Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex

Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.     

Determination of the residue of quizalofop-p-tefuryl in soybean by HPLC

A HPLC method was developed for the analysis of quizalofop-P-tefurylof in soybean. The samples were extracted with methanol-water (volume ratio), The extracts were cleaned up with a column of silica gel. The final residue was detected by HPLC, using a UV detector. The recoveries from the analytical method for soybean were 84.32%–89.25%. Variable coefficients were 0.49%∼1.51%. This method proved to be simple, reliable and accurate. __________ Translated from Chinese Journal of Chromatography, 2005, 23(2)(in Chinese)     

Diastereoselective allylation of planar chiral substituted ferrocenecarboxaldehyde: an efficient entry to chiral ferrocenyl ligands

2,2′-Disubstituted ferrocenecarboxaldehydes are subjected to zinc-mediated allylation to form homoallylic ferrocenyl alcohols. The effects of ortho-substituted functional groups on facial selectivities of planar chiral aldehydes were studied and it was found that the corresponding homoallylic alcohols were obtained as single diastereomers in excellent yields.     

含聚硅氧烷链双马来酰亚胺的合成与表征

合成了Ｎ－（４－羟基苯基）马来酰亚胺和含聚硅氧烷链双马来酰亚胺，并用ＦＴＩＲ、１ＨＮＭＲ、元素分析、ＧＰＣ、ＤＴＡ和ＴＧ对其进行了表征。     

Reduction of nitroaromatics to arylnitrenium ions by vinyl halide cations

The title reduction of nitroaromatics ArNO(2) by vinyl halide radical cations CH(2)[double bond]CH-X(+*)(X = Cl or Br) to form arylnitrenium ions ArNH(+) involves a change in oxidation number of nitrogen from +3 to -1. This novel reaction provides a new route for the generation of arylnitrenium ions, a highly selective method for the detection of explosives in mixtures, and offers clues to the carcinogenic activity of nitroaromatics in vivo.     

Detection of explosives on solid surfaces by thermal desorption and ambient ion/molecule reactions

A simple, fast and direct method is presented for detecting traces of solid explosives on cotton swabs or in particulate samples: ions are transferred into a mass spectrometer after thermal desorption and corona discharge chemical ionization in ambient air; specificity is enhanced using ambient ion/molecule reactions or by conventional tandem mass spectrometry.     

Oxidation of Styrene with Molecular Oxygen in Supercritical CO2

The oxidation of styrene with molecular oxygen catalyzed by PdCl2 CuCl2 has been investigated in supercritical CO2 with a batch reactor. The oxidative system of styrene contains four components at the beginning and seven components during the reaction. The critical temperature, critical pressure, and critical density at different conversions are determined by using a high-pressure view cell. The effect of phase behavior on the conversion and selectivity were studied. Experimental results showed that the critical parameters of the reaction mixture at fixed initial molar ratio changed with the conversion of reactant. The conversion of styrene reached maximum near the critical density of the reaction mixture. Product selectivity also varied with density of reaction mixture and could be tuned to some degree.     

Selective binding of steroids by 2,2'-biquinoline-4,4'-dicarboxamide-bridged bis(beta-cyclodextrin): fluorescence enhancement by guest inclusion

A novel bis(beta-cyclodextrin) was synthesized, and its binding behavior with steroids was investigated to demonstrate that the cooperative co-inclusion of guest and tether by two cyclodextrin moieties is operative to afford the highest molecular selectivity of up to 3.6 for deoxycholate over taurocholate.     

Self-assembling a molecular pegboard

This paper describes the design, construction, and application of a self-assembled, chemically addressable DNA nanogrid composed of DNA tiles of nanometer dimensions. This self-assembled structure permits precise placement of molecules at predetermined locations on a "molecular pegboard". We used the indexed DNA nanogrids to identify single molecules of DNA that hybridize at particular locations.     

Improving the quality of 3D-QSAR by using flexible-ligand receptor models

To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to achieve minimal docking energies; (2) the receptor atoms are spatially moveable in the process of genetic evolving in order to avoid improper initial receptor shapes; and (3) void receptor sites are specially favored in order to obtain open receptor models that allow large gaps. Advantages of an open model include less noise information, a smaller risk of overfitting, and ease of locating the key interaction sites. The latter two features, inherited from the previous FLARM 1.0 method, can improve the predictive ability of the 3D-QSAR models, while the first feature is newly implemented to relieve the uncertainty caused by improper conformation and alignment. Three FLARM 2.0 case studies were performed, and the results show that FLARM 2.0 models are highly predictive and robust. FLARM 2.0 pseudoreceptor models can correspond well with the pharmacophore models and/or the binding sites of the real protein receptors.