Characterization of the Binding of Methylene Blue to DNA by Spectroscopic Methods

ABSTRACT

Methylene blue (MB) binds to the double helical DNA with a high affinity, as deduced from the absorption and fluorescence spectral data. Extensive hypochromism and red shifts in the absorption spectra were observed when MB binds to calf thymus DNA(CT DNA), which suggested the intercalation mechanism of MB into DNA bases. Upon binding to DNA, the fluorescence from MB was efficiently quenched by the DNA bases, with no shifts in the emission maximum. The large increases in the polarization upon binding to CT DNA supported the intercalation of MB into the helix. Ferrocyanide quenching studies showed that the magnitude of K_sv of the bound MB was lower than that of the free MB. The results of competitive binding studies showed that ethidium bromide could be displaced by MB from ethidium-DNA complex. The results of all above further studies also proved the intercalation of MB into DNA base stack.     

DNA小沟结合药物DB818的分子动力学模拟和结合自由能分析

采用分子动力学模拟了DNA小沟结合芳香二脒药物DB818形成的复合物. 通过5 ns的模拟研究表明: DB818药物分子可紧密结合在DNA的AATTC小沟区域, 和双螺旋d[CGCGAATTCGCG]2形成稳定的复合物. 由于噻吩硫原子的弱电负性, 使DB818能够以更大的伸展程度与DNA的小沟结合, 形成更强的结合力. DB818苯并咪唑的氮原子能够与DNA 7位和19位T碱基上的氧原子形成两个稳定的氢键, 同时, DB818末端氨基氮原子分别与DNA 的20位T碱基的氧原子和9位C碱基的氧原子形成两个氢键. 另外, 运用MM_PBSA方法计算了DB293-DNA和DB818-DNA复合物的结合自由能, 计算结合能与实验值能较好的吻合, 通过比较其结合自由能, 从热力学能量角度说明了DB818有较大的熵值与较小的焓值贡献, 从而与DNA小沟结合的结合力比DB293强. 本文在分子水平上提供了DB818直接与双螺旋DNA相互作用的结构及复合物的动态变化情况, 为设计出更高生物活性的DNA小沟结合剂提供一定的理论依据.     

Classification and Prediction of Sodium and Potassium Coronates Stability in Aqueous-Organic Media by Exploratory Data Analysis Methods

Russian Journal of General Chemistry - Linear Fisher classification functions, canonical linear discriminant functions, and trees (rules) for classification and prediction of the stability of...     

Oxygen Binding,Activation, and Reduction to Water by Copper Proteins

Copper active sites play a major role in biological and abiological dioxygen activation. Oxygen intermediates have been studied in detail for the proteins and enzymes involved in reversible O(2) binding (hemocyanin), activation (tyrosinase), and four-electron reduction to water (multicopper oxidases). These oxygen intermediates exhibit unique spectroscopic features indicative of new geometric and electronic structures involved in oxygen activation. The spectroscopic and quantum-mechanical study of these intermediates has defined geometric- and electronic-structure/function correlations, and developed detailed reaction coordinates for the reversible binding of O(2), hydroxylation, and H-atom abstraction from different substrates, and the reductive cleavage of the O-O bond in the formation water.     

X射线荧光光谱法测定硅石中主次量元素组分

以Li_2B_4O_7、LiBO_2和LiF(质量比为45∶10∶5)为混合熔剂,NH_4NO_3为氧化剂,LiBr为脱模剂,熔融制作样片,采用硅质砂岩、石英岩标准样品和配制标准样品作为校准样品,建立了熔融制样-X射线荧光光谱法(XRF)测定硅石中主次量成分(SiO_2、Al_2O_3、TFe_2O_3、MgO、CaO、K_2O、MnO、TiO_2、P_2O_5)的快速分析方法。对样品制备以及分析测试过程中的条件进行了优化,在最优条件下,对标准样品(GBW03112、GBW07835)进行重复测定,相对标准偏差RSD2%。同时对3个混合配制的硅石标准样品进行分析,结果与参考值无显著性差异。     

大洋底多金属结核样品中主、次、微量元素的X射线荧光光谱测定

制定了一个用X射线荧光光谱法测定大洋底多金属结核样品中主、次、微量元素的分析方法。样品用石墨坩埚、混合熔剂低倍稀释熔融,用人工标样作为校准标准。计算了COLA方程的理论α系数,用于校正28个分析元素的吸收-增强效应。本法测定结果与化学法结果相吻合。     

X-射线荧光光谱法测定白云石中主次量组分

采用粉末压片x-射线荧光光谱法测定白云石中氧化镁、氧化钙、二氧化硅、三氧化二铝、三氧化二铁和二氧化钛含量。采用校正曲线和基体校准一体的回归方程进行谱线重叠干扰校正和基体效应校正。将白云石样品进行磨细处理,在压片机上制成样片,直接在X-射线荧光光谱仪上按照选定的分析条件,以标准样品做工作曲线,利用工作曲线测定样品含量。通过与国家标准化学法以及熔片法对照,分析结果与标准值、熔片法结果吻合,主含量元素测定结果相对误差不超过10％,同一样品12次测定结果相对标准偏差不超过10％。该方法简便、快速、准确、重现性好。     

X射线荧光光谱法分析镁砂中的主次成分

采用镁砂标准样品作为校准样品,建立了熔融制样X射线荧光光谱法测定镁砂中MgO,Al2O3,SiO2,CaO,P2O5,Fe2O3的方法。采用熔融法为样品片和校准片的制备方法,选择四硼酸锂-偏硼酸锂(67+33)为助熔剂,1.00mL LiBr溶液为脱模剂,熔融温度为1 100℃,熔融时间20min。对镁砂样品测定的相对标准偏差(RSD)小于3%,对不同镁砂标准样品进行测定,方法的测定结果与认证值相吻合。     

Analysis of DSC Data Relating to Proteins Undergoing Irreversible Thermal Denaturation

New approaches to the analysis of differential scanning calorimetry (DSC) data relating to proteins undergoing irreversible thermal denaturation have been demonstrated. The experimental approaches include obtaining a set of DSC curves at various scanning rates and protein concentrations, and also reheating experiments. The mathematical methods of analysis include construction of a linear anamorphosis and simultaneous fitting of a theoretical expression for the dependence of the excess heat capacity on temperature to a set of experimental DSC curves. Different kinetic models are discussed: the one-step irreversible model, the model including two consecutive irreversible steps, the Lumry and Eyring model with a fast equilibrating first step, and the whole kinetic Lumry and Eyring model. This revised version was published online in July 2006 with corrections to the Cover Date.     

Understanding the Peculiarities of Azide and Thiocyanate Binding in Proteins: Use of the Small Molecule Structural Data

Abstract

The complexation and supramolecular recognition of two polyfunctional anions, thiocyanate and azide, have been analysed using the X-ray structural data retrieved from the Brookhaven Protein Database (for macromolecules) and the Cambridge Structural Database (for small molecule structures). The following structural aspects have been considered: - hydrogen-bond acceptor function of the anions; - analysis of the coordination features of anions with the metals; - influence of metal complexation on the H-donor accepting properties of the anions. Lastly, a comparison of the modes of binding of the two anionic substrates was carried out. Their extraordinary activity as hydrogen-bond acceptors allows these anions to serve as a strong bridge between different molecular fragments. The coordination of thiocyanate or azide anion by the metal atoms in coordination compounds gives rise to a redistribution of anionic charge in both entities which in turn, controls the hydrogen-bonding acceptor properties of the terminal atom of the anion. The results presented in this paper provide structural information of the role of anion binding in proteins and to our knowledge, afford the first study of the binding behaviour of thiocyanate and azide in systematic manner.     

基于DNA和小沟结合染料DAPI快速检测水样中Hg2+

设计了一条DNA序列作为专一识别Hg2+的探针,结合小沟结合染料DAPI,构建了一种新型无标记荧光降低型核酸适体传感器。无Hg2+时DNA折叠成稳定的茎-环结构,DAPI插入茎部位有强荧光发射;Hg2+存在时DNA发生结构转变,DAPI释放荧光降低。结果表明:在最佳实验条件下,体系荧光降低百分数和Hg2+浓度正相关,在较低的浓度范围(0.5~50 nmol/L)仍呈良好的线性关系,实际检出限为0.5 nmol/L。该方法操作简单、对于环境水样中Hg2+的快速实时检测具有潜在的应用前景。     

Analysis of Diazofluorene DNA Binding and Damaging Activity: DNA Cleavage by a Synthetic Monomeric Diazofluorene

The lomaiviticins and kinamycins are complex DNA damaging natural products that contain a diazofluorene functional group. Herein, we elucidate the influence of skeleton structure, ring and chain isomerization, D‐ring oxidation state, and naphthoquinone substitution on DNA binding and damaging activity. We show that the electrophilicity of the diazofluorene appears to be a significant determinant of DNA damaging activity. These studies identify the monomeric diazofluorene 11 as a potent DNA cleavage agent in tissue culture. The simpler structure of 11 relative to the natural products establishes it as a useful lead for translational studies.     

Light‐Triggered Capture and Release of DNA and Proteins by Host–Guest Binding and Electrostatic Interaction

The development of an effective and general delivery method that can be applied to a large variety of structurally diverse biomolecules remains a bottleneck in modern drug therapy. Herein, we present a supramolecular system for the dynamic trapping and light‐stimulated release of both DNA and proteins. Self‐assembled ternary complexes act as nanoscale carriers, comprising vesicles of amphiphilic cyclodextrin, the target biomolecules and linker molecules with an azobenzene unit and a charged functionality. The non‐covalent linker binds to the cyclodextrin by host–guest complexation with the azobenzene. Proteins or DNA are then bound to the functionalized vesicles through multivalent electrostatic attraction. The photoresponse of the host–guest complex allows a light‐induced switch from the multivalent state that can bind the biomolecules to the low‐affinity state of the free linker, thereby providing external control over the cargo release. The major advantage of this delivery approach is the wide variety of targets that can be addressed by multivalent electrostatic interaction, which we demonstrate on four types of DNA and six different proteins.     

X射线荧光光谱法测定金红石中主次组分

采用Li2B4O7和LiBO2的混合熔剂(67∶33)熔融制样,波长色散X射线荧光光谱法测定金红石中TiO2,TFe,P,SiO2,Al2O3,MnO,CaO,Cr2O3,MgO,ZrO2,HfO2等组分。实验中样品和熔剂的质量比为1∶14,以溴化锂(LiBr)作脱模剂,采用高频熔炉在1 150℃熔融90s进行制样,所得熔片均匀、强度高、成型良好。方法用于金红石实际样品的测定,结果同参考值或化学分析方法的结果相吻合,相对标准偏差(RSD,n=10)P为3.8%、Al2O3为2.8%,其它均小于2%,能够满足实际测定工作的需要。     

Binding of Copper(II) to Pectins by Electrochemical Methods

The interaction between Cu(II) and pectin extracted from citrus fruit was studied in KNO₃ 0.10 mol dm^?3 at 25 °C and pH 5.5, using ion selective electrode potentiometry and voltammetry, namely differential pulse polarography and square‐wave voltammetry. Although many independent variables may affect Cu(II)‐polymer interactions such as charge density, polymer concentration and copper to polymer concentration ratio, a good fitting was observed for the model with ML and ML₂ complex species, when M:L total concentration (mol dm^?3) ratio varies from 0.2 to 2.7 and the ligand concentration is in the range (0.2 to 1) g dm^?3, i.e., (0.4 to 2)×10^?3 mol COO^? dm^?3. The complex parameters found in these conditions were log β_CuL=3.5±0.1 and log β_CuL2= 8.0±0.2. For lower total ligand and total metal ion concentrations, used in voltammetry, the interaction Cu(II)‐pectin is affected by a cooperative mode (increase of metal ion‐ligand affinity) when the total metal ion concentration increases and by an anti‐cooperative mode when the total ligand concentration increases, possibly due to different conformations of the polymer.     

X射线荧光光谱法测定黏土中的主次组分

采用熔融玻璃片制样,选用标准样品,以经验α系数和散射线内标法校正元素谱线重叠干扰和基体效应,使用ZSX Primus Ⅱ X射线荧光光谱仪对黏土样品中的Al₂O₃、SiO₂、Fe₂O₃、CaO、MgO、K₂O、Na₂O、MnO、P₂O₅、TiO₂、Cu、Cr等组分进行测定,分析结果与标准值和化学值相吻合,12次测定的相对标准偏差小于10%.     

Tailoring the NIR-II Photoluminescence of Single Thiolated Au25 Nanoclusters by Selective Binding to Proteins**

Atomically precise gold nanoclusters are a fascinating class of nanomaterials that exhibit molecule-like properties and have outstanding photoluminescence (PL). Their ultrasmall size, molecular chemistry, and biocompatibility make them extremely appealing for selective biomolecule labeling in investigations of biological mechanisms at the cellular and anatomical levels. In this work, we report a simple route to incorporate a preformed Au₂₅ nanocluster into a model bovine serum albumin (BSA) protein. A new approach combining small-angle X-ray scattering and molecular modeling provides a clear localization of a single Au₂₅ within the protein to a cysteine residue on the gold nanocluster surface. Attaching Au₂₅ to BSA strikingly modifies the PL properties with enhancement and a redshift in the second near-infrared (NIR-II) window. This study paves the way to conrol the design of selective sensitive probes in biomolecules through a ligand-based strategy to enable the optical detection of biomolecules in a cellular environment by live imaging.     

X射线荧光光谱法测定石灰岩和白云岩中主次量组分

建立用X射线荧光光谱法同时测定石灰岩和白云岩中主次量组分(CaO、MgO、Al2 O3、SiO2、Fe2O3、TiO2、K2O、Na2O、MnO、P2O5)的快速分析方法,在优化条件下,采用国家标准样品建立的标准工作曲线和基体校准一体回归方程进行谱线重叠干扰和基体效应校正.实验结果表明,各元素的检出限在80～280μg...