Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

One of the main factors that can affect the quality of microarray results is the microarray hybridization specificity. The key factor that affects hybridization specificity is the design of the probes. In this paper, we described a novel oligonucleotide probe containing deoxyinosines aimed at improving DNA hybridization specificity. We compared different probes to determine the distance between deoxyinosine base and SNPs site and the number of deoxyinosine bases. The new probe sequences contained two set of deoxyinosines (each set had two deoxyinosines), in which the interval between SNP site and each set of deoxyinosines was two bases. The new probes could obtain the highest hybridization specificity. The experimental results showed that probes containing deoxyinosines hybridized effectively to the perfectly matched target and improved the hybridization specificity of DNA microarray. By including a simple washing step after hybridization, these probes could distinguish matched targets from single‐base‐mismatched sequences perfectly. For the probes containing deoxyinosines, the fluorescence intensity of a match sequence was more than eight times stronger than that of a mismatch. However, the intensity ratio was only 1.3 times or less for the probes without deoxyinosines. Finally, using hybridization of the PCR product microarrays, we successfully genotyped SNP of 140 samples using these new labeled probes. Our results show that this is a useful new strategy for modifying oligonucleotide probes for use in DNA microarray analysis.     

电磁轴承系统的刚度阻尼特性分析

分析了电磁轴承系统的刚度阻尼特性与系统结构参数及其控制器频响特性之间的关系。给出了系统控制电流的相位对系统稳定性和刚度阻尼特性的影响。提出了电磁轴承系统的复阻尼概念，以及部分刚度阻尼特性指标的实际意义和计算方法。     

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Chemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide‐Based Inhibitors

Sirtuins are NAD⁺‐dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide‐based inhibitors that interact with the NAD⁺ binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X‐ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5.     

Mode Specificity,Bond Selectivity,and Product Energy Disposal in X + CH4/CHD3 (X=H,F, O(3P), Cl,and OH) Hydrogen Abstraction Reactions: Perspective from Sudden Vector Projection Model

Reactions between methane and various radicals have become the workhorse in our understanding of mode specificity and bond selectivity in bimolecular reactions. In this work, the recently proposed Sudden Vector Projection (SVP) model is used to gain insight into the existing experimental and theoretical data on these reactions. The SVP model attributes mode specificity and bond selectivity to the coupling of reactant modes/bonds with the reaction coordinate at the transition state. In the sudden limit, the strength of the coupling can be simply computed by projecting the corresponding reactant normal mode vector onto that of the imaginary frequency mode at the saddle point. In addition, the SVP model can be used to predict energy disposal in the products, thanks to microscopic reversibility. It is shown that most of the mode‐specific and bond‐selective chemistry in X + CH₄/CHD₃ (X=H, F, O(³P), Cl, and OH) reactions can be reasonably understood with this simple model.     

ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators

Two-component systems (TCS) are signaling machinery that consist of a histidine kinases (HK) and response regulator (RR). When an environmental change is detected, the HK phosphorylates its cognate response regulator (RR). While cognate interactions were considered orthogonal, experimental evidence shows the prevalence of crosstalk interactions between non-cognate HK–RR pairs. Currently, crosstalk interactions have been demonstrated for TCS proteins in a limited number of organisms. By providing specificity predictions across entire TCS networks for a large variety of organisms, the ELIHKSIR web server assists users in identifying interactions for TCS proteins and their mutants. To generate specificity scores, a global probabilistic model was used to identify interfacial couplings and local fields from sequence information. These couplings and local fields were then used to construct Hamiltonian scores for positions with encoded specificity, resulting in the specificity score. These methods were applied to 6676 organisms available on the ELIHKSIR web server. Due to the ability to mutate proteins and display the resulting network changes, there are nearly endless combinations of TCS networks to analyze using ELIHKSIR. The functionality of ELIHKSIR allows users to perform a variety of TCS network analyses and visualizations to support TCS research efforts.     

Intracellular lectins are involved in quality control of glycoproteins

Glycoprotein quality control is categorized into three kinds of reactions; the folding of nascent glycoproteins, ER-associated degradation of misfolded or unassembled glycoproteins, and transport and sorting of correctly folded glycoproteins. In all three processes, N-glycans on the glycoproteins are used as tags that are recognized by intracellular lectins. We analyzed the functions of these intracellular lectins and their sugar-binding specificities. The results clearly showed that the A, B, and C-arms of high mannose-type glycans participate in the folding, transport and sorting, and degradation, respectively, of newly synthesized peptides. After correctly folded glycoproteins are transported to the Golgi apparatus, N-glycans are trimmed into Man₃GlcNAc₂ and then rebuilt into various complex-type glycans in the Golgi, resulting in the addition of diverse sugar structures that allow glycoproteins to play various roles outside of the cells.     

A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism

Structure-based virtual screening techniques require reliable scoring functions to discriminate potential substrates effectively. In this study we compared the performance of GOLD, PMF, DOCK and FlexX scoring functions in FlexX flexible docking to cytochrome P450cam binding site. Crystal structures of protein-substrate complexes were most effectively reproduced by the FlexX/PMF method. On the other hand, the FlexX/GOLD approach provided the best correlation between experimental binding constants and predicted scores. Binding modes selected by the FlexX/PMF approach were rescored by GOLD to obtain a reliable measure of binding energetics. The effectiveness of the FlexX/PMF/GOLD method was demonstrated by the correct classification of 32 out of the 33 experimentally studied compounds and also in a virtual HTS test on a library of 10,000 compounds. Although almost all the available functions were developed to be general, our study on cytochrome P450cam substrates suggests that careful selection or even tailoring the scoring function might increase the prediction power of virtual screens significantly. The FlexX/PMF/GOLD methodology was tested on cytochrome P450 3A4 substrates and inhibitors. This preliminary study revealed that the combined function was able to recognise 334 out of the 345 compounds bound to 3A4.     

The use of a radiation inactivation method for characterization of the structure and catalytic properties of enzymes

The use of a radiation inactivation method for studies of the properties of enzymes of different classes is discussed. The possibilities of characterization of enzymes on the basis of the radiation-chemical parameters concerned are described.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp. 2828–2836, December, 1996.     

Aminolysis ofO-alkylO-4-nitropyenyl chloromethylphosphonates in reverse micellar solutions of the nonionic surfactant

The reaction ofn-hexylamine withO-alkylO-4-nitrophenyl chloromethylphosphonates in toluene solutions of poly(ethylene glycol)-600 monolaurate (PM) has been studied by spectrophotometry. The reverse micelles of the nonionic surfactant increase more than tenfold the observed rate constant of aminolysis. The catalytic activity of the surfactant is practically independent of the alkyl radical length of phosphonate. An increase in the concentration of amine results in a decrease in the catalytic efficiency. The character of the dependence of the rate constant on the concentration of PM is affected by the alkyl chain length of the substrate. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1735–1738, September, 1998.