Auto-orientation of G-wire DNA on mica

Scanning probe microscopy was used to examine the orientation of Tet1.5 quadruplex DNA polymers, a.k.a. “G-wires”, after adsorption onto freshly cleaved Phyllosilicate micas. The G-wires appear to have a preferential orientation at 60° intervals after thorough rinsing and slow drying. The angles the G-wires made with the fast scan direction of the SPM probe were measured and the frequency-angle information was quantitatively characterized by an empirical correlation coefficient. Careful measurements indicate the Tet1.5 G-wires orient along the b lattice vector of mica, the next nearest neighbor potassium vacancy. A model is proposed to explain this auto-orientation affect due to alignment of the G-wires’ phosphate backbone through magnesium tether cations. Pairs of adjacent, parallel phosphate groups of the G-wires (0.95 nm apart) appear to align with the next nearest neighbor potassium vacancy sites of mica (0.90 nm apart). This behavior is not observed in solution. The potential for using the auto-orientation phenomena in the development of high-density biomolecular nano-electronic devices is explored.     

Characterization of Aldehyde Dehydrogenases Applying an Enzyme Assay with In Situ Formation of Phenylacetaldehydes

Herein, different dehydrogenases (DH) were characterized by applying a novel two-step enzyme assay. We focused on the NAD(P)⁺-dependent phenylacetaldehyde dehydrogenases because they produce industrially relevant phenylacetic acids, but they are not well studied due to limited substrate availability. The first assay step comprises a styrene oxide isomerase (440 U mg^?1 _protein) which allows the production of pure phenylacetaldehydes (>70 mmol L^?1) from commercially available styrene oxides. Thereafter, a DH of interest can be added to convert phenylacetaldehydes in a broad concentration range (0.05 to 1.25 mmol L^?1). DH activity can be determined spectrophotometrically by following cofactor reduction or alternatively by RP-HPLC. This assay allowed the comparison of four aldehyde dehydrogenases and even of an alcohol dehydrogenase with respect to the production of phenylacetic acids (up to 8.4 U mg^?1 _protein). FeaB derived from Escherichia coli K-12 was characterized in more detail, and for the first time, substituted phenylacetaldehydes had been converted. With this enzyme assay, characterization of dehydrogenases is possible although the substrates are not commercially available in sufficient quality but enzymatically producible. The advantages of this assay in comparison to the former one are discussed.     

Effects of caffeine on stereoselectivities of high cell density biotransformations of cyclic beta-keto esters with Saccharomyces cerevisiae

Caffeine affects the stereoselectivity of microbial high cell density reductions with commercial grade Saccharomyces cerevisiae (Baker's yeast). Cyclic beta-keto esters ethyl 2-oxocyclopentanoate (1) and ethyl 2-oxocyclohexanoate (3) were shown to be reduced with increased diastereoselectivity (1: 90.1 --> 92.1% de, 3: 75.0 --> 90.0% de) after addition of caffeine. Effects on enantioselectivity were less pronounced (1: 97.3 --> 98.5% ee, 3: 90.1 --> 92.1% ee). The observations are ascribed to the action of caffeine on cellular calcium homeostasis. These effects are accompanied by caffeine-induced cell-death, which preferably takes effect on pre-stressed cells which were found to decrease diastereoselectivity.     

The Schur–Potapov Algorithm for Sequences of Complex p × q Matrices. II

This is the second and final part of a paper which appeared in a preceding issue of this journal. Herein the methods developed in the earlier sections of this paper are used first to develop a number of applications. A central theme of this paper is to study the interplay between functions from and their sequence of SP-parameters. In particular, we describe how certain summability properties of the SP-parameters are expressed in terms of the associated functions from . As a byproduct of our investigations on the interplay between the SP-algorithm for p × q Schur functions and the SP-algorithm for sequences of complex p × q matrices we present a new approach to the nondegenerate matricial Schur problem. Our method complies with the basic strategy in Schur’s classical paper [138] because it does not make use of any tools outside of the theory of Schur functions and Schur sequences. A closer look at the behaviour of distinguished subclasses of with respect to the SP-algorithm enables us to handle the corresponding versions of the matricial Schur problem restricted to these subclasses. Submitted: August 17, 2006. Accepted: September 13, 2006.     

Comparison of water isotope-ratio determinations using two cavity ring-down instruments and classical mass spectrometry in continuous ice-core analysis

We present a detailed comparison between subsequent versions of commercially available wavelength-scanned cavity ring-down water isotope analysers (L2120-i and L2130-i, Picarro Inc.). The analysers are used in parallel in a continuous mode by adaption of a low-volume flash evaporation module. Application of the analysers to ice-core analysis is assessed by comparison between continuous water isotope measurements of a glacial ice-core from Severnaya Zemlya with discrete isotope-ratio mass spectrometry measurements performed on parallel samples from the same ice-core. The great advances between instrument versions, particularly in the measurement of δ²H, allow the continuous technique to achieve the same high level of accuracy and precision obtained using traditional isotope spectrometry techniques in a fraction of the experiment time. However, when applied to continuous ice-core measurements, increased integration times result in a compromise of the achievable depth resolution of the ice-core records.     

Reversal of selectivity in gold-catalyzed cyclizations of 3,3-disubstituted 1,4-diynes

A general synthetic access to 3,3-disubstituted 1,4-diynes bearing a quaternary carbon center from acetylacetone was developed. The compounds were cyclized to the corresponding enol ethers by cationic gold complexes. The reactions occur in complete exo-selectivity in contrast to compounds incorporating an alkoxy substituent in the 3-position. A mechanistic rationale for this reversal of selectivity is provided.     

Inverse electron-demand Diels-Alder reactions for the selective and efficient labeling of RNA

We report the first example of RNA labeling based on inverse electron-demand Diels-Alder reactions. Both chemically synthesized and enzymatically transcribed RNAs were successfully modified with biotin or a fluorescent label. This approach works efficiently under mild conditions in water and does not require transition metals.     

Ultrafast charge-transfer dynamics of donor-substituted truxenones

The photophysics of two donor-substituted truxenone derivatives has been studied by femtosecond time-resolved transient absorption spectroscopy. The systems consist of a central truxenone acceptor with three triarylamine (TARA) branches which act as electron donors. Upon excitation in the visible regime an electron is transferred from the donor to the acceptor, generating a charge-separated state. This state can be probed via the characteristic absorption of the TARA radical cation around 700 nm. A second absorption band around 420 nm exhibits the same kinetics and is assigned to an absorption of the radical anion of the truxenone moiety. The back electron transfer and the recovery of the ground state can be interpreted within the framework of Marcus theory. To study the dependence of the back electron transfer on the electronic coupling, the distance between the donor and the acceptor was adjusted. Two solvents were employed, dimethylsulfoxide and dichloroethane. A biexponential decay of the bands assigned to the charge-separated state was observed, with time constants in the picosecond range. Surprisingly, the rates for electron back transfer do not follow the simple picture of the donor-acceptor distance being the determining factor. The observations are explained within a model that additionally takes steric interactions between the donor and the acceptor into account.