A Carbazole Derivative Synthesis for Stabilizing the Quadruplex Structure

A new molecule of 3,6‐Bis(1‐methyl‐4‐vinylpyridium iodine)carbazole ( BMVC ) was synthesized for stabilizing the quadruplex structure of human telomeric sequence of d(T₂AG₃)₄ in vitro. Mixing BMVC with the DNA can raise the melting temperature of the d(T₂AG₃)₄ by ～ 13 °C, implying that BMVC could be a useful telomerase inhibitor. In addition, the fluorescence of the BMVC increased significantly upon interacting with the d(T₂AG₃)₄ which may be useful as a G‐quadruplex specific marker.     

Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T

The interactions between human telomere sequence and a typical highly selective G-quadruplex ligand ThT were studied at the single-molecule level through α-hemolysin protein nanopore.     

基于磁性微球的无标记化学发光端粒传感新技术

近年来无标记型DNA传感技术的研究已成为病原基因测定和基因疾病诊断等领域新的研究热点之一. 基于磁性微球分离和富集的方法, 建立了一种新型的无标记化学发光检测技术, 并成功地应用于特定序列DNA——端粒的检测. 首先采用dT₂₀修饰的磁性微球, 与连接有dA₂₀的捕获探针DNA杂交, 然后再与端粒进行第二步杂交反应. 磁性分离洗涤后, 利用端粒中富含的G碱基与3,4,5-三甲氧基苯乙二醛反应产生特异性化学发光, 从而实现特定序列 DNA——端粒的无标记检测. 实验结果表明: 该法具有操作简便、分析快速、灵敏度高、专属性好等特点. 目标DNA浓度在5×10^－9～1×10^－7 mol/L浓度范围内具有良好的线性关系, 相关系数为0.9918.     

线性DNA复制后5′端空缺的填补

介绍了近年来线性DNA复制后5′端空缺填补问题的研究进展及其在控制细胞的衰老、癌变等方面的重要作用。对5′端空缺填补的问题，认为不论何种填补方式，DNA都是通过特殊的末端顺序，在3′端形成模板引物结构而完成空缺的填补。     

Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.     

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence {"type":"entrez-nucleotide","attrs":{"text":"T30695","term_id":"612793"}}T30695 (5′TGGGTGGGTGGGTGGG3′), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.     

Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome)

Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases.