SELEX and dynamic combinatorial chemistry interplay for the selection of conjugated RNA aptamers

SELEX (for Systematic Evolution of Ligands by Exponential enrichment) has proven to be extraordinarily powerful for the isolation of DNA or RNA aptamers that bind with high affinity and specificity to a wide range of molecular targets. However, the modest chemical functionality of nucleic acids poses some limits on the versatility of aptamers as binders and catalysts. To further improve the properties of aptamers, additional chemical diversity must be introduced. The design of chemical modifications is not a trivial task. Recently, dynamic combinatorial chemistry (DCC) has been introduced as an alternative to traditional combinatorial chemistry. DCC employs equilibrium shifting to effect molecular evolution of a dynamic combinatorial library of molecules. Herein, we describe an original process that combines DCC and SELEX for the in vitro selection of modified aptamers which are conjugated to chemically diverse small-molecules. Its successful application for the selection of small-molecule conjugated RNA aptamers that bind tightly to the transactivation-response (TAR) element of HIV-1 is presented.     

Radiative heat transfer at nanoscale: Closed-form expression for silicon at different doping levels

Radiative heat transfer at the nanoscale is becoming an important technological issue with the development of nano electromechanical systems (NEMS). In this article, we derive asymptotic expressions to compute near-field radiative heat transfer between two planes of silicon. We identify two physical mechanisms that give the dominant contribution at small gaps. For intrinsic and low-doped silicon, the main contribution is due to evanescent waves coming from propagating waves undergoing frustrated total internal reflections at the interfaces. For doping levels larger than N_e=10¹⁶ cm^?3 surface mode coupling contributes to the heat transfer. Asymptotic expressions are also given in that case. In all cases, we compare analytical formulas with exact numerical calculations when varying the temperature and the doping concentration. We also give their range of validity.     

Use of 4-bromo pyridazine 3,6-dione for building 3-amino pyridazine libraries

An efficient method for preparation of 4,6 or 5,6 disubstituted 3-aminopyridazines was easily carried out starting from easily available 4-bromo-pyridazine-3,6-dione, and using combination of both amination and Pd(0) cross-coupling reactions under microwave irradiation.     

Interstack Interactions in Potassium Bis(1,2-Cyclobutenedione 3,4-dithiolato) Palladate. Crystal Structure

Abstract

Potassium bis(1,2-cyclobutenedione 3,4-dithiolato) palladate (Pd(dithiosquarato)₂K₂) crystallizes in the monolinic system, space group P2₁/c, a = 8.046(2), b = 15.235(4), c = 6.289(1). The dithiosquarate entities are stacked in parallel columns separated by potassium cations and water molecules. π-interactions within a stack are evidenced by the short stacking distance (3.51 Å). Further interstack interactions involve close S…O or O…O interstack contacts. (～3.5 Å). As a result, the structural arrangement is nearly two-dimensional. Conductivity measurements carried out on pressed pellets show a semi-conductive behavior (σ = 2 × 10^?5 Ω^?1 cm¹).     

A numerical evaluation of Rayleigh's theory applied to scattering by randomly rough dielectric surfaces

Abstract

We present a numerical simulation of scattering by one-dimensional randomly rough surfaces. It is based on the use of plane-wave expansions to describe the Melds on the surface (i.e. Rayleigh hypothesis). Accuracy and convergence properties of two different numerical implementations are studied. Some examples of results for a dielectric and a metallic Gaussian rough surface are shown to be in good agreement with calculations by a rigorous numerical method. The Rayleigh method appears to be a fast computation tool for dielectric surfaces with slopes of less than 0.2.     

Image encryption based on fractional chaotic pseudo-random number generator and DNA encryption method

Nonlinear Dynamics - Nonlinear dynamic systems and chaotic systems have been quite exhaustively researched in the domain of cryptography. However, the possibility of using fractional chaotic...     

Template-directed excimer formation via specific non-covalent interactions between pyrene guanidinium derivatives and nucleic acids

Structurally distinct guanidinium derivatives were evaluated for their ability to interact non-covalently with various nucleic acid sequences. Among the evaluated derivatives, 4-[(pyrene-1-ylmethyl)amino]butyl] guanidinium (pbg) was found to demonstrate strong excimer emission upon nucleic acid addition and high levels of discrimination between ds- and ss-DNA. The intensity of excimer emission proved to be dependent on the length of the linker probe as well as the oligonucleotide length and sequence. In particular, G-quadruplex prone structures were found to induce the highest excimer emissions among all nucleic acids tested.     

Stereospecific cyclodehydration of 1,4-sulfanylalcohols to thiolanes: mechanistic insights

A series of thiolanes were prepared by cyclodehydration of sulfanylalcohols in the presence of catalytic amounts of p-toluenesulfonic acid or by using K10 clay. The sulfur heterocycles were synthesised in good to excellent yields using either a conventional Dean-Stark method or microwave irradiation under solvent-free conditions. The reaction could be performed regio- and stereoselectively and its mechanism was investigated by means of enantio- and diastereomerically enriched substrates. In contrast to previous studies, our results are consistent with an intramolecular S_N2-type mechanism as a general pathway.     

Comparison of solid-phase extraction sorbents for sample clean-up in the analysis of organic explosives

In this study, a method was developed for determination of steroid hormones (17beta-estradiol, estrone, 17alpha-ethynylestradiol) in tap and sewage water samples from Sweden. Sample preparation and analysis were performed by a hollow-fibre microporous membrane liquid-liquid extraction (HF-MMLLE) set-up combined with gas chromatography-mass spectrometry (GC-MS). In this approach, only the organic liquid in the lumen (10microL) of the hollow-fibre membrane was utilised for depleting extraction. Several parameters were studied, including: type of organic solvent, sample pH, salt and humic acid content. The optimised method allowed the determination of the analyte at the low ngL(-1) level in tap and sewage water. A linear plot gave correlation coefficients better than 0.995 and resulted in a method limit of detection of 1.6, 3 and 10ngL(-1) for 17beta-estradiol, estrone, and 17alpha-ethynylestradiol, respectively, in sewage water. Enrichment factors were over 1400 after derivatisation. The repeatabilities at 50 and 600ngL(-1) were better than 10% and 6%, respectively.     

Molecular transfer of surfactant bilayers: widening the range of substrates

Handling nanometer-thick films and nano-objects remains a challenge. Applying self-assembly properties of surfactants to nanomaterials manipulation may be the key to the fast, easy, cost-effective growth of 2D and 3D nanostructures. Newton black films (NBFs) are self-assembled bilayers of surfactant, well-organized, but fragile objects. To render such films amenable to practical applications, it is necessary to find ways to transfer them onto solid substrates. A method developed recently to transfer NBFs onto a solid substrate while preserving their molecular organization (Benattar, J.-J.; Nedyalkov, M.; Lee, F. K.; Tsui, O. K. C. Angew. Chem., Int. Ed. 2006, 45, 4186) is broadened here to different surfaces. The method requires hydrophobic, planar, atomically smooth surfaces. This study presents the adhesion of a fluorinated NBF surfactant onto hydrophobically treated silica and silicon surfaces (with etching or silanization). The structures of the free-standing film, bare substrates, and transferred films are investigated using X-ray reflectivity. The homogeneity of the surfaces before and after bilayer deposition is examined by atomic force microscopy (AFM). Multiple transfers are tested and described for the future development of more complex architectures involving many surfactant layers and inserted nanosized objects.