G-四链体-氯化血红素DNA酶在传感器设计中的应用

G-四链体-氯化血红素(hemin)DNA酶是一种由特定的核酸G-四链体与hemin结合后形成的具有过氧化物酶活性的人工模拟酶。作为一类重要的DNA酶,G-四链体-hemin DNA酶近年来在分析化学领域受到了越来越多的关注。目前这类DNA酶已被用在了多种传感器,包括金属离子传感器、适配体传感器、酶传感器、DNA传感器及药物传感器的设计当中。本文对G-四链体-hemin DNA酶在传感器设计中的应用进行了系统的介绍和评述,并对其未来的发展进行了初步的展望。     

色胺修饰竹红菌素及其稀土离子配位聚合物与DNA相互作用研究

利用紫外-可见吸收光谱、荧光光谱、圆二色谱(CD)等方法研究了色胺修饰竹红菌素(DTrpHA)及其稀土离子配位聚合物(Y³⁺-DTrpHA, La³⁺-DTrpHA)与小牛胸腺DNA (CT DNA)和G-四链体22AG的相互作用.结果表明, DTrpHA及其配位聚合物中的色胺基团和竹红菌素基团均参与和双链CT DNA的作用,作用方式主要为沟槽作用.与G-四链体DNA作用后, DTrpHA及其配位聚合物中的色胺基团均具有较大的减色效应(> 45%)和峰位红移(≥ 4 nm),说明色胺基团与G-四链体采用外部堆积作用方式结合;而竹红菌素基团的减色效应相对较小且无明显峰位变化,表明竹红菌素基团采用非特异性作用方式与G-四链体的环区碱基或糖-磷酸骨架结合. G-四链体22AG的构象主要为分子内反平行结构,加入DTrpHA及其配位聚合物对G-四链体22AG的构象影响较小. Y³⁺-DTrpHA比DTrpHA和La³⁺-DTrpHA与G-四链体具有更强的相互作用. Y³⁺-DTrpHA使得CT DNA的熔解温度(T_m)上升了仅1.9 ℃,而使G-四链体的熔解温度上升了13.1 ℃.荧光嵌插剂置换实验 (FID)结果表明, Y³⁺-DTrpHA对G-四链体具有良好亲和性,具有较小的^G4DC₅₀值(使噻唑橙/G-四链体体系荧光下降50%所需配体或配合物的浓度)和较高的G-四链体选择性.     

血红素/G-四链体DNA酶的活性增强研究及其在生物传感器中的应用进展

血红素/G-四链体DNA酶是一类具有类过氧化物酶活性的DNA分子,因其具有出色的活性、易修饰性和可编程性,被广泛应用于生物传感器等领域。 本文先是简要介绍了G-四链体的结构,再主要综述了增强血红素/G-四链体DNA酶活性的策略及基于血红素/G-四链体DNA酶的生物传感器在生物标志物、微生物与生物毒素以及金属离子检测中的应用,并展望了血红素/G-四链体DNA酶的未来发展趋势。     

人体端粒中(3+1)混合结构G-四链体稳定性的分子动力学模拟

利用分子动力学模拟方法, 考察了人体端粒中(3+1)混合结构G-四链体的结构及稳定性问题. 讨论了配位K+离子、药物分子(端粒抑素)和溶剂水分子对G-四链体的Hoogsteen氢键结构、π-π堆积作用的影响. 研究表明, K+离子与鸟嘌呤碱基上O6原子的配位作用减弱了对角鸟嘌呤间O6-O6的静电排斥作用, 使得相邻的四个鸟嘌呤能够以Hoogsteen氢键结合的方式形成具有近平面结构的稳定G-四平面. 另一方面, G-四平面间、G-四平面与药物分子间的π-π堆积作用降低了G-四链体复合物的总能, 有利于其稳定存在. 此外, 溶剂水分子主要分布在G-四链体的TTA环、骨架和糖环的周围, 使其位移涨落增大; 然而, 在3 ns动力学模拟中, 由于水分子没有进入到G-四链体的空腔中, 溶剂水对G-四平面的结构影响不明显.     

钌配合物与G-四链体DNA的相互作用研究进展

人体端粒由富含鸟嘌呤(G)的DNA重复序列组成,该序列在一定条件下可以形成G-四链体DNA结构。小分子化合物诱导该结构的形成并使之稳定,可以抑制端粒酶活性而达到抗肿瘤的目的。因此,G-四链体DNA稳定剂的设计和筛选是近年来生物无机化学的重要前沿研究领域之一。在金属配合物中,钌配合物由于具有丰富的光化学、光物理特性以及生物活性,其作为G-四链体DNA稳定剂引起人们的高度关注。本文以近年一些代表性的研究工作为例,对钌配合物与G-四链体DNA相互作用方面的研究进展进行了综述。     

利用对G-四链体环部的构型调节进行传感器的设计

对鸟嘌呤碱基G重复序列之间连接环结构对G-四链体形成的影响进行了研究。发现在连接环较长,DNA链不易形成G-四链体的情况下,可以通过将环序列设计成双链结构的方式促进G-四链体的重新形成。这就为传感器的设计提供了一个新途径,即可以利用目标分子对环部双链的调节作用控制G-四链体DNA酶的活性。为证明这一点,在双链区域引入T-T碱基错配,破坏双链结构使DNA链不能形成G-四链体。Hg2+对T-T错配的稳定作用可以促进双链结构的形成,DNA链重新折叠成G-四链体,得到的G-四链体与氯化血红素(Hemin)结合后形成具有过氧化物酶活性的G-四链体DNA酶,据此构建了Hg2+传感器。利用此传感器可在10~700 nmol/L范围内实现Hg2+的定量检测,检出限为8.7 nmol/L。在此基础上,利用半胱氨酸可以将Hg2+从T-Hg2+-T碱基对上竞争下来的能力,设计了一种半胱氨酸的检测方法。此方法可以在20~600 nmol/L范围内实现半胱氨酸的定量检测,检出限为14 nmol/L。     

分子内裂分G-四链体脱氧核糖核酸酶用于Hg2+的特异性定量检测

G-四链体DNA酶是由核酸G-四链体与氯化血红素(Hemin)结合后形成的一种具有过氧化物酶活性的人工酶,利用这种DNA酶,可进行多种化学及生物传感器的设计。为提高G-四链体DNA酶类Hg2+传感器的选择性,本研究在传感器的设计过程中引入了分子内裂分G-四链体,即将形成G-四链体的富G序列拆分成两部分,分别放置在Hg2+探测序列的两端。在无Hg2+存在时,部分富G序列被包埋在某一分子内二倍体结构中,无法形成G-四链体。而在Hg2+存在下,Hg2+对T-T碱基错配的稳定能力可以促使Hg2+探测序列形成分子内二倍体结构,并伴随着原有分子间二倍体结构的破坏及分子内裂分G-四链体的生成。利用生成的裂分G-四链体与Hemin作用后检测体系酶活性的提高,实现Hg2+传感器的设计。利用该传感器,可在50～500 nmol/L及2.0～7.5μmol/L两个浓度范围内实现Hg2+的定量检测,检出限为47 nmol/L。由于裂分G-四链体DNA酶的使用强化了传感器对Hg2+的依赖性,极大地提高了设计的Hg2+传感器的选择性。对实际水样的加标回收结果显示,回收率为97.5%～104.5%,证明此传感器可以满足实际水样中痕量Hg2+的分析要求。     

Loop长度对G-四链体DNA识别和结合肿瘤细胞的能力的影响

G-四链体是由富含鸟嘌呤(G)的核酸通过π-π堆积形成的核酸二级结构.前期研究发现,G-四链体DNA对肿瘤细胞具有普遍识别和结合能力,且具有如抗肿瘤增殖等生物学活性,但G-四链体DNA的结构对其识别和结合肿瘤细胞的能力的影响还未见报道.本文采用圆二色光谱和凝胶电泳对不同连接环(loop)长度G-四链体DNA的结构和稳定...     

靶向G-四链体的小分子配体在癌症治疗中应用的研究进展

G-四链体是一类由Hoogsteen氢键维持稳定的,富含鸟嘌呤的DNA或RNA二级结构。人类基因组中存在大量潜在的形成G-四链体的序列,所形成的G-四链体结构能够调控基因组的稳定性、DNA复制和基因表达,其中包括很多与癌症相关基因。因此寻找能够诱导DNA的G富集区域形成G-四链体结构的配体,进而筛选潜在抗癌药物的先导化合物,已成为癌症治疗研究的热点之一。本文对近年来发现和设计的以G-四链体为靶点的小分子配体,按照靶向的G-四链体结构类型和配体的分子结构进行分类,综述了这类化合物在癌症治疗方面的研究进展,分析了相关靶向治疗存在的问题,并对未来的研究方向进行了展望。     

G-四链体DNA稳定剂的研究进展

人体端粒由富含鸟嘌呤(G)的DNA重复序列组成,该序列在一定的条件下可以形成G-四链体DNA的结构.小分子化合物诱导该结构的形成并使之稳定,不但可以抑制端粒酶的活性或降低癌基因的转录表达而达到抗肿瘤的目的,还可以作为G-四链体DNA的探针,辅助G-四链体DNA生物功能的研究及与之相关疾病的诊断.因此,G-四链体DNA稳定剂的设计是近年来化学生物学的重要前沿领域之一.到目前为止,G-四链体DNA稳定剂主要可分为有机小分子化合物和金属配合物.本文重点综述这两方面特别是后者的最新研究进展.     

Small change in a G-rich sequence,a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations

NMR study has shown that DNA oligonucleotide d(G(3)T(4)G(4)) adopts an asymmetric bimolecular G-quadruplex structure in solution. The structure of d(G(3)T(4)G(4))(2) is composed of three G-quartets, overhanging G11 residue and G3, which is part of the loop. Unique structural feature of d(G(3)T(4)G(4))(2) fold is the orientation of the two loops. Thymidine residues T4-T7 form a diagonal loop, whereas T15-T18 form an edge type loop. The G-quadruplex core of d(G(3)T(4)G(4))(2) consists of two stacked G-quartets with syn-anti-anti-anti alternation of dG residues and one G-quartet with syn-syn-anti-anti alternation. Another unusual structural feature of d(G(3)T(4)G(4))(2) is a leap between G19 and G20 over the middle G-quartet and chain reversal between G19 and G20 residues. The presence of one antiparallel and three parallel strands reveals the hitherto unknown G-quadruplex folding motif consisting of antiparallel/parallel strands and diagonal as well as edge type loops. Further examination of the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)) showed that it forms a bimolecular G-quadruplex in the presence of K+, Na+, and NH4+ ions with the same general fold.     

Insight into How Telomeric G‐Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin

The toxic oxidative damage of G‐quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label‐free and nanopore‐based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)_n). The nanopore‐based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single‐molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (K_a)≈10⁶ m ^?1) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of K_a to approximately 10⁷ m ^?1. Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π–π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H₂O₂ in the catalytic cycle. Our studies developed a label‐free and single‐molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative‐damage property in cellular oxidative disease and anticancer therapeutics.     

Exploring the Parallel G-Quadruplex Nucleic Acid World: A Spectroscopic and Computational Investigation on the Binding of the c-myc Oncogene NHE III1 Region by the Phytochemical Polydatin

Trans-polydatin (tPD), the 3-β-D-glucoside of the well-known nutraceutical trans-resveratrol, is a natural polyphenol with documented anti-cancer, anti-inflammatory, cardioprotective, and immunoregulatory effects. Considering the anticancer activity of tPD, in this work, we aimed to explore the binding properties of this natural compound with the G-quadruplex (G4) structure formed by the Pu22 [d(TGAGGGTGGGTAGGGTGGGTAA)] DNA sequence by exploiting CD spectroscopy and molecular docking simulations. Pu22 is a mutated and shorter analog of the G4-forming sequence known as Pu27 located in the promoter of the c-myc oncogene, whose overexpression triggers the metabolic changes responsible for cancer cells transformation. The binding of tPD with the parallel Pu22 G4 was confirmed by CD spectroscopy, which showed significant changes in the CD spectrum of the DNA and a slight thermal stabilization of the G4 structure. To gain a deeper insight into the structural features of the tPD-Pu22 complex, we performed an in silico molecular docking study, which indicated that the interaction of tPD with Pu22 G4 may involve partial end-stacking to the terminal G-quartet and H-bonding interactions between the sugar moiety of the ligand and deoxynucleotides not included in the G-tetrads. Finally, we compared the experimental CD profiles of Pu22 G4 with the corresponding theoretical output obtained using DichroCalc, a web-based server normally used for the prediction of proteins’ CD spectra starting from their “.pdb” file. The results indicated a good agreement between the predicted and the experimental CD spectra in terms of the spectral bands’ profile even if with a slight bathochromic shift in the positive band, suggesting the utility of this predictive tool for G4 DNA CD investigations.     

Enantioselective Diels–Alder reactions with left-handed G-quadruplex DNA-based catalysts

Since the discovery of left-handed G-quadruplex (L-G4) structure formed by natural DNA, there has been a growing interest in its potential functions. This study utilised it to catalyse enantioselective Diels-Alder reactions, considering its different optical rotation compared to an ordinary G4. It was determined that when L-G4 was used with a combination of copper(II) ions, there was a good enantioselectivity (?52% ee) without further addition of ligands. When further consideration was given by adding G4 ligands, G4 was further stabilised, even obtaining a better enantioselectivity (up to ?80% ee). Moreover, when using ligands that have regulatory effects on G4, the ee value can be adjusted. In this work, a minimal left-handed G4 was reported. A follow-up study was also conducted, which recovers that the minimal left-handed G4 remains its catalytic effect and enantioselectivity, but is not so effective as the former case. This indicates that a complete G4 structure is relatively conducive to chiral catalysis.     

Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra

The infrared (IR) and vibrational circular dichroism (VCD) spectra of guanosine-5'-hydrazide ( G-1), a powerful hydrogelator, have been measured and analyzed on the basis of ab initio modeling. B3LYP/6-31G** DFT calculations predict that G-1, forming a clear solution in deuterated DMSO, is present in monomeric form in this solvent, whereas strong gelation in a phosphate buffer is due to the formation of a guanine-quartet structure, ( G-1)4, in which the four G-1 are linked by hydrogen-bonded guanine moieties and stabilized by an alkali metal cation. The B3LYP/6-31G** IR and VCD spectra of the nearly planar G-quartet, whose structure is slightly distorted from the C4h symmetry, in which the G-bases interact via four Hoogsteen-type hydrogen bonds and a sodium cation is positioned in the middle of the G-quartet, are in very good agreement with the experimental spectra, indicating that this structure is the predominant structure in the gel state. The geometric parameters are discussed. This study is the first to use IR and VCD spectroscopies coupled with DFT calculations to elucidate the structure of a supramolecular species in a gel state and shows the VCD spectroscopy as a powerful method for investigating the structure of complex supramolecular self-assemblies where the use of other structural methods is limited.     

Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes

G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavage and/or modification of G4s by functional-NDIs. This is the case of NDI-Cu-DETA, a copper(II) complex able to cleave G4s in the closest proximity to the target binding site. Herein, we present two original Cu(II)-NDI complexes, inspired by NDI-Cu-DETA, differently functionalized with 2-(2-aminoethoxy)ethanol side-chains, to selectively drive redox-catalyzed activity towards parallel G4s. The selective interaction toward parallel G4 topology, controlled by the presence of 2-(2-aminoethoxy)ethanol side chains, was already firmly demonstrated by us using core-extended NDIs. In the present study, the presence of protonable moieties and the copper(II) cavity, increases the binding affinity and specificity of these two NDIs for a telomeric RNA-G4. Once defined the copper coordination relationship and binding constants by competition titrations, ability in G4 stabilization, and ROS-induced cleavage were analyzed. The propensity in the stabilization of parallel topology was highlighted for both of the new compounds HP2Cu and PE2Cu. The results obtained are particularly promising, paving the way for the development of new selective functional ligands for binding and destructuring parallel G4s.     

Assessing The Key Photophysical Properties of Triangulenium Dyes for DNA Binding by Alteration of the Fluorescent Core

Four-stranded G-quadruplex (G4) DNA is a non-canonical DNA topology that has been proposed to form in cells and play key roles in how the genome is read and used by the cellular machinery. Previously, a fluorescent triangulenium probe ( DAOTA-M2 ) was used to visualise G4s in cellulo, thanks to its distinct fluorescence lifetimes when bound to different DNA topologies. Herein, the library of available triangulenium probes is expanded to explore how modifications to the fluorescent core of the molecule affect its photophysical characteristics, interaction with DNA and cellular localisation. The benzo-bridged and isopropyl-bridged diazatriangulenium dyes, BDATA-M2 and CDATA-M2 respectively, featuring ethyl-morpholino substituents, were synthesised and characterised. The interactions of these molecules with different DNA topologies were studied to determine their binding affinity, fluorescence enhancement and fluorescence lifetime response. Finally, the cellular uptake and localisation of these optical probes were investigated. Whilst structural modifications to the triangulenium core only slightly alter the binding affinity to DNA, BDATA-M2 and CDATA-M2 cannot distinguish between DNA topologies through their fluorescence lifetime. It is argued theoretically and experimentally that this is due to reduced effectiveness of photoinduced electron transfer (PET) quenching. This work presents valuable new evidence into the critical role of PET quenching when using the fluorescence lifetime of triangulenium dyes to discriminate G4 DNA from duplex DNA, highlighting the importance of fine tuning redox and spectral properties when developing new triangulenium-based G4 probes.     

Separation of Trp-Arg and Arg-Trp using G-quartet-forming DNA oligonucleotides in open-tubular capillary electrochromatography

DNA oligonucleotides that form intramolecular G-quartet structures were investigated as stationary phase reagents for separation of mixtures of the isomeric dipeptides Trp-Arg and Arg-Trp in open-tubular capillary electrochromatography (OTCEC). The oligonucleotides included a thrombin-binding aptamer that forms a biplanar G-quartet structure and an oligonucleotide that forms a 4-plane G-quartet structure. Fluorescence, circular dichroism and UV-visible absorbance spectroscopies were used in batch solution studies to indicate interactions between the dipeptides and the biplanar G-quartet structure. Results for OTCEC separations were compared with results obtained for capillary zone electrophoresis separations on a bare capillary. Temperature studies suggest that resolution is improved when the G-quartet structure is partially destabilized, but control experiments in which potassium chloride was not included in the mobile phase indicate that the G-quartet structure nevertheless plays a role in the separations.     

硫黄素T与侧翼连接双链DNA的G-四链体高特异性作用

富G碱基的DNA序列在离子诱导下可形成G-四链体(G4),基于这一构型转化设计了大量的传感检测平台。其中的荧光检测平台是基于G4与荧光小分子的相互作用。但是,G4与荧光小分子的有效结合依赖于G4构型和体系中存在的离子种类和离子浓度,尤其是高Na⁺浓度(140 mmol·L^-1)。那么如何实现G4与荧光小分子普适性地有效结合,并不依赖于体系中的Na⁺和Na⁺浓度,是一个难题。在本研究中,以最简单的富G DNA序列凝血酶适体链TBA (thrombin binding aptamer)为例,在3’端和5’端分别增加10个碱基(TBA-10 bp),K⁺诱导TBA-10 bp形成K⁺稳定TBA (K⁺-TBA,G4)并衔接含有10个互补碱基对的双链DNA (K⁺-TBA-10 bp)。相较于K⁺-TBA,硫磺素T与K⁺-TBA-10 bp结合后的荧光强度增加了100倍,相互作用强度增加了1000倍,而且与体系中的Na⁺ (5-140 mmol·L^-1)无关。结合荧光光谱,紫外吸收光谱和圆二色光谱发现硫磺素T特异性的嵌合于K⁺-TBA和双链DNA衔接处的空腔内。有趣的是,这一结合模式不受G4构型的影响。该研究结果为研究G4与荧光小分子的有效结合提供了新视角,也为拓展G4在生物功能和生化检测领域的应用提供了实验依据。