亚甲基蓝与DNA相互作用的电化学研究

近年来,小分子化合物与DNA相互作用的研究是生命科学研究的热门话题。特别是一些药物和毒物分子与DNA的作用[1-2],如何影响DNA的生理和化学物理性质,如何影响DNA的转译和复制,都是十分重要的课题。在医药研究中,DNA与靶向分子相互作用的研究不仅对阐述一些抗肿瘤、抗病毒药物及     

核酸适体靶向的膜蛋白识别与功能调控研究进展

膜蛋白在细胞生命活动中发挥着重要作用, 研究并调控细胞膜蛋白的结构和功能有助于阐明生命活动的基本规律, 为新型药物研发和高效疾病诊治提供研究基础. 核酸适体是一类特殊的寡核苷酸序列, 因具有特异性识别靶标的能力而被广泛用于生物传感领域. 将核酸适体与DNA纳米技术相结合, 利用DNA分子可程序化设计、 可功能化修饰等优势, 发展核酸适体靶向的膜蛋白识别与功能调控方法可为研究膜蛋白相互作用提供有力工具. 本文介绍了基于核酸适体靶向识别的DNA纳米技术在膜蛋白识别及细胞功能调控中的研究进展, 并对核酸适体靶向的膜蛋白识别及功能调控领域面临的挑战进行了分析, 对其应用前景进行了展望.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

不可逆电活性药物米托蒽醌与脱氧核糖核酸的相互作用

研究了抗癌新药米托蒽醌(MXT)的电化学行为及与脱氧核糖核酸(DNA)的相互作用，推导了适用于研究不可逆电活性分子与DNA相互作用的电化学公式，运用该公式可以简便、快速地测定靶向分子与DNA的结合常数和结合位点数。实验发现，MXT与小牛胸腺DNA的结合以蒽醌母核的嵌插作用为主，同时，烃氨基侧链与骨架磷酸基团之间的静电吸引对母核起稳定作用，使化合物易于嵌入DNA的平面结构。MXT与DNA相互作用引起的峰电流的变化可以用于分析测定DNA。     

基于氧化石墨烯的Ag~+与核酸中C-C碱基错配的相互作用研究

基于氧化石墨烯,以修饰了荧光分子的单链DNA为探针,利用荧光光谱和圆二色光谱研究了Ag+对双螺旋DNA中C-C碱基错配特异性识别,并建立了检测Ag+的荧光方法。荧光光谱表明Ag+能与带C-C错配碱基的双螺旋DNA作用,使原本被氧化石墨烯淬灭的标记在DNA上的荧光分子的荧光得到恢复。圆二色光谱表明Ag+能与双螺旋DNA中的C-C碱基错配相互作用,形成更稳定的C-Ag+-C结构。在最佳实验条件下,体系荧光强度的变化与Ag+的浓度在30.0~250.0 nmol/L之间呈良好的线性关系,方法检出限为19.1 nmol/L。为研究Ag+与核酸分子的相互作用及其在环境中对生物分子的影响等方面提供了重要依据。     

基于DNA的细胞膜功能化

细胞膜在细胞与外界环境间的物质运输、能量转换和信息传递等过程中起着重要作用,研究和控制细胞膜上的分子的相互作用,对理解和操控细胞的生理功能具有重要意义。脱氧核糖核酸(Deoxyribonucleic acid, DNA)分子具有精确自组装和可编程的特性,是一种研究生物膜分子相互作用的新工具。本综述中,我们概括了DNA分子修饰细胞膜的方法,随后介绍了基于DNA分子的监测、控制细胞膜分子相互作用的工作以及DNA分子介导细胞连接的研究,并分析了上述研究的局限性。最后,我们对基于DNA的细胞膜功能化研究进行总结与展望,以期促进对细胞膜功能的新认识,获得控制细胞功能的新方法。     

基于钌多吡啶类配合物的DNA分子光开关及生物传感研究

DNA结构具有多态性,利用小分子化合物对不同结构的DNA分子进行识别及调控具有重要的生物学意义.本文主要针对近年来钌多吡啶配合物作为DNA分子光开关的研究进行综述,内容包括DNA分子光开关的机制,不同结构DNA的分子光开关,DNA分子光开关的开关循环控制策略和钌多吡啶类配合物及与纳米材料相结合作为生物传感器的研究.     

环丙沙星铽荧光配合物与DNA的相互作用及染色新方法

合成了环丙沙星铽荧光配合物,并研究其与DNA分子的相互作用.对比DNA分子吸附配合物分子前后的显微红外及荧光光谱发现,以环丙沙星分子为配体的稀土配合物同DNA间存在相互作用,这种作用诱导了DNA二级结构的构象变化.基于这种相互作用,研究了环丙沙星铽配合物对口腔粘膜组织切片的荧光染色,得到了同经典的苏木精-伊红染色法类似的反差效果.     

水溶性卟啉及金属卟啉在DNA中的研究进展

近年来, 卟啉及金属卟啉与DNA的相互作用已成为研究的热点. 通过对卟啉及金属卟啉与DNA相互作用的研究将有助于更深地认识DNA本身的结构和功能, 有助于卟啉及金属卟啉在医学上的应用, 对认识很多疾病的治病机制和药物的设计也起到非常重要的作用. 本文阐述了卟啉及金属卟啉与DNA相互作用的方式和影响因素, 并将水溶性卟啉及金属卟啉分为三类: 具有吡啶基或铵基的阳离子型卟啉及金属卟啉, 具有磺酸基或羧基的阴离子型卟啉及金属卟啉, 以及非离子型的卟啉及金属卟啉. 重点论述了这三类水溶性卟啉及金属卟啉与DNA之间的相互作用, 以及这三类水溶性卟啉及金属卟啉在DNA中的应用研究进展.     

OAP-H2O2-HRP酶促反应产物与DNA相互作用的光谱及电化学研究

脱氧核糖核酸(DNA)是生物的基本遗传物质，对其研究是生命科学研究领域中极其重要的内容，其中有关DNA靶向分子与DNA之间相互作用的研究一直是一个比较活跃的领域，继Bard等用电化学方法对溶液中的电活性物质与DNA相互作用进行研究之后，又有许多相关的研究成果相继报道。3-氨基酚噁嗪(AP，即寻霉素A)与放线菌素D的生成有关，放线菌素D在伴随DNA指导RNA的合成中起作用，AP被用作放线菌素D的行为模型，对放线菌素D还原成1个N-10中心阴离子提供信息。     

A Personal History of Quadruplex–Small Molecule Targeting

The story behind some of the early studies in the laboratory of Stephen Neidle on quadruplex‐binding small molecules and the structural studies on quadruplexes and their complexes is presented and discussed in the context of his earlier work on drug–DNA interactions. More recent studies and future directions in the rational design of small molecules targeting telomeric and gene promoter quadruplexes are also described.     

Feeling Inter‐ or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions

Single‐molecule force spectroscopy (SMFS) opens new avenues for elucidating the structures and functions of large coiled molecules such as synthetic and biopolymers at the single‐molecule level. In addition, some of the features in the force–extension curves (i.e. force spectra) are closely related to primary/secondary structures of the molecules being stretched. For example, the long force plateau in the DNA stretching curve is related to the double‐helix structure. These features can be regarded as the force fingerprints of individual macromolecules. These force fingerprints can therefore be used as indicators/criteria of single‐molecule manipulation during the measurement of some unknown intra‐ or intermolecular interactions. By comparing the force spectra of a single polymer chain before and after interaction with other molecules, the mode/strength of such molecular interactions can be derived. This Review focuses on recent advances in AFM‐based SMFS studies on molecular interactions in both synthetic and biopolymer systems using a single macromolecular chain as probe, including interactions between nucleic acids and proteins, mechanochemistry of covalent bonds, conformation‐regulated enzymatic reactions, adsorption and desorption of biopolymers on a flat surface or from the nanopore of a carbon nanotube, and polymer interactions in the condensed state.     

Tetrapeptides induce selective recognition for G-quadruplexes when conjugated to a DNA-binding platform

3,6-Bis-peptide acridine and acridone conjugates have been designed and synthesised to selectively interact with G-quadruplex DNA. The ligand properties are peptide sequence dependent, the highest discrimination being obtained with the FRHR tetrapeptide (up to >50-fold specificity). Molecular modeling studies have helped us rationalise the data and suggest that human telomeric quadruplex DNA can readily accommodate tetrapeptides, and furthermore that FRHR contributes to stabilization of the complex by non-bonded interactions within the TTA loop pockets of the quadruplex. These studies indicate that targeting distinct features of a G-quadruplex with hybrid molecules is a promising strategy for discriminating between quadruplex and duplex DNA.     

Gemini表面活性剂(12-6-12)和DNA的相互作用

应用紫外光谱、荧光探针、zeta 电位、动态光散射和凝胶电泳等方法探讨了阳离子gemini 表面活性剂C₁₂H₂₅N⁺(CH₃)₂―(CH₂)₆―(CH₃)₂N⁺C₁₂H₂₅·2Br^-(12-6-12)与DNA之间的相互作用. 研究结果表明, 与传统表面活性剂相比, 偶联表面活性剂特殊的分子结构使其与DNA的作用更强烈. DNA引导表面活性剂在其链周围形成类胶束结构, 开始形成类胶束时对应的表面活性剂临界聚集浓度(CAC)比纯表面活性剂临界胶束浓度(CMC)低两个数量级. CAC与DNA的浓度无关, 而与表面活性剂之间的疏水作用以及表面活性剂与DNA之间的静电吸引作用密切相关. Zeta 电位和凝胶电泳结果显示了DNA链所带负电荷逐渐被阳离子表面活性剂中和的过程. 借助原子力显微镜(AFM)成功观察到了松散的线团状DNA, 球状体随机地分散在DNA链上形成类似于串珠的结构、尺寸较大的球形复合物以及其由于吸附多余的表面活性剂重新带正电而被溶解得到的较小DNA/12-6-12聚集体. 圆二色(CD)光谱结果显示, 12-6-12可以诱导DNA的构象发生改变.     

Bioactive Structure of Membrane Lipids and Natural Products Elucidated by a Chemistry‐Based Approach

Determining the bioactive structure of membrane lipids is a new concept, which aims to examine the functions of lipids with respect to their three‐dimensional structures. As lipids are dynamic by nature, their “structure” does not refer solely to a static picture but also to the local and global motions of the lipid molecules. We consider that interactions with lipids, which are completely defined by their structures, are controlled by the chemical, functional, and conformational matching between lipids and between lipid and protein. In this review, we describe recent advances in understanding the bioactive structures of membrane lipids bound to proteins and related molecules, including some of our recent results. By examining recent works on lipid‐raft‐related molecules, lipid–protein interactions, and membrane‐active natural products, we discuss current perspectives on membrane structural biology.     

Sugar–Edge Interactions in a DNA–RNA G‐Quadruplex: Evidence of Sequential C−H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding

DNA G‐quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti‐dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA–RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3′‐side within the quadruplex core strongly suggest the presence of C8?H???O hydrogen‐bonding interactions with the O2′ position of the C2′‐endo ribonucleotide. A geometric analysis of reported high‐resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.     

Differences in affinity of arylstilbazolium derivatives to tetraplex structures

Research into the interactions of small molecules (ligands) with DNA is a very important field of biochemistry. A ligand interacts with a DNA structure in many ways, depending on the structural features of the ligand (the presence of rings, substituent groups, length of bonds, etc.) or nucleic acid (number and association of strands, base sequence etc.). This study reports on an investigation of the preferential binding of arylstilbazolium ligands to a four-stranded DNA. For this purpose, an equilibrium dialysis was used. Equilibrium dialysis is a versatile method which enables many DNA structures to be investigated at the same time. A dozen different DNA structures of (single-stranded, double-stranded (duplex), triple-stranded (triplex), and four-stranded (tetraplex)) were involved in experiments with each ligand. Following the dissociation of DNA-ligand complexes by SDS, the concentration of the ligand bound was calculated from fluorescence and absorbance calibration curves. As a result, the amount of the ligand bound was directly related to the ligand-binding affinity. Equilibrium dialysis was used as a powerful tool to indicate which of the arylstilbazolium ligands investigated was the best therapeutic agent targeting G-quadruplex. Arylstilbazolium derivatives demonstrated strong interactions with the DNA samples used in the assay. The most interesting finding was a selective, preferential binding of anthryl derivative to c-MYC DNA (c-MYC is a DNA sequence that appears in an oncogene). Furthermore, as this derivative binds preferentially to one of the triplexes investigated, it can find an application in the TFO-triplex forming oligonucleotides which are used in gene therapy.     

Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids

DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T−T/U−U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.     

Bismuth Film Electrode as Sensing Platform for IgE–anti‐IgE Interactions

In this study, a bismuth film was used as a sensing platform for immunoreaction assay which includes the interactions between IgE and anti‐IgE molecules. For preparing this assay, IgE was deposited on a carbon paste electrode via bismuth(III) cations without using any membrane or functional reagent. The immobilized reagents and interaction of anti‐IgE on this formation were monitored by using atomic force microscopy technique and electrochemical impedance spectroscopy. Then some experimental parameters like the effect of IgE amount and the IgE–anti‐IgE interaction time were optimized. Under the optimal experimental conditions, the binding of anti‐IgE was also examined by following current decrease in differential pulse voltammograms of neutral red.     

Structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat: evidence for A-tetrad formation from NMR and molecular dynamics simulations

The structure of the intermolecular DNA quadruplex d(TTAGGGT)4, based on the human telomeric DNA sequence d(TTAGGG), has been determined in solution by NMR and restrained molecular dynamics simultations. The core GGG region forms a highly stable quadruplex with G-tetrads likely stabilised by K+ ions bound between tetrad plains. However, we have focused on the conformation of the adenines which differ considerably in base alignment, stability and dynamics from those in previously reported structures of d(AGGGT)4 and d(TAGGGT)4. We show unambiguously that the adenines of d(TTAGGGT)4 are involved in the formation of a relatively stable A-tetrad with well-defined glycosidic torsion angles (anti), hydrogen bonding network (adenine 6-NH2-adenine N1) defined by interbase NOEs, and base stacking interactions with the neighbouring G-tetrad. All of these structural features are apparent from NOE data involving both exchangeable and non-exchangeable protons. Thus, context-dependent effects appear to play some role in dictating preferred conformation, stability and dynamics. The structure of d(TTAGGGT)4 provides us with a model system for exploiting in the design of novel telomerase inhibitors that bind to and stabilise G-quadruplex structures.