Study on the interaction of trypsin with some DNAs and their analytical application by resonance Rayleigh scattering spectra

When trypsin reacts with Herring sperm DNA (hsDNA), Salmon sperm DNA (sDNA), and Calf thymus DNA (ctDNA) to form a complex, the resonance Rayleigh scattering (RRS) was remarkably enhanced and new RRS spectra appear. These new spectra have similar characteristics of RRS spectra. The maximum RRS peaks are at 307 nm (hsDNA, sDNA) and 290 nm (ctDNA), and other peaks are at 350 nm. The scattering intensity is proportional to the concentration of DNA or trypsin; so this intereaction can be used to determine trypsin using DNA or DNA using trypsin. In the determination of DNA using trypsin, the linear ranges for hsDNA, sDNA, and ctDNA are 0–2.3, 0–2.5, and 0–1.9 μg·mL⁻¹, and the detection limits are 0.4, 0.7, and 1.1 ng·mL⁻¹, respectively. In the determination of trypsin using hsDNA, the linear range is 0–30.0 μg·mL⁻¹, and the detection limit is 39.0 ng·mL⁻¹. In this paper, the intereaction conditions were optimized. The affecting factors, chemical properties of the complex, and the composition ratio of trypsin with DNA were investigated. Using trypsin as RRS probe, a sensitive method for the determination of trace amounts of DNA was developed. Translated from Chemical Journal of Chinese Universities, 2006, 27(3) (in Chinese)     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

A new route for the functionalisation of wood through transesterification reactions

A novel transesterification reaction between acetylated maritime pine sapwood (Pinus pinaster Soland) and methyl benzoate (MB), in the presence of dibutyltin oxide (DBTO) as a catalyst, was performed. Reaction was confirmed by Fourier-transform infrared spectroscopy (FTIR) and ¹³C nuclear magnetic resonance cross-polarisation with magic-angle spinning (NMR CP MAS) analysis: signals corresponding to benzoylated wood were identified and, when transesterification was performed with ethyl trimethylsilylacetate (ETMSA), characteristic trimethylsilyl groups were detected. The acetyl/benzoyl exchange rate was found to increase with increasing amount of DBTO, temperature and reaction time and a concurrent deterioration of the woody material was evidenced.     

Stochastic resonance is applied to quantitative analysis for weak chromatographic signal of glyburide in plasma

Based on the theory of stochastic resonance, a new method carried on the quantitive analysis to weak chromatographic signal of glyburide in plasma, which was embedded in the noise background and the signal-to-noise ratio (SNR) of HPLC-UV is enhanced remarkably. This method enhances the quantification limit to 1 ng ml⁻¹, which is the same as HPLC-MS, and makes it possible to detect the weak signal accurately by HPLC-UV, which was not suitable before. The results showed good recovery and linear range from 1 to 50 ng ml⁻¹ of glyburide in plasma and the method can be used for quantitative analysis of glyburide.     

Combined use of liquid chromatography-nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry for the characterization of an acarbose degradation product

Directly coupled LC-MS and LC-NMR were applied to identify and structurally characterize an acarbose degradation product A in acidic media. A comparative analysis of the stop-flow LC-NMR (1H and TOCSY) and LC-MS data provided evidence that A is structurally related to acarbose, differing from the parent compound in a number of subunits present in the molecule. Spectral analysis revealed that A was the alpha-glucosidase inhibitor amylostatin XG. Complementary information obtained from the two methods led to the structural elucidation of A which was later corroborated by high-resolution NMR spectroscopy of the isolated molecule.     

IR Study of p–π Conjugation in 2-Substituted 4-Methylene-1,3-dioxolanes and 4-Methyl-1,3-dioxoles

Selected group frequencies of the IR spectra of a number of 2-substituted 4-methylene-1,3-dioxolanes (a) and their endocyclic isomers, 2-substituted 4-methyl-1,3-dioxoles (b), have been studied to establish their usefulness as a measure of the strength of p– conjugation in the O—C=C moieties of the title compounds. In the exo compounds (a), the C=C stretching frequencies C=C and the in-phase, out-of-plane bending (wagging) frequencies CH₂ w of the =CH₂ group were found to be linearly related, besides to each other, also to the electron-donating character of the substituents and the ¹³C NMR chemical shift of the C atom of the exocyclic CH₂ group. This suggests that the two IR group frequencies of the exo isomers are linearly related to the strength of p– conjugation in the O—C=C moiety. The C=C stretching absorption of the exo compounds in the 1600–1700 cm^–1 region appeared as a doublet, shown to arise from Fermi resonance of the C=C fundamental with the CH₂ w overtone. The C=C frequencies of the endo compounds support some previous findings of an unexpected strength of p– conjugation in the 2-alkoxy derivatives. Finally, DFT calculations at the B3LYP/6-31G* level of theory are shown to give accurate predictions of the effect of 2-substituents on the group frequencies.     

Nuclear magnetic resonance studies of sulfur inversion in bis(cyclopentadienyl)-molybdenum and -tungsten complexes with dithioethers

The metallocene thioether derivatives [Cp₂M(MeSCH₂CH₂SMe)][PF₆]₂ (1, M = MO; 2, M = W), [Cp₂Mo(SCH₂CH₂SMe)][PF₆] (3) and [Cp₂M(SCH₂CH₂S)] (4, M = Mo; 5, M = W) exhibit temperature-dependent fluxional behavior in solution, owing to the pyramidal sulfur inversion process. The activation energies for this process were determined from proton band-shape analysis in the cases of 1 (54.9 ± 2 kJ mol⁻¹), 2 (51.2 ± 4.6 kJ mol⁻¹) and 3 (30.0 ± 3.1 kJ mol⁻¹). Extended Hückel calculations on related model complexes suggest that local inversion at the sulfur atoms, rather that an inversion of the complete S---C---C---S chain, is responsible for the observed fluxional behaviour.     

Immobilization of antibody fragment for immunosensor application based on surface plasmon resonance

Biosurface fabrication using the Fab′ fragment of immunoglobulin (IgG) was carried out by self-assembly (SA) technique. The pepsin-digested monoclonal antibody (Mab) against bovine insulin containing the F(ab′)₂ fragment and residual proteins was separated using affinity chromatography and dialysis. To prevent the nonspecific binding of F(ab′)₂ onto gold (Au) substrate, the native disulfide bridge was reduced using dithiothreitol (DTT) to convert F(ab′)₂ into Fab′, which made the immobilization to be carried out via the native thiol (–SH) group. The fabricated biosurface using SA technique showed the formation of stable thin film through AFM topography. Through the concentration change of DTT and Fab′, the absorption characteristics against the Au surface were investigated using surface plasmon resonance (SPR) with the flow cell. The amount of immobilized antibody fragment and the antigen binding capacity were regulated with respect to the reduction state and concentration of F(ab′)₂. Based on the biosurface of the fabricated Fab′, the insulin-detection was carried out by the measurement of SPR. The proposed antibody surface could successfully detect the bovine insulin at the concentration from 100 ng/mL to 10 μg/mL.     

The use of the isotropic orientation factor in fluorescence resonance energy transfer (FRET) studies of the actin filament

A Dale-Eisinger style analysis (R. E. Daleet al., Biophys. J. 26, 161, 1979) is used to produce three-dimensional plots that display the limits on the average orientation factor k ² that is required to calculate molecular distances in F-actin from fluorescence resonance energy transfer measurements. Maxima and minima plots are generated for the transfer of energy from a donor to a single acceptor and for transfer to multiple acceptors that are related by F-actin helical symmetry. The analysis is performed in terms of dipole cone half-angles rather than depolarization factors, in order to facilitate the modeling of the multiple acceptor problem. Calculations are carried out under the restrictive condition of a single electric dipole moment per fluorophore. In addition, both surface and volume averaging of the donor and acceptor dipoles are considered. Comparisons between the plots show that for the multiple acceptor cases with F-actin symmetry, there is a great reduction in the range for maxima and minima limits on k ². The calculations also suggest guidelines for the choice of fluorescence label that will result in an average orientation factor occurring within acceptable limits, i.e., inside the limits for which k ²=2/3 may be employed. Thus, without having detailed knowledge of the mean donor or acceptor dipole relative orientations, the use of k ²=2/3 in radial coordinate studies of F-actin is more than reasonable and is fairly assured of being correct.