DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Efficient primer strand extension beyond oxadiazole carboxamide nucleobases

Two oxadiazole carboxamide deoxyribonucleoside analogues are described that can be incorporated and efficiently extended by Taq DNA polymerase. The primer strand extension beyond oxadiazole nucleoside analogues occurs at rates similar to the values observed for the canonical Watson-Crick base pairs irrespective of the template nucleobase. These distinctive chemical effects in DNA polymerase extensions are attributed to the smaller size and unique electronic properties of the oxadiazole nucleobase.     

A combination chemical and enzymatic approach for the preparation of azole carboxamide nucleoside triphosphate

Alternative substrates for DNA and RNA polymerases offer an important set of biochemical tools. Many of the standard methods for nucleoside triphosphate synthesis fail in the cases of nonpurine and nonpyrimidine nucleosides. An efficient preparation of the 5'-O-tosylates for both the deoxy- and ribonucleosides enabled preparation of the diphosphate esters by displacement with tris(tetra-n-butylammonium) pyrophosphate. Enzymatic synthesis of the azole carboxamide deoxyribonucleoside triphosphate was based on ATP as the phosphate donor, nucleoside diphosphate kinase as the catalyst, coupled with phosphoenol pyruvate (PEP) and pyruvate kinase as an ATP regeneration system. Ribonucleoside triphosphate synthesis required PEP as the phosphate donor and pyruvate kinase as the catalyst. An optimized purification procedure based upon boronate affinity gel was developed to yield highly purified nucleoside triphosphates. The strategy outlined here provides a new and efficient method for preparation of nucleoside 5'-triphosphate and is likely applicable to a broad variety of base and sugar modified nucleoside analogues.     

A short regiospecific total synthesis of furoventalene,a marine natural benzofuran

Synthesis of a naturally occurring irregular isoprenoid benzofuran, furoventalene ( 3 ), has been achieved in high yield via the nickel catalyzed coupling of 4-methyl-3-penten-1-ylmagnesium bromide ( 1 ) with 3-methyl-6-chlorobenzofuran ( 2 ).     

Roughness effects in low-<Emphasis Type="Italic"> Re</Emphasis><Subscript><Emphasis Type="Italic"> θ</Emphasis></Subscript> open-channel turbulent boundary layers

This paper reports velocity measurements obtained on a smooth and two geometrically different types of rough surfaces in an open channel. The measurements were obtained using a laser-Doppler anemometer. The recent boundary layer theory proposed by George and Castillo (1997) and conventional scaling laws are used to analyze the data. The present flow shows a strong structural similarity to a canonical turbulent boundary layer in the inner layer. The results demonstrate that surface roughness increases the wake parameter. Surface roughness also enhances the levels of turbulence intensities, Reynolds shear stress and triple correlations over most of the boundary layer, but decreases the stress anisotropy.     

Roughness effects on turbulent plane wall jets in an open channel

This paper reports the effects of surface roughness on the mean flow characteristics for a turbulent plane wall jet created in an open channel. The velocity measurements were obtained using a laser Doppler anemometer over smooth and transitionally rough surfaces. The power law proposed by George et al. (2000) was used to determine the friction velocity. Both conventional scaling and the momentum–viscosity scaling proposed by Narasimha et al. (1973) were used to analyze the streamwise evolution of the flow. The results show that surface roughness increases the skin friction coefficient and the inner layer thickness, but the jet half-width is nearly independent of surface roughness.     

An Improved Method for Site‐Specific End Modification of Zeolite L for the Formation of Zeolite L and Gold Nanoparticle Self‐Assembled Structures

The ability to site‐selectively modify micro‐ and nanosized particles has allowed for directed self‐assembly in two and three dimensions. Site‐selective modification of particles can be a complicated task requiring the pre‐organization of particles or enhanced particle fabrication methods. The aluminum silicate, zeolite L has been reported to undergo site‐specific modification at the zeolite channel entrances, post‐fabrication in a solution‐based method. The process by which the channel entrances are site selectively modified is explored here. The preliminary step of charging the zeolite channels with aqueous acid allows for catalysis of covalent bond formation at the channel entrances. Three new end‐specific modification reagents are described based on silanol and silyl ether functional groups. These reagents are purified by column chromatography and characterized by¹H NMR spectroscopy and high resolution mass spectrometry (HRMS); they provide for reliable end modification of zeolites L. Preferential reactivity at the channel entrances is also observed. The utility of the approach is demonstrated by modifying zeolite L with adamantane at the channel entrances. Site‐specific self‐assembly with β‐cyclodextrin coated gold nanoparticles can be triggered with a chemical stimulus. The resulting multivalent host‐guest interactions give gold clustered nanoparticles at the ends of the micrometer‐sized zeolites.     

Inelastic electron scattering from 6Li near the α-d threshold

The form factor for the alpha-deuteron continuum in ⁶Li has been measured in the excitation region within 2 MeV of threshold, for momentum transfers q < 1.2 fm^?1. The results are interpreted in terms of an α-d cluster model. The monopole breakup appears to be predominant near threshold, but the influence of the J = 2⁺ (4.31 MeV) quadrupole resonance becomes important a few MeV above threshold. The form factor for the C2 transition to the 3⁺ (2.185 MeV) state is also presented.