Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach

Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.     

Thermodynamic equilibrium between locally excited and charge-transfer states through thermally activated charge transfer in 1-(pyren-2′-yl)-o-carborane

Reversible conversion between excited-states plays an important role in many photophysical phenomena. Using 1-(pyren-2′-yl)-o-carborane as a model, we studied the photoinduced reversible charge-transfer (CT) process and the thermodynamic equilibrium between the locally-excited (LE) state and CT state, by combining steady state, time-resolved, and temperature-dependent fluorescence spectroscopy, fs- and ns-transient absorption, and DFT and LR-TDDFT calculations. Our results show that the energy gaps and energy barriers between the LE, CT, and a non-emissive ‘mixed’ state of 1-(pyren-2′-yl)-o-carborane are very small, and all three excited states are accessible at room temperature. The internal-conversion and reverse internal-conversion between LE and CT states are significantly faster than the radiative decay, and the two states have the same lifetimes and are in thermodynamic equilibrium.

Reversible conversion between excited-states is key to many photophysical phenomena. We studied the equilibrium between LE and CT states by time-resolved and temperature-dependent fluorescence, fs- and ns-transient absorption, and LR-TDDFT calculations.     

Facile one‐pot method of initiator fixation for surface‐initiated atom transfer radical polymerization on carbon hard spheres

An efficient and novel one‐pot process is developed to immobilize the atom transfer radical polymerization (ATRP) initiators onto the surface of fully pyrolyzed carbon hard spheres (CHSs) via a radical trapping process from the in situ thermal decomposition of bis(bromomethylbenzoyl)peroxide. The CHSs do not require any additional preparative treatment prior to the initiator immobilization. Styrene and methyl methacrylate are polymerized onto initiator‐immobilized CHSs by surface‐initiated atomic transfer radical polymerization (SI‐ATRP). Samples are characterized using Fourier transform infrared, thermogravimetric analysis, scanning electron microscopy, and transmission electron microscopy. These methods of characterization confirmed that all the CHSs are coated with a uniform layer of grafted polymer. This efficient, one‐pot immobilization of ATRP‐initiators represents an exceptionally simple route for the rapid preparation of various polymer‐coated carbon‐based nanomaterials using SI‐ATRP. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3314–3322     

Open Chain Chiral Macrolide Building Blocks by Opening of Deoxygenated 1,6-Anhydrosugars with 1,3-Propanedithiol

Chiral building blocks for macrolides and related natural products are obtained from 1,6-anhydrosugars by conversion of the bicyclic acetals 2 or 12 into the open chain chiral 1,3-dithianes 6 and 13. Branched precursors can be obtained by opening of the ?erný epoxide 1 with the 1,3-dithiane anion to yield 7, followed by ring opening with 1,3-propanedithiol to the bis-1,3-dithiane 8.     

A Novel One Pot Synthesis of o‐Nitrophenylacetic Acid and Unexpected p‐Nitrobenzoic Acid by HNO3‐Mediated CH2 Extrusion Reaction of Phenylacetic Acid

The HNO₃‐mediated CH₂ extrusion reactions of phenylacetic acid lead to one pot synthesis of unexpected commercially important product 4‐nitrobenzoic acid through the formation of 4‐nitrophenylacetic acid and 2‐nitrophenylacetic acid.     

Excitation of defect modes from the extended photonicband-gap structures of 1D photonic lattices

This paper stuides numerically the model equation in a one dimensional defective photonic lattice by modifying the potential function to a periodic function. It is found that defect modes (DMs) can be regarded as Bloch modes which are excited from the extended photonic band-gap structure at Bloch wave-numbers with k x = 0. The DMs for both positive and negative defects are considered in this method.     

Well-posed variational inequalities

In this paper, we introduce the concept of well-posedness for general variational inequalities and obtain some results under pseudomonotonicity. It is well known that monotonicity implies pseudomonotonicity, but the converse is not true. In this respect, our results represent an improvement and refinement of the previous known results. Since the general variational inequalities include (quasi) variational inequalities and complementarity problems as special cases, results obtained in this paper continue to hold for these problems.     

Galvanomagnetic study of the quantum-well valence band of germanium in the Ge<Subscript>1−x</Subscript>Si<Subscript>x</Subscript>/Ge/Ge<Subscript>1−x</Subscript>Si<Subscript>x</Subscript> potential well

The structure of the quantum-well valence band in a Ge(111) two-dimensional layer is calculated by the self-consistent method. It is shown that the effective mass characterizing the motion of holes along the germanium layer is almost one order of magnitude smaller than the mass for the motion of heavy holes along the [111] direction in a bulk material (this mass is responsible for the formation of quantum-well levels). This creates a unique situation in which a large number of subbands appear to be populated at moderate values of the layer thickness d _w and the hole concentration p _s . The depopulation of two or more upper subbands in a 38-nm-thick germanium layer at a hole concentration p _s = 5 × 10¹⁵ m^?2 is revealed from the results of measuring the magnetoresistance in a strong magnetic field aligned parallel to the germanium layers. The destruction of the quantum Hall state at a filling factor ν = 1 indicates that the two lower subbands merge together in a self-formed potential profile of the double quantum well. It is demonstrated that, in a quasi-two-dimensional hole gas, the latter effect should be sensitive to the layer strain.