Determination of DNA structure in solution: enzymatic deuteration of the ribose 2' carbon

An enzymatic solution to the problem of obtaining 13C/15N-labeled nucleotides that are deuterated uniquely at the H2' ' position within the ribose ring is presented. Selective deuteration occurs with an overall yield of >80%. The deuteron at the H2' ' position allows measurement of the scalar and residual dipolar couplings for the bond vectors attached to the C2' carbon of each ribose sugar. These data allow the accurate determination of sugar conformation. Interesting DNA double helices of 2-3 turns are now within the reach of solution NMR spectroscopy. As an example, these labeled nucleotides are incorporated uniquely at positions 6-14 in a 20-bp DNA sequence containing the adenovirus major late promoter.     

Photolysis of p-benzoquinone in N2 matrices at 12K: a novel decomposition pathway

Photolysis of _p-benzoquinone in N₂ matrices at 12K has been found to give acetylene and CO; 1,4-naphthoquinone and 9,10-anthraquinone, however, are inert under similar conditions.     

A critical comparison of approximation methods and models for equilibrium properties of low-barrier hydrogen bonds

Recent experimental evidence has led to the conclusion that short, strong hydrogen bonds can stabilize transition states of enzyme catalyzed biochemical reactions. Evidence for such hydrogen bonds is the low value of the isotopic fractionation factor, phi, which is defined as the equilibrium constant for the generic reaction, R-H + DOH <--> R-D + HOH, where H is the hydrogen atom participating in the low-barrier hydrogen bond in a molecule R-H. In this work we assess two approximation methods for computing the isotopic fractionation factors for single and multidimensional systems containing a low-barrier hydrogen bond. These methods are WKB and an approach that corrects the classical partition function via a quantum correction factor. We find that the latter approach is universally accurate and applicable in both single and multidimensional systems containing a low-barrier hydrogen bond. We also assess two different models for the coupling of a molecule's low-barrier hydrogen bond to other degrees of freedom, both internal and external to the molecule, and show that each leads to a lowering of the fractionation factor.     

Synthesis of the branched-chain sugar aceric acid: a unique component of the pectic polysaccharide rhamnogalacturonan-II

Described herein is the synthesis of 3-C-carboxy-5-deoxy-L-xylose (aceric acid), a rare branched-chain sugar found in the complex pectic polysaccharide rhamnogalacturonan-II. The key synthetic step in the construction of aceric acid was the stereoselective addition of 2-trimethylsilyl thiazole to 5-deoxy-1,2-O-isopropylidene-alpha-L-erythro-pentofuran-3-ulose (2), which was prepared from L-xylose. The thiazole group was efficiently converted into the required carboxyl group via conventional transformations. Aceric acid was also synthesized by dihydroxylation of a 3-C-methylene derivative of 2 followed by oxidation of the resulting hydroxylmethyl group. The C-2 epimer of aceric acid was also synthesized using thiazole addition chemistry, starting from L-arabinose.     

The dependence of ultrasound contrast agents backscatter on acoustic pressure: theory versus experiment

Experimental investigations have not fully explored the interaction between ultrasound beams and microbubble contrast agents. Moreover theoretical investigations have not solved the problem of the microbubble oscillation. A simple in-vitro system based on a commercial scanner (ATL UM9) was used to insonate (3 MHz transmission) diluted contrast suspensions of Definity and Quantison at different acoustic pressures (0.27-1.52 MPa). The experimental data were referred to a blood mimicking fluid in order to extract an estimate of their scattering cross-section. The results were compared with the solutions of the three main bubble oscillatidn models, Rayleigh-Plesset, Herring and Gilmore. Non-linear solutions of the above models were produced numerically using the Mathematica Package Software. The experiments showed that both agents provided a linear increase in scattering cross-section with increasing acoustic pressure. The thick shelled Quantison provided an increasing number of scatterers with increasing acoustic pressure, which proved that free bubbles leaked out of the shell. At high acoustic pressures both Quantison and Definity scattering cross-sections were almost identical, and were probably that of a free bubble. The Rayleigh-Plesset model provided a scattering cross-section almost independent of acoustic pressure. On the contrary the scattering cross-sections calculated by the Herring and Gilmore models solutions displayed a definite dependence on acoustic pressure of an order higher than one, which is slightly higher than the order of dependence exhibited by the experimental data. However, the increase of the experimentally measured scattering cross-section with acoustic pressure was sharper than the calculated one by the above two models. This is most probably due to the fact that the models simulated damped and not free bubble oscillations. In conclusion the Rayleigh-Plesset model was inadequate in describing the bubble oscillations even at small diagnostic acoustic pressures. The Herring and Gilmore models could simulate the dependence of the scattering cross-section of encapsulated microbubbles on acoustic pressure. However the contribution of free bubble oscillations has still to be modelled.