Monte Carlo Simulation of the Assembly of bis‐Biotinylated DNA and Streptavidin

We present Monte Carlo simulations of the self‐assembly of bivalent bis‐biotinylated DNA molecules with the tetravalent biotin‐binding protein streptavidin (STV). By fitting the STV binding probabilities for the four possible valencies, the modelling correctly reproduces the dependencies of various network parameters experimentally observed in an earlier study. The combined results from the experimental and theoretical studies suggest that the binding probability for divalent STV formation is about 50 times larger than for the formation of trivalent and about 200 times larger than for tetravalent STV. In accordance with the experimental results, the modelling also indicates that the mixture of an equimolar ratio of DNA and STV leads to a maximum in size of the oligomeric DNA–STV clusters formed. Furthermore, we found a percolation transition in which the DNA cluster size increases rapidly with increasing DNA concentration resulting in the formation of a single supercluster at elevated concentrations. This behaviour coincides with the occurrence of an immobile band previously observed in electrophoretic experiments, indicating the formation of extremely large DNA–STV aggregate networks.     

Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d,e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.

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Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden

Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.

     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Study on the Interaction between Gatifloxacin Mesylate and Salmon Sperm DNA by Fluorescence Method

The interaction between gatifloxacin mesylate (GM) and salmon sperm DNA was studied by fluorescence spectrometry and ultra‐violet (UV) spectrometry. Additions of salmon sperm DNA to GM solution resulted in its strong fluorescence quenching and UV absorbance decrease due to the strong interaction between GM and salmon sperm DNA. Both the maximum fluorescence emission wavelength and the maximum UV absorbance wavelength of GM did not change with the increasing concentration of salmon sperm DNA, indicating no intercalative binding existed between them. The Stern‐Volmer plot indicated that the fluorescence‐quenching constant at different temperatures or different salmon sperm DNA concentration ranges was different. Effects of ionic strength and I^? on the fluorescence quenching of GM by salmon sperm DNA indicated that electrostatic interaction and groove binding coexisted between them.     

白藜芦醇的电化学行为及其与DNA的相互作用

采用电化学方法研究了白藜芦醇在pH=2~13的缓冲溶液中的电化学行为、抗氧化能力及其与DNA的相互作用. 研究结果表明， 在2.011的溶液中, 白藜芦醇产生的P4和P5波分别是其二价和三价阴离子的还原波. 在最佳实验条件下, 微分脉冲极谱图上IP3在8.0×10-8~2.0×10-6 mol/L范围内与白藜芦醇的浓度呈线性关系, 检出限为4×10-8 mol/L. 将该法用于中药虎杖中白藜芦醇含量的测定, 结果与高效液相色谱法一致.     

透明导电玻璃(ITO)基材自加热传感静态芯片聚合酶链反应(PCR)

利用商品化ITO玻璃导电层的温阻效应, 无需任何微加工手段, 实现了自加热和传感的芯片温度自动程序控制, 最大程度地减小了传感滞后对温度控制稳定性的影响, 温度控制的稳定性达到了0.2 ℃, 升温速度最快可达20 ℃/s以上, 在冷却风扇辅助下降温速度最快达到了8 ℃/s. 芯片温控单元的引线从传统的两对(一对用于传感, 一对用于加热)减少为一对. 通过在该芯片上直接构建多个开放微池反应器的方法成功地实现了λDNA 157 bp片段的并行扩增. 将该芯片置于倒置荧光显微镜样品台上, 以蓝色(575 nm)发光二极管为光源, 以光电倍增管为检测手段检测了dsDNA和SYBR Green Ⅰ嵌合物的荧光强度随温度的实时变化曲线.     

基于超星学习通平台的有机化学录播课教学实践

由于新型冠状病毒肺炎疫情,高校延期开学。为了实现"停课不停教、停课不停学",需要积极开展在线教学。本文基于超星学习通平台,开展了有机化学课程录播课教学实践,为高校教师网络教学提供一定的参考。     

生物质裂解产物的制备及HPLC检测其成分的虚拟仿真实验开发

In order to improve university laboratory teaching and practical education under the background of information technology, as well as overcome the difficulty for practical training, develop a virtual simulation experiment platform for rapid pyrolysis of natal materials and high-performance liquid chromatographic (HPLC) detection of its components. The experiment integrates the actual operation process of the plant to produce cleaved products by rapid pyrolysis of biomass with HPLC detection. The virtual experiment is divided into biomass sample pretreatment, rapid biomass pyrolysis, bio-oil extraction, and HPLC determination of complex components, making the biomass cleavage workshop "real" through simulation. This virtual simulation experiment fully integrates the utilization of biomass resources and basic chemistry courses (such as organic chemistry, instrumental analysis, chemical engineering principles, etc.), which are widely involved in agricultural and forestry majors with advantageous characteristics value.     

Hydrolysis of DNA by cerium(IV)/EDTA complex

Homogeneous solutions are formed from equimolar amounts of Ce(NH₄)₂(NO₃)₆ and EDTA. These solutions hydrolyze single-stranded DNA far more efficiently than double-stranded DNA. In contrast, Ce(IV) hydroxide gel, obtained in the absence of EDTA, hydrolyzes both single-stranded and double-stranded DNAs at almost the same rates. In order to achieve this substrate-specificity sufficiently, the mole ratio of EDTA to Ce(NH₄)₂(NO₃)₆ must be 1.0 or greater. By using this remarkable specificity of Ce(IV)/EDTA complex, gap-site in substrate DNA is selectively hydrolyzed. The scission-site is modulated by use of appropriate combination of oligonucleotide additives. The reactions have been kinetically analyzed.     

Chromatography of plasmid DNA

Liquid chromatography plays a central role in process-scale manufacturing of therapeutic plasmid DNA (pDNA) for gene therapy and DNA vaccination. Apart from its use as a preparative purification step, it is also very useful as an analytical tool to monitor and control pDNA quality during processing and in final formulations. This paper gives an overview of the use of pDNA chromatography. The specificity of pDNA purification and the consequent limitations to the performance of chromatography are described. Strategies currently used to overcome those limitations, as well as other possible solutions are presented. Applications of the different types of chromatography to the purification of therapeutic pDNA are reviewed, and the main advantages and disadvantages behind each technique highlighted.