溴化乙锭标记DNA电化学探针的研究

以乙基-(3-二甲基丙基)碳化二亚胺盐酸盐(EDC)为偶联活化剂,将电化学活性物质溴化乙锭(Ethidiumbromide,EB)成功地标记在人工合成的含有21个碱基的寡聚DNA片段上,制备成EB标记DNA探针;用电化学方法将待测样品DNA片段固定在石墨电极表面,在一定的温度、pH值和离子强度条件下与EB标记DNA探针进行杂交反应,从而对靶序列DNA片段进行识别和测定.此外,还讨论了该探针的电化学性质、荧光光谱、待测DNA片段在石墨电极表面的电化学固定、DNA链碱基长度对EB标记DNA电化学探针的影响以及探针的选择性、重现性和寿命,结果令人满意.     

吖啶黄与脱氧核糖核酸加成反应机理及其在微量DNA测定中的应用

研究了微量脱氧核糖核酸与吖啶黄的加成反应,并对反应条件作了优化,基于在pH6.5的B-R缓冲溶液中,脱氧核糖核酸(DNA)浓度与吖啶黄最大吸收波长444 nm处的吸光度线性降低的关系,建立了测定微量DNA的方法。在小于8.0 mg.L-1浓度范围内呈现良好的线性关系,相关系数为0.999 8,对3个模拟试样中DNA含量作了测定,结果的RSD值及回收率的测定结果分别在1.4%~3.0%及98.3%~104.0%之间。对此加成反应的机理也作了初步探讨。     

荧光染料探针与脱氧核糖核酸作用机理研究

核酸与各类物质的相互作用与探测核酸的结构与功能密切相关,是揭示核酸的生物功能和一些药物的作用机制的重要途径。本文研究了染料ZR、甲酚红、苏木色精等DNA的作用,给出它们在不同结合数下的生成常数。此外,还求取了它们的能量转移效率,给体－受体之间的距离。     

Ethidium Binding to Salmonella enterica ser. Typhimurium Cells and Salmon Sperm DNA

Bacterial resistance to antibiotics due to increased efficiency of the efflux is a serious problem in clinics of infectious diseases. Knowledge of the factors affecting the activity of efflux pumps would help to find the solution. For this, fast and trustful methods for efflux analysis are needed. Here, we analyzed how the assay conditions affect the accumulation of efflux indicators ethidium (Et⁺) and tetraphenylphosphonium in Salmonella enterica ser. Typhimurium cells. An inhibitor phenylalanyl-arginyl-β-naphtylamide was applied to evaluate the input of RND family pumps into the total efflux. In parallel to spectrofluorimetric analysis, we used an electrochemical assessment of Et⁺ concentration. The results of our experiments indicated that Et⁺ fluorescence increases immediately after the penetration of this indicator into the cells. However, when cells bind a high amount of Et⁺, the intensity of the fluorescence reaches the saturation level and stops reacting to the accumulated amount of this indicator. For this reason, electrochemical measurements provide more trustful information about the efficiency of efflux when cells accumulate high amounts of Et⁺. Measurements of Et⁺ interaction with the purified DNA demonstrated that the affinity of this lipophilic cation to DNA depends on the medium composition. The capacity of DNA to bind Et⁺ considerably decreases in the presence of Mg²⁺, Polymyxin B or when DNA is incubated in high ionic strength media.     

Optical,Redox, and DNA‐Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA

The phenanthridinium chromophores 5‐ethyl‐6‐phenylphenanthridinium ( 1 ), 5‐ethyl‐6‐methylphenanthridinium ( 2 ), 3,8‐diamino‐5‐ethyl‐6‐methylphenanthridinium ( 3 ), and 3,8‐diamino‐5‐ethyl‐6‐(4‐N,N‐diethylaminophenyl)phenanthridinium ( 4 ) were characterized by their optical and redox properties. All dyes were applied in titration experiments with a random‐sequence 17mer DNA duplex and their binding affinities were determined. The results were compared to well‐known ethidium bromide ( E ). In general, this set of data allows the influence of substituents in positions 3, 6, and 8 on the optical properties of E to be elucidated. Especially, compound 4 was used to compare the weak electron‐donating character of the phenyl substituent at position 6 of E with the more electron‐donating 4‐N,N‐diethylaminophenyl group. Analysis of all of the measurements revealed two pairs of chromophores. The first pair, consisting of 1 and 2 , lacks the amino groups in positions 3 and 8, and, as a result, these dyes exhibit clearly altered optical and electrochemical properties compared with E . In the presence of DNA, a significant fluorescence quenching was observed. Their binding affinity to DNA is reduced by nearly one order of magnitude. The electronic effect of the phenyl group in position 6 on this type of dye is rather small. The properties of the second set, 3 and 4 , are similar to E due to the presence of the two strongly electron‐donating amino groups in positions 3 and 8. However, in contrast to 1 and 2 , the electron‐donating character of the substituent in position 6 of 3 and 4 is critical. The binding, as well as the fluorescence enhancement, is clearly related to the electron‐donating effect of this substituent. Accordingly, compound 4 shows the strongest binding affinity and the strongest fluorescence enhancement. Quantum chemical calculations reveal a general mechanism related to the twisted intramolecular charge transfer (TICT) model. Accordingly, an increase of the twist angle between the phenyl ring in position 6 and the phenanthridinium core opens a nonradiative channel in the excited state that depends on the electron‐donating character of the phenyl group. Access to this channel is hindered upon binding to DNA.     

Self‐Assembled Multilayers of Polyethylenimine and DNA: Spectrophotometric and Electrochemical Characterization and Application for the Determination of Acridine Orange Interaction

This work deals with the study of the interaction between acridine orange (AO) and calf‐thymus double stranded DNA (dsDNA) present in supramolecular architectures built on gold electrodes modified with mercapto‐1‐propanesulfonic acid (MPS) by self‐assembling of polyethylenimine and dsDNA. The optimal conditions for building the supramolecular architecture were obtained from UV‐vis spectrophotometric experiments. The electrochemical studies were performed by adsorptive transfer square wave voltammetry from the evaluation of the oxidation signal of AO accumulated within the multistructure. The effect of the number of PEI‐dsDNA bilayers (Au/MPS/(PEI‐dsDNA)_n) on the accumulation and electrooxidation of AO is also discussed.     

吖啶-多胺类缀合物的合成、 抗肿瘤活性及与DNA键合作用

设计合成了系列吖啶-多胺类衍生物(ACP1~ACP6), 并通过四甲基偶氮唑蓝(MTT)染色法研究了化合物对K562(人白血病细胞)、 A549(人肺癌细胞)和Hela(人宫颈癌细胞)细胞株的体外抗肿瘤活性. 结果显示, 化合物对肿瘤细胞具有一定的抑制作用, 尤其是化合物ACP2的抗肿瘤活性优于阳性对照顺铂. 通过UV-Vis光谱、 荧光光谱、 圆二色谱和热变性实验研究了合成化合物与小牛胸腺DNA(Ct-DNA)的键合作用. 结果表明, 三乙烯四胺修饰的化合物ACP2具有较好的抗肿瘤活性, 与DNA分子具有较强的结合能力.     

Study of interactions between DNA-ethidium bromide (EB) and DNA-acridine orange (AO), in solution, using hanging mercury drop electrode (HMDE)

The interaction of ethidium bromide (EB) and acridine orange (AO) with double stranded (ds), thermally denatured (ss) and supercoiled (sc) DNA, in solution, was studied by alternating current voltammetry (AC voltammetry) at the hanging mercury drop electrode (HMDE) in 0.3 M NaCl+50 mM sodium phosphate buffer (pH 8.5). Their interaction with DNA is shown to be time dependent and completely different. The changes at peak 2 (peak at −1.20 V) of dsDNA form and the appearance of peak 3 (peak at −1.42 V) in scDNA form are presented as criteria declaring the different mechanism of interaction of EB and AO with DNA. Additionally, the appearance of a new peak at around −0.44 V as a result of DNA and AO interaction, differentiates the studied behaviors. The comparison of the electrochemical behaviors of these compounds highlights the differences in the mechanism of interaction.     

A TriPPPro-Nucleotide Reporter with Optimized Cell-Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells

The metabolic labeling of nucleic acids in living cells is highly desirable to track the dynamics of nucleic acid metabolism in real-time and has the potential to provide novel insights into cellular biology as well as pathogen-host interactions. Catalyst-free inverse electron demand Diels–Alder reactions (iEDDA) with nucleosides carrying highly reactive moieties such as axial 2-trans-cyclooctene (2TCOa) would be an ideal tool to allow intracellular labeling of DNA. However, cellular kinase phosphorylation of the modified nucleosides is needed after cellular uptake as triphosphates are not membrane permeable. Unfortunately, the narrow substrate window of most endogenous kinases limits the use of highly reactive moieties. Here, we apply our TriPPPro (triphosphate pronucleotide) approach to directly deliver a highly reactive 2TCOa-modified 2′-deoxycytidine triphosphate reporter into living cells. We show that this nucleoside triphosphate is metabolically incorporated into de novo synthesized cellular and viral DNA and can be labeled with highly reactive and cell-permeable fluorescent dye-tetrazine conjugates via iEDDA to visualize DNA in living cells directly. Thus, we present the first comprehensive method for live-cell imaging of cellular and viral nucleic acids using a two-step labeling approach.     

Construction of Organelle-Like Architecture by Dynamic DNA Assembly in Living Cells

The design of controllable dynamic systems is vital for the construction of organelle-like architectures in living cells, but has proven difficult due to the lack of control over defined topological transformation of self-assembled structures. Herein, we report a DNA based dynamic assembly system that achieves lysosomal acidic microenvironment specifically inducing topological transformation from nanoparticles to organelle-like hydrogel architecture in living cells. Designer DNA nanoparticles are constructed from double-stranded DNA with cytosine-rich stick ends (C-monomer) and are internalized into cells through lysosomal pathway. The lysosomal acidic microenvironment can activate the assembly of DNA monomers, inducing transformation from nanoparticles to micro-sized organelle-like hydrogel which could further escape into cytoplasm. We show how the hydrogel regulates cellular behaviors: cytoskeleton is deformed, cell tentacles are significantly shortened, and cell migration is promoted.     

Chromophore-Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells

The spatial arrangement of chromosome within the nucleus is linked to genome function and gene expression regulation. Existing genome-wide mapping methods often rely on chemically crosslinking DNA with protein baits, which raises concerns of artifacts being introduced during cell fixation. By genetically targeting a photosensitizer protein to specific subnuclear locations, we achieved blue-light-activated labeling of local DNA with a bioorthogonal functional handle for affinity purification and sequence identification through next-generation sequencing. When applied to the nuclear lamina in human embryonic kidney 293T cells, it revealed lamina-associated domains (LADs) that cover 37.6 % of the genome. These LADs overlap with heterochromatin hallmarks and are depleted with CpG islands. This simple labeling method avoids the harsh treatment of chemical crosslinking and is generally applicable to the genome-wide high-resolution mapping of the spatial chromosome organization in living cells.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

吖啶橙染料在表面活性剂存在时溶液状态的光谱研究

应用紫外－可见吸收光谱和荧光光谱，研究了激光染料吖淀橙（ＡＯ）的溶液状态以及添加表面活性剂时吖啶橙染料的溶液状态变化，并应用Ｋａｓｈａ理论推算出二聚体时的状态，结果表明：在吖啶橙溶液中，ＡＯ二聚体的α＝４９°，ｒ＝１．３９ｎｍ。     

Determination of Sodium Hexametaphosphate in Beverages Based on the Fluorescence Quenching of Acridine Orange

Sodium hexametaphosphate was shown to form a complex with acridine orange by electrostatic interactions that induce fluorescence quenching. Analysis of fluorescence intensity showed that the process was dominated by static quenching, which was confirmed by absorption spectra and lifetime of the excited state. The decreased fluorescence intensity was directly proportional to the concentration of sodium hexametaphosphate between 8.0 × 10^?7 and 1.1 × 10^?5 mol L^?1 with a limit of detection of 5.3 × 10^?7 mol L^?1. Beverages were analyzed for sodium hexametaphosphate with recoveries between 91.7% and 108.3%.     

荧光光谱法研究核黄素与鲱鱼精DNA的相互作用

在B-R缓冲溶液中, 以吖啶橙(AO)作荧光探针研究了核黄素(RF)与DNA的相互作用. 在pH值为7.25时, 荧光光谱研究表明, RF与DNA发生作用生成了复合物, 其结合比为n_RF∶n_DNA＝5∶1, 28 ℃时RF与DNA的结合常数K＝2.53×10⁶ L/mol; 并运用双倒数法求得RF与DNA相互作用的 为－6.06×10⁴ J/mol, 为－78.70 J/(mol•K), 28 ℃时的 为－3.69×10⁴ J/mol. 同时通过粘度法、盐效应和Scatchard法等研究了RF与DNA的作用方式, 确定了在该实验条件下RF与鲱鱼精DNA之间主要为沟面和静电作用方式.     

A Telomerase-Assisted Strategy for Regeneration of DNA Nanomachines in Living Cells

DNA nanomachines have been engineered into diverse personalized devices for diagnostic imaging of biomarkers; however, the regeneration of DNA nanomachines in living cells remains challenging. Here, we report an ingenious DNA nanomachine that can implement telomerase (TE)-activated regeneration in living cells. Upon apurinic/apyrimidinic endonuclease 1 (APE1)-responsive initiation of the nanomachine, the walker of the nanomachine moves along tracks regenerated by TE, generating multiply amplified signals through which APE1 can be imaged in situ. Additionally, augmentation of the signal due to the regeneration of the nanomachines could reveal differential expression of TE in different cell lines. To the best of our knowledge, this is the first proof-of-concept demonstration of the use of biomarkers to assist in the regeneration of nanomachines in living cells. This study offers a new paradigm for the development of more applicable and efficient DNA nanomachines.     

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.     

Synthesis and Evaluation of Europium Complexes that Switch on Luminescence in Lysosomes of Living Cells

A set of four luminescent Eu^III complexes bearing an extended aryl-alkynylpyridine chromophore has been studied, showing very different pH-dependent behaviour in their absorption and emission spectral response. For two complexes with pK_a values of 6.45 and 6.20 in protein-containing solution, the emission lifetime increases very significantly following protonation. By varying the gate time during signal acquisition, the ‘switch-on’ intensity ratio could be optimised, and enhancement factors of between 250 to 1330 were measured between pH 8 and 4. The best-behaved probe showed no significant emission dependence on the concentration of endogenous cations, reductants, and serum albumin. It was examined in live-cell imaging studies to monitor time-dependent lysosomal acidification, for which the increase in observed image brightness due to acidification was a factor of 50 in NIH-3T3 cells.     

Spectral Studies on the Binding Behavior of Cationic Dyes and Surfactants with Bacterial Polysaccharide of Klebsiella K43

The binding behavior of acidic capsular polysaccharide (SPS), isolated from Klebsiella serotype K43, with oppositely charged dyes and surfactants have been studied by way of absorbance and emission spectroscopic measurements. Each repeating unit of the SPS consists of three D-mannose, one D-galactose, and one D-glucuronic acid residue. The anionic polysaccharide exhibited chromotropic character and induced strong metachromasy in the cationic dye, pinacyanol chloride (PCYN) through the formation of a 1:1 stoichiometric complex. Evaluation of thermodynamic parameters, viz., changes in free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), for the formation of dye-polymer complex and studies on the effect of different cosolvents were also evaluated to shed light on the binding nature as well as the extent of stability of the dye-polymer complex. Fluorescence of the cationic dye acridine orange (AO) was quenched with the progressive addition of SPS, which was found to be of Stern-Volmer type. Cationic surfactants in their pure form as well as in the mixed state with nonionic surfactant (Tween-20), replaced the dye bound to the polymer matrices; thus the original band intensities of the dyes could be reverted. Such studies revealed the involvement of both electrostatic as well as hydrophobic interactions between the dye-polymer as well as surfactant-polymer aggregates.