Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system

We have studied the migration of DNA in pulsed field agarose gels under a variety of electrophoresis conditions. We have made use of an instrument which can generate electric fields of any orientation, magnitude, or duration to compare different separation techniques for DNA molecules of from 1 to several thousand kilobase pairs. We discuss the capabilities of the system and present results of gel runs in which electrophoresis conditions were changed individually or in combination. The mobility of DNA in pulsed field gels is shown to reflect a number of interdependent physical parameters.     

Oxidation-Induced Structural Alterations and Its Effect on Chaperone Function of Rat Lens α-Crystallin

An ascorbate-FeCl₃-EDTA-H₂O₂ system was used to oxidize rat lens α-crystallins. Under this oxidative insult, the chaperone activity of α-crystallin toward γ-crystallin was shown to decrease significantly, which is quite different from the result reported by Wang and Spector. (Invest. Ophthalmol. Vis. Sci. 1995 , 36, 311-321.) Fluorescence spectroscopy and circular dichroism were employed to characterize the structural changes of oxidized α-crystallin. It was found that fluorescence intensity of l-anilinonaphthalene-8-sul-phonate (ANS) bound to oxidized α-crystallin increased comparing to that bound to normal α-crystallin, suggesting oxidation causes the exposure of more hydrophobic regions. Further, α-crystallin's fluorescence intensity in response to tryptophan residues showed a pseudo first order decline. Amino acid analysis of normal versus oxidized α-crystallin confirmed actual decline in tryptophan levels, showing about 80% of tryptophan being modified after 10-hour oxidation. Circular dichroism showed both changes in the secondary and tertiary structures of oxidized α-crystallin, characterized by a large loss of aromatic-type amino acid interactions and a large loss of β-sheet structure. In conclusion, modified tryptophan, secondary and tertiary structural changes of α-crystallin correlate best with the reduction of chaperone function, the curves all showing a linear slope for 10 hours, then plateauing. These results indicate that the decrease of α-crystallin chaperone activity is attributed to the structural changes.     

Static ultrasonic oscillations induced degradation and its effect on the linear rheological behavior of novel propylene based plastomer melts

The ultrasonic degradation of novel propylene based plastomer (DP) melts with different melt viscosities was conducted in a “static” ultrasonic device where the samples were taken from various distances from the tip of an ultrasonic probe. The effects of ultrasonic time, oscillation temperature, ultrasonic intensity and the distance from the ultrasonic probe tip on the degradation behavior of DP melts as well as the ultrasonic degradation effect on the linear rheological behavior of DP melts were studied. The results show that the increase of initial melt viscosity of DP (higher molecular weight) has greater impact on the ultrasonic degradation of DP melt. The molecular weight and intrinsic viscosity of DP decrease with the increase of ultrasonic oscillation time and they approach to a limiting value. The molecular weight distribution of DP increases after ultrasonic degradation. Decreasing oscillation temperature and distance from probe tip and increasing ultrasonic intensity lead to an increase in the degradation of DP melt. The linear rheological behavior measurements of the samples obtained near the ultrasonic probe tip show that ultrasonic oscillations decrease the complex viscosity, zero shear viscosity, viscoelastic moduli, cross modulus, relaxation time and the slope of log G′ − log G″ for DP melts.     

Determination of phenolic compounds using high-performance liquid chromatography with Ce-Tween 20 chemiluminescence detection

A novel method for the simultaneous determination of phenolic compounds such as salicylic acid, resorcinol, phloroglucinol, p-hydroxybenzoic acid, 2,4-dihydroxybenzoic acid, and m-nitrophenol by high-performance liquid chromatography (HPLC) coupled with chemiluminescence (CL) detection was developed. The procedure was based on the chemiluminescent enhancement by phenolic compounds of the cerium(IV)-Tween 20 system in a sulfuric acid medium. The separation was carried out with an isocratic elution or with a gradient elution using a mixture of methanol and 1.5% acetic acid. For six phenolic compounds, the detection limits (3σ) were in the range 1.40-5.02 ng/ml and the relative standard deviations (n=11) for the determination of 0.1 μg/ml compounds were in the range 1.9-2.9%. The CL reaction was well compatible with the mobile phase of HPLC, no baseline drift often occurred in HPLC-CL detection was observed with a gradient elution. The method has been successfully applied to the determination of salicylic acid and resorcinol in Dermatitis Clear Tincture and p-hydroxybenzoic acid in apple juices.     

Complexation of silver and co-recovered metals with novel aza-crown ether macrocycles by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is used to evaluate the metal binding selectivities of an array of novel caged macrocycles for silver, gold, copper, nickel, zinc, iron, lead, manganese and alkali metal ions. It is found that five of the new compounds display silver selectivity, and their relative affinities for various metals depend on the type, number, and arrangement of heteroatoms (N, O), the cavity size, and the presence of aromatic substituents. Alkali metal cation binding studies are used to evaluate the size-selectivities of the cavities of the macrocycles. Electronic structure calculation by B3LYP density function theory methods were used to model the metal complexes. The presence of nitrogen atoms in the macrocyclic ring is essential for silver selectivity over other transition metals and alkali metal ions, and the presence of aromatic groups also enhances silver avidity. Macrocycle 3, a triaza-18-crown-6 analog modified with two phenyl groups and a cage group, is capable of selective extraction of Ag+ from aqueous solutions in the presence of other transition metal ions and the most common alkali and alkaline earth metal ions.     

Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters

The multicanonical basin hopping (MUBH) method, which uses a multicanonical weight in the basin hopping (BH) Monte Carlo method, was found to be very efficient for global optimization of large-scale systems such as Lennard-Jones clusters containing more than 150 atoms. We have implemented an asynchronous parallel version of the MUBH method using the message passing interface (MPI) to take advantage of the full usage of multiprocessors in either a homogeneous or heterogeneous computational environment. Based on the intrinsic properties of the Monte Carlo method, this MPI implementation used the task parallelism to minimize interthread data communication. For a Co nanocluster consisting of N atoms, we have applied the asynchronous multicanonical basin hopping (AMUBH) method (for 181 < N < or = 200), together with BH (for 2 < or = N < 150) and MUBH (for 150 < or = N < or = 180), to search for the molecular configuration of the global energy minimum. AMUBH becomes the only practical computational scheme for locating the energy minimum within realistic computational time for a relatively large cluster.     

Polarographic Behaviour and Determination of Kinetic Parameters of Lead-Pamoate Complex in Dimethyl Sulfoxide

The polarography of lead ion in dimethyl sulfoxide (DMSO) was investigated in the DMSO concentration range 0–80 vol.%. The complex species identified were Pb₂(DMSO)⁴⁺₃, Pb(DMSO)²⁺₃ and Pb(DMSO)²⁺₆ in [DMSO]<10 vol.%, 10< [DMSO]<43 vol.% and [DMSO]>43 vol.%, respectively. In the presence of pamoic acid, the reduction of lead ion in DMSO was two-electron reversible diffusion-controlled at pH≤6.0, but it became irreversible at pH>6.0. The complex species identified was Pb(D_m)₂(P_m)₃(OH)^6? at pH>6.0. The rate constants of electro-reduction and electro-oxidation, activation energies were determined. The hydrolysis constants of lead ion in dimethyl sulfoxide concentration 40–70 vol.% at pH 4.5–6.0 were found to be of the order of 10^?6. The stability constants of the Pb(DMSO)²⁺₃ and Pb(DMSO)²⁺₀ were also determined to be of the orders of 10¹ and 10⁵, respectively.     

Novel diastereoselective synthesis of (E)- and (Z)-allylsilanes via organoboranes

A simple, novel diastereoselective synthesis of both (E)- and (Z)-allylsilanes via organoboranes is developed. (E)-1-Alkenylboronate esters easily prepared from the corresponding terminal alkynes via hydroboration with dibromoborane-methyl sulfide complex followed by treatment with 1,3-propane diol readily react with trimethylsilylmethyllithium at −78 °C in methanol followed by reaction with iodine in methanol to produce the corresponding (Z)-allylsilanes in high yields (72-80%) and in high stereochemical purities (98% as evidenced by CMR spectral data). Similarly, the (Z)-1-alkenylboronate esters react with trimethylsilylmethyllithium at −78 °C in methanol followed by treatment with iodine in methanol to produce the corresponding (E)-allylsilanes in moderate yields (57-65%) in high stereochemical purities (>98% as revealed by CMR spectral data).     

蒙特卡洛模拟退火与距离限制相结合的方法在多肽溶液构象分析中的应用

多维核磁共振技术的飞速发展议得其在生物大分子结构测定方面的应用已经达到可以与【射线晶体学并驾齐驱的地步．蛋白质结构堆积紧密，较适合于用核磁共振方法给出确定的结构．与蛋白质不同的是多肽的柔性较大，在溶液中可能存在多种构象，核磁共振实验给出的只是平均信息＊．利用核磁，（振数据构建分子结构模型常用的方法有距离几何、分子动力学等，在由核磁共振NOESZ得到的距离信息足够多时可以给出较好的结果问．由于多肽本身的特点：柔性较大，由核磁共振得到的距离信息较少等，利用距离几何、分子动力学方法进行构象搜索时容易陷入…     

Synthesis of proline-modified analogues of the neuroprotective agent glycyl-l-prolyl-glutamic acid (GPE)

The synthesis of ten proline-modified analogues of the neuroprotective tripeptide GPE is described. Five of the analogues incorporate a proline residue with a hydrophobic group at C-2 and two further analogues have this side chain locked into a spirolactam ring system. The pyrrolidine ring was also modified by replacing the γ-CH₂ group with sulfur and/or incorporation of two methyl groups at C-5.