A simple method of identifying symmetric substructures of proteins

Accurate identifications of internal symmetric substructures of proteins are needed in protein evolution study and protein design. To overcome the difficulties met by previous methods, here we propose a simple quantitative one by using a similarity matrix plus Pearson's correlation analysis. The distance root-mean-square deviation (dRMSD) is used to measure the similarity of two substructures in a protein. We applied this method to the proteins of the beta-propeller, jelly roll, and beta-trefoil families and the results show that this method cannot only detect the internal repetitive structures in proteins effectively, but also can identify their locations easily.     

A single molecule detection method for understanding mechanisms of electric field-mediated interstitial transport of genes

The interstitial space is a rate limiting physiological barrier to non-viral gene delivery. External pulsed electric fields have been proposed to increase DNA transport in the interstitium, thereby improving non-viral gene delivery. In order to characterize and improve the interstitial transport, we developed a reproducible single molecule detection method to observe the electromobility of DNA in a range of pulsed, high field strength electric fields typically used during electric field-mediated gene delivery. Using agarose gel as an interstitium phantom, we investigated the dependence of DNA electromobility on field magnitude, pulse duration, pulse interval, and pore size in the interstitial space. We observed that the characteristic electromobility behavior, exhibited under most pulsing conditions, consisted of three distinct phases: stretching, reptation, and relaxation. Electromobility depended strongly on the field magnitude, pulse duration, and pulse interval of the applied pulse sequences, as well as the pore size of the fibrous matrix through which the DNA migrated. Our data also suggest the existence of a minimum pulse amplitude required to initiate electrophoretic transport. These results are useful for understanding the mechanisms of DNA electromobility and improving interstitial transport of genes during electric field-mediated gene delivery.     

A method for calculating effective charges in the water molecule

A method for calculating the effective charges of the hydrogen, oxygen, and nitrogen atoms in the water and ammonia molecules in the crystalline state was developed.     

A glass nanopore electrode for single molecule detection

<正>We have developed a simple method for fabricating robust and low noise glass nanopore electrodes with pore size 10±5 nm to detect single molecules.β-Cyclodextrin was used as model compound for characterization.In 1.0 mol/L NaCl solution,the molecules generated current pulses of 2-5 pA with noise level less than 0.8 pA.A slide mode and a plug mode were suggested for the way ofβ-cyclodextrin single molecule moving into the glass nanopores.     

A simple method for estimating the superaromatic stabilization energy of a super-ring molecule

A simple graph-theoretical method is proposed for readily estimating the degree of extra stabilization due to macrocyclic conjugation (superaromaticity). This method is based theoretically on the concept of circuit resonance energy previously defined for cyclic pi systems. We confirmed that kekulene and related super-ring molecules are essentially nonsuperaromatic, with very small superaromatic stabilization energies.     

A modified gran method for determination of equivalence points in potentiometric precipitation titrations

Gran's method is frequently applied in potentiometric titration to obtain a more precise estimate of the equivalence point, particularly when the analyte concentration is too low to give well defined end-points. With precipitation reactions, however, when the analyte concentration is comparable to the solubility of the precipitate, even the use of Gran's method will not avoid significant errors. A correction term is introduced and a computer program outlined to overcome this problem. Titrations of 10^-4 M chloride are used for illustration.     

A new method for the detection of ATP using a quantum-dot-tagged aptamer

Fluorescence resonance energy transfer (FRET) between a quantum dot as donor and an organic fluorophore as acceptor has been widely used for detection of nucleic acids and proteins. In this paper, we developed a new method, characterized by 605-nm quantum dot (605QD) fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease, to detect adenosine triphosphate (ATP). The new method involved the use of three different oligonucleotides: 3′-biotin-modified DNA that binds to streptavidin-conjugated 605QD; 3′-Cy5-labelled DNA; and a capture DNA consisting of an ATP aptamer and a sequence which could hybridize with both 3′-biotin-modified DNA and 3′-Cy5-labelled DNA. In the absence of the target ATP, the capture DNA binds to 3′-biotin-modified DNA and 3′-Cy5-labelled DNA, bringing quantum dot and Cy5 into close proximity for greater FRET efficiency. When ATP is introduced, the release of the 3′-Cy5-labelled DNA from the hybridization complex took place, triggering 605QD fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease. Taken together, the virtue of FRET pair 605QD/Cy5 and the property of aptamer-specific conformation change caused by aptamer–ATP interaction, combined with the fluorescence intensity change of both 605QD and Cy5, provide prerequisites for simple and convenient ATP detection. Zhang Chen and Guang Li contributed equally to this work.     

A least-squares method applied to the hydrogen molecule

A least-squares approach is proposed to remedy some of the weaknesses of the method of moments. It is shown by an application to the hydrogen molecule that the least-squares procedure yields reliable results in cases where the method of moments fails. The prediction of equilibrium internuclear distances by the least-squares method is also found to be more reliable than the corresponding results obtained by the method of moments.     

茶叶中的茶多酚荧光检测方法

以石墨烯量子点为荧光探针,基于二氧化锰纳米片与石墨烯量子点之间发生有效的荧光共振能量转移,构建了一种茶叶中茶多酚含量的荧光检测新方法。MnO2纳米片使石墨烯量子点的荧光淬灭,而茶多酚能与MnO2发生氧化还原反应,将其还原成Mn^2+,使体系荧光恢复。茶多酚含量与荧光强度增量在20~750μg/mL范围内成线性相关,线性方程为F=1.0574c-114.9,线性相关系数为R=0.9936。将该方法用于茶叶中茶多酚含量的检测,结果与国标法接近。方法有望应用于食品中其它抗氧化物质的实时检测。     

Development and validation of a rapid method for the detection of latrunculol A in plasma

Latrunculol A is a recently discovered 6,7-dihydroxy analog of the potent actin inhibitor latrunculin A. Latrunculol A has exhibited greater cytotoxicity than latrunculin A against both murine and human colon tumor cell lines in vitro. Currently, there are no reports regarding the bioavailability of latrunculol A in vivo. This study was undertaken as a prelude to pharmacokinetic assessments and it is the first work where bioavailability of latrunculol A was studied. In the present work, a simple plasma preparation and a rapid HPLC method have been developed. Mouse plasma containing latrunculol A was first treated by acetonitrile and then centrifuged at 14,000 rpm at 4 °C for 25 min. The supernatant was injected in an HPLC system comprising a Waters Symmetry NH₂ column, a mobile phase of acetonitrile/water (95/5, v/v), a flow rate of 1.0 mL/min, at 220 nm. The method was validated by parameters including a good linear correlation, a limit of quantification of 9 ng/mL, and a good precision with a coefficient variation of 1.65, 1.86, and 1.26% for 20, 400, and 800 ng/mL, respectively. With this simple method, excellent separation and sensitivity of latrunculol A are achieved, thus allowing a rapid analysis of the plasma samples for absorption, distribution, and metabolism studies.     

A routine method for the determination of plutonium in urine with a low detection limit

A radiochemical method for the determination of plutonium in urine is described. The steps involved are a) co-precipitation of plutonium, b) wet ashing, c) hydrolysis, d) extraction from 2M HNO₃ into capillary polypropylene columns coated with tri-n-octyl phosphineoxide 0.5M in toluene, and e) back-extraction of plutonium from the organic phase, f) electroplating onto stainless steel disks and spectrometry, since plutonium is extracted together with small amounts of uranium naturally occurring in urine. High quality deposits for spectrometry are obtained because iron interference is eliminated before back-extraction. The radiochemical recovery of²³⁹Pu is 55.6±7.5% and the detection limit is 1.0 mBq per liter of urine.     

Using a nanopore for single molecule detection and single cell transfection

We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity.     

An improved synthesis of a fluorescent gabapentin-choline conjugate for single molecule detection

Voltage-gated calcium ion channels comprise pore-forming α₁ and auxiliary α₂δ, β, and γ subunits. They are important molecular devices involved in a variety of cell functions. Fluorescently labeled acylcholine analogues are important in studies such as ion channel regulation. Cy3-3-acetylcholine has recently been synthesized for single molecule detection studies; albeit in an extremely low overall yield (0.06%). In this work, an alternative route to that used in the previous Cy3-3-acetylcholine synthesis was developed with a 90% yield at a significantly lower material cost.     

A simple empirical method for the estimation of activation energies in radical molecule metathesis reactions

Several new empirical methods are presented for the prediction of activation energies E of the metathetical transfer reaction of single bonded atoms in radical-molecule reactions of the type A· + BC → AB + C· The methods assign additive contributions to E for the endgroups A· and C·, neglecting the effect of the transferred atom B. Most of the predicted values agree to within l kcal mol^?1 with the experimental activation energies (average error = 0.82 and standard deviation = 1.02 kcal mol^?1). This is comparable to the best of the more complex schemes available for such estimation.     

A self-consistent Hirshfeld method for the atom in the molecule based on minimization of information loss

Based on the so-called Hirshfeld atom in the molecule scheme, a new AIM method is presented. The method is similar to the Hirshfeld-I scheme, with the AIM weight function being constructed by minimizing the information loss upon formation of the molecule, but now requiring explicitly that the promolecular densities integrate to the same number of electrons as the AIM densities. This new weight function leads to a new iterative AIM scheme, and the resulting operative scheme is examined and discussed. The final results indicate that the newly proposed method does not perform as well as the Hirshfeld-I method.     

A quantitative application of the J-based configuration analysis method to a flexible small molecule

An example of the use of the J-based configuration analysis method to determine relative stereochemistry of a small molecule related to reboxetine is described. This study was complicated by the fact that the molecule did not exhibit J-couplings and NOEs consistent with a single conformation, but rather an ensemble average. A quantitative fitting procedure using predicted couplings and NOEs from all possible conformers was used. This gave a clear indication of the stereochemistry, and the populations of the conformers involved.     

An SCF-CI method for determining the potential energy surface of a triatomic molecule

A self-consistent-field (SCF)-configuration interaction (CI) (SCF-CI) method for determining the potential energy surface of a triatomic molecule from the observed vibrational band origins has been suggested. By this method, the SCF-CI procedure in the internal coordinates is used to calculate the vibrational bond origins and their first derivatives with respect to parameters in the potential energy function using the exact vibrational Hamiltonian, and the optimizer LMF in the nonlinear-squares problem is employed to optimize parameters in the potential energy function. This approach is used to optimize the potential energy function of the water molecule. The standard deviation of this fitting to the 70 observed band origins is 1.154cm-1.     

Strategies for constructing the calibration set for a near infrared spectroscopic quantitation method

Three strategies for the construction of calibration sets have been tried, with the objective to develop and to validate a NIR quantitation method.The first two approaches consist of the use of two types of samples, named: samples of laboratory obtained by mixing the ingredients that compose the drug, and doped samples obtained by under- and over-dosed production samples. In order to improve the prediction results, production samples have been added to each calibration model. The ensuing models were validated with a view to determine their fitness for purpose. However, spectral differences between the laboratory samples and doped samples resulted in spurious predictions in quantifying samples of one type using the model developed from samples of the other.Such differences were studied in depth and a third procedure has been proposed, based on a calibration model constructed with an unique type of sample (laboratory sample) for later to correct it with a few doped samples. This corrected model has a good predictive ability on production samples.     

Quasi-stationary detection of transient absorption of a dissociating molecule

Using the forth harmonic of a Nd-YAG laser at 266 nm TlI was dissociated and the dissociation was observed by a transient absorption due to a transition from the repulsive potential, which correlates to T1 (6p ² P _3/2) and I, to the repulsive potential with the asymptote T1 (7s) and I. The experiment is performed with quasi-stationary spectroscopy in the nanosecond time domain, but detects transients effects by asymmetric absorption profiles in the frequency domain. Simulations applying Bloch equations with time dependent molecular energies are able to reproduce the observations and give information on the difference potential between the two molecular states involved and the transition dipole moment. The results are also in good agreement with fs experiments from other authors.