrating its sensitivity to gaseous analytes including water and methanol.     

Poly(dimethylsiloxane) contamination in microcontact printing and its influence on patterning oligonucleotides

It is well-established that, during microcontact printing (muCP) using poly(dimethylsiloxane) (PDMS)-based stamps, some unexpected siloxane fragments can be transferred from the stamp to the surface of the sample. This so-called contamination effect coexists with the delivery of the molecules constituting the ink and by this way influences the printing process. The real impact of this contamination for the muCP technique is still partially unknown. In this work, we investigate the kinetics of this contamination process through the surface characterization of both the sample and the stamp after imprinting. The way both the curing conditions of the PDMS material and the contact time influence the degree of contamination of the surface is investigated on silicon and glass substrates. We propose a cleaning process of the stamp during several hours which eliminates any trace of contamination during printing. We show that hydrophobicity recovery of PDMS surfaces after hydrophilic treatment using oxygen plasma is considerably slowed down when the PDMS material is cleaned using our procedure. Finally, by comparing cleaned and uncleaned PDMS stamps, we show the influence of contamination on the quality of muCP using fluorescent DNA molecules as an ink. Surprisingly, we observe that the amount of DNA molecules transferred during muCP is higher for the uncleaned stamp, highlighting the positive impact of the presence of low molecular weight siloxane fragments on the muCP process. This result is attributed to the better adsorption of oligonucleotides on the stamp surface in presence of these contaminating molecules.     

Controlled intracellular localization and enhanced antisense effect of oligonucleotides by chemical conjugation

Oligonucleotides can be covalently linked to peptides composed of any sequence of amino acids by solid phase fragment condensation. The peptides incorporated into the conjugates include nuclear localizing signals (NLS), nuclear export signals (NES), membrane fusion domain of some viral proteins and some designed peptides with amphipathic character. Evaluation of biological properties of DNA-peptide conjugates indicated that (a) the conjugates could bind to target RNA and dsDNA with increased affinity, (b) the conjugates were more resistant to cellular nuclease degradation, (c) the conjugate-RNA hybrids could activate RNase H as effectively as native oligonucleotides, (d) the conjugates with fusion peptides showed largely enhanced cellular uptake, (e) the conjugates with NLS could be predominantly delivered into the cell nucleus, (f) the conjugates with NES could be localized in the cytoplasm. As a result, antisense oligonucleotides conjugated with NLS could inhibit human telomerase in human leukemia cells much more strongly than phosphorothioate oligonucleotides.     

Controlled lateral spreading and pinning of oil droplets based on topography and chemical patterning

Geometric pinning sites can be used to control the lateral spreading and pinning of oils on surfaces. The geometric pinning effect combined with lithographic surface chemistry patterning allows controlling the shapes of oil droplets. We study the confinement effect on test structures of various protruding and intruding geometries, and employ scanning electron microscopy analysis to study the shape of the meniscus at the edges of the chemical patterns. Nanopillar and micropillar topographies are compared, revealing that it is a necessity for accurate oil patterns that the length scale of the roughness is smaller than the resolution of the surface chemistry pattern. We also find that there exists a critical, geometry-dependent threshold contact angle, below which the geometric confinement does not work, as olive oil with a static advancing contact angle of 57° accurately replicated the chemical pattern on top of nanopillar topography, but hexadecane with a static advancing contact angle of 50° penetrated the pinning sites and wetted the whole surface.     

High‐density quantum dots composites and its photolithographic patterning applications

With the growing interest in quantum dots (QDs), many applications are emerging recently. In particular, the display industry has shown widespread interest in using QDs as the next generation colorants. One application is to replace conventional color filters with QD‐based color conversion films to significantly improve color purity and luminous efficiency. However, QD blending which is capable of photolithographic patterning is a very challenging problem due to its low dispersion property and aggregations in polar medias. Herein, we report a photo‐patternable QD dispersion that can produce fine patterns through a photolithography process. First, the QDs dispersed in a nonpolar solvent, for example, chloroform or hexane, were separated and dried to obtain a QD powder. And then, the dispersion characteristics of the QD powders were investigated after mixing commercial dispersants and UV curable oligomers. Furthermore, the QD dispersion was investigated up to 30 wt.% of QDs by mixing with various commercial additives. We have studied the optical property changes of QDs during the photocuring process and the heating process prior to actual application. And, we have studied the surface characteristics of the fine QDs patterns after patterning process. As a result, it was confirmed that QDs are able to be well dispersed up to 30 wt.%.     

Cooperative hybridization of oligonucleotides

Nucleic acids have been demonstrated to be versatile nanoscale engineering materials with the construction of dynamic DNA structures, motors, and circuits. These constructions generally rely on the clever use and integration of relatively few reaction mechanisms and design primitives. Here, cooperative hybridization is introduced as a mechanism in which two oligonucleotides of independent sequence can stoichiometrically, simultaneously, and cooperatively hybridize to a DNA complex. Cooperative hybridization is rigorously characterized and modeled and is shown to implement digital concentration comparison with amplification, as well as digital Boolean logic. These designs, based on cooperative hybridization, excel in being robust to impurities and not requiring oligonucleotide purification.     

Synthesis of aminoglycoside-modified oligonucleotides

[structure: see text] To study the structural requirements of aminoglycoside binding to nucleic acids, compound 1-an analogue of the naturally occurring nucleoside J-was synthesized. When incorporated into oligodeoxynucleotides, 1 leads to thermal stabilization of the resulting duplexes. The increase in pairing affinity is stronger with complementary RNA than with DNA.     

Stepwise synthesis of oligonucleotides

Russian Chemical Bulletin -     

Flow-induced patterning of Langmuir monolayers

Insoluble monolayers on water have been patterned at the macroscopic scale (i.e., at the centimeter scale of the flow apparatus) as well as the mesoscopic scale (i.e., down to the micron scale resolvable via optical microscopy). The macroscopic patterning at the air/water interface results from a hydrodynamic instability leading to a steadily precessing flow pattern. The velocity field is measured, and the associated shear stress at the interface is shown to be locally amplified by the flow pattern. The resulting hydrodynamic effects on two different monolayer systems are explored: (1) the pattern in a model monolayer consisting of micron-size, surface-bound particles is visualized to show that the particles are concentrated into isolated regions of converging flow with high shear, and (2) Brewster angle microscopy of a Langmuir monolayer (vitamin K1) shows not only that the monolayer is patterned at the macroscopic scale but also that the localized high-shear flow further patterns the monolayer at the mesoscale.     

Solid-phase enzymatic synthesis of oligonucleotides

[formula: see text] The controlled and selective synthesis of oligonucleotides on the solid phase is possible under mild aqueous conditions using the enzyme T4 RNA ligase, the resins being tentagel or kieselguhr/polydimethylacrylamide.     

Fluorous affinity purification of oligonucleotides

[structure: see text] Nucleoside phosphoramidites bearing a fluorous dimethoxytrityl (FDMT) group were used to synthesize fluorous-tagged oligonucleotides, which were subjected to solid-phase extraction using a pH-stable fluorinated adsorbent. On-column detritylation afforded the purified oligonucleotides. The fluorous affinity purification method offers one-pass loading without ammonia removal, high selectivity for the removal of failure sequences, high recoveries (typically 70-100%), and the ability to purify long oligonucleotides (e.g., 50-100-mers).     

Diels--Alder bioconjugation of diene-modified oligonucleotides

In an effort to offer complementary technology for covalent biomolecule modification (bioconjugation), we have developed a method that exploits the aqueous acceleration of Diels--Alder reactions for this purpose. Three different diene phosphoramidite reagents have been synthesized that enable diene modification of synthetic oligonucleotides prepared by the phosphoramidite method. Clean and efficient Diels--Alder cycloaddition of these diene oligonucleotides with maleimide dieneophiles was carried out, and the labeled oligonucleotide bioconjugates were characterized by HPLC and electrospray mass spectrometry. Dieneophile stoichiometry, temperature, and pH are all parameters that were shown to influence the efficiency of the process.     

Self-assembly patterning of silica colloidal crystals

We developed a self-assembly process of silica particles to fabricate desired patterns of colloidal crystals having high feature edge acuity and high regularity. A micropattern of colloidal methanol prepared on a self-assembled monolayer in hexane was used as a mold for particle patterning, and slow dissolution of methanol into hexane caused shrinkage of molds to form micropatterns of close-packed SiO2 particle assemblies. This result is a step toward the realization ofnano/micro periodic structures for next-generation photonic devices by a self-assembly process.