Reversible pH Switch of Two‐Quartet G‐Quadruplexes Formed by Human Telomere

A four‐repeat human telomere DNA sequence without the 3′‐end guanine, d[TAGGG(TTAGGG)₂TTAGG] (htel1‐ΔG23) has been found to adopt two distinct two G‐quartet antiparallel basket‐type G‐quadruplexes, TD and KDH⁺ in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH⁺ form is distinctive with unique protonated T18?A20⁺?G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G‐quadruplexes in general. Specific stacking interactions amongst two G‐quartets flanking base triples and base pairs in TD and KDH⁺ forms are reflected in 10 K higher thermal stability of KDH⁺. Populations of TD and KDH⁺ forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1‐ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.     

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.     

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.     

Use of an automated capillary DNA sequencer to investigate the interaction of cisplatin with telomeric DNA sequences

The determination of the sequence selectivity of DNA-damaging agents is very important in elucidating the mechanism of action of anti-tumour drugs. The development of automated capillary DNA sequencers with fluorescent labelling has enabled a more precise method for DNA sequence specificity analysis. In this work we utilized the ABI 3730 capillary sequencer with laser-induced fluorescence to examine the sequence selectivity of cisplatin with purified DNA sequences. The use of this automated machine enabled a higher degree of precision of both position and intensity of cisplatin-DNA adducts than previously possible with manual and automated slab gel procedures. A problem with artefact bands was overcome by ethanol precipitation. It was found that cisplatin strongly formed adducts with telomeric DNA sequences.     

Naphthalene Diimides Carrying Two β-Cyclodextrins Prefer Telomere RNA G-Quadruplex Recognition

Newly synthesized naphthalene diimide carrying two β-cyclodextrins (NDI-β-CyDs) showed improved specificity for the parallel G-quadruplex structure alongside the hybrid G-quadruplex structure. Specifically, the highest binding affinity of NDI-β-CyDs for the telomere RNA G-quadruplex was observed. The binding simulation indicated that β-cyclodextrins might be available for loop nucleobase inclusion under its complex.     

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.