Recognition and detection of oligonucleotides in the presence of chromosomal DNA based on entrapment within conducting-polymer networks

Overlapping voltammetric signals, accrued from redox processes of nucleobases, do not permit discrimination between short oligonucleotides and chromosomal DNA molecules when conventional electrochemical techniques are used. This article describes a new genoelectronic route for discriminating between short oligonucleotides and chromosomal DNA, based on the polypyrrole (PPy) doping process. Such a route relies on the profound effect of short nucleic acid dopants upon the redox activity of PPy, and hence on the square-wave voltammetric signal of the polymer-modified electrode in a blank electrolyte solution. The electropolymeric growth of PPy thus serves for preferential accumulation (by doping) of short oligonucleotides. High selectivity is demonstrated for voltammetric measurements of oligo(dG)₂₀ and oligo(dT)₂₀ in the presence of otherwise interfering ss- and ds-DNA. The signals for the oligonucleotides are also not affected by a large excess of chloride or phosphate ions. The response of the new preconcentration (doping)–medium-exchange–voltammetric protocol is proportional to the concentration of the oligonucleotide dopant. Such a new recognition process, based on the doping of conducting-polymer networks, enhances the scope of electroanalysis of nucleic acids.     

Measuring the crystallinity index of cellulose by solid state 13C nuclear magnetic resonance

The crystallinity index of cellulose is an important parameter to establish because of the effect this property has on the utilization of cellulose as a material and as a feedstock for biofuels production. However, it has been found that the crystallinity index varies significantly depending on the choice of instrument and data analysis technique applied to the measurement. We introduce in this study a simple and straightforward method to evaluate the crystallinity index of cellulose. This novel method was developed using solid state ¹³C NMR and subtraction of the spectrum of a standard amorphous cellulose. The crystallinity indexes of twelve different celluloses were measured and the values from this method were compared with the values obtained by other existing methods, including methods based on X-ray diffraction. An interesting observation was that the hydration of the celluloses increased their crystallinity indexes by about 5%, suggesting that addition of water increased cellulose order for all the cellulose samples studied.     

Adiabatic ionization potential and electron affinity of formaldehyde

The adiabatic ionization potential and electron affinity for CH₂O have been calculated using high levels of ab initio molecular orbital theory. Harmonic vibrational frequencies and zero-point energies also have been predicted. At the CCSD(T)/6-311++G(3df,3pd) level of theory, the adiabatic ionization potential is calculated as 10.82 eV as compared to the experimental literature value of 10.8887±0.0030 eV. The electron affinity is calculated to be −0.96 eV, compared to the experimental literature value of −0.65±0.05 eV.     

A trapping principle and convergence result for finite element approximate solutions of steady reaction/diffusion systems

We consider nonlinear elliptic systems, with mixed boundary conditions, on a convex polyhedral domain Ω ⊂ R ^N . These are nonlinear divergence form generalizations of Δu = f(·, u), where f is outward pointing on the trapping region boundary. The motivation is that of applications to steady-state reaction/diffusion systems. Also included are reaction/diffusion/convection systems which satisfy the Einstein relations, for which the Cole-Hopf transformation is possible. For maximum generality, the theory is not tied to any specific application. We are able to demonstrate a trapping principle for the piecewise linear Galerkin approximation, defined via a lumped integration hypothesis on integrals involving f, by use of variational inequalities. Results of this type have previously been obtained for parabolic systems by Estep, Larson, and Williams, and for nonlinear elliptic equations by Karátson and Korotov. Recent minimum and maximum principles have been obtained by Jüngel and Unterreiter for nonlinear elliptic equations. We make use of special properties of the element stiffness matrices, induced by a geometric constraint upon the simplicial decomposition. This constraint is known as the non-obtuseness condition. It states that the inward normals, associated with an arbitrary pair of an element’s faces, determine an angle with nonpositive cosine. Drăgănescu, Dupont, and Scott have constructed an example for which the discrete maximum principle fails if this condition is omitted. We also assume vertex communication in each element in the form of an irreducibility hypothesis on the off-diagonal elements of the stiffness matrix. There is a companion convergence result, which yields an existence theorem for the solution. This entails a consistency hypothesis for interpolation on the boundary, and depends on the Tabata construction of simple function approximation, based on barycentric regions. This work was supported by the National Science Foundation under grant DMS-0311263.     

Cubist algebras

We construct algebras from rhombohedral tilings of Euclidean space obtained as projections of certain cubical complexes. We show that these ‘Cubist algebras’ satisfy strong homological properties, such as Koszulity and quasi-heredity, reflecting the combinatorics of the tilings. We construct derived equivalences between Cubist algebras associated to local mutations in tilings. We recover as a special case the Rhombal algebras of Michael Peach and make a precise connection to weight 2 blocks of symmetric groups.     

Chemoselective functionalization of α-carbolines at the C-2, C-3, C-4, and C-6 positions using Suzuki-Miyaura reactions

The synthesis of 2-, 3-, 4-, and 6-substituted pyrido[2,3-b]indoles (α-carbolines) by palladium-catalyzed cross-coupling reactions from the corresponding halopyrido[2,3-b]indoles is described. A sequential and a one-pot chemoselective double Suzuki-Miyaura coupling route is presented for the synthesis of symmetrically and unsymmetrically disubstituted pyrido[2,3-b]indoles.