A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay

Protein in, DNA out: A "binding-induced molecular translator" is able to convert an input target protein into an output DNA that can be readily detected and potentially be used to assemble DNA nanodevices. Successful molecular translation is mediated by binding-induced DNA assembly on a gold nanoparticle (AuNP) scaffold, thereby achieving efficient target-dependent strand displacement.     

基于DNA四面体纳米结构探针的电化学生物传感器检测DNA甲基化

该文以DNA四面体纳米结构探针(TSP)为捕获探针,将辣根过氧化物酶标记的IgG抗体结合在纳米金颗粒表面(AuNPs-IgG-HRP)作为信号分子,构建了一种新型DNA甲基化电化学传感器。利用一步热变性法组装成TSP后,通过Au—S键固定在修饰纳米金颗粒的金电极表面,经过靶标DNA杂交、5-甲基胞嘧啶(5-mc)抗体及AuNPs-IgG-HRP结合后,用差分脉冲伏安法(DPV)进行检测。采用循环伏安法(CV)和电化学阻抗谱(EIS)对修饰电极的构建过程进行电化学表征。探究了杂交时间、5-mc抗体浓度、IgG-HRP加入体积、氢醌(HQ)和过氧化氢(H₂O₂)浓度对传感器的影响。在最佳条件下,该传感器对甲基化DNA的线性响应范围为1.0×10^-15～1.0×10^-10 mol/L,检出限(S/N=3)为4.4×10^-16 mol/L。该传感器具有良好的选择性和稳定性,为DNA甲基化检测提供了新方法。     

DNA甲基化电化学分析

DNA甲基化是目前研究最多的DNA表观遗传修饰之一.大量研究表明,DNA甲基化会引起DNA结构、稳定性以及DNA与蛋白质相互作用方式的改变,从而影响基因表达,进而引起多种神经退行性疾病、免疫系统疾病甚至癌症.因此,发展简易、灵敏、准确、可靠的方法进行DNA甲基化的分析是至关重要的.本文简单介绍了DNA甲基化的分析方法,重点综述了DNA甲基化的电化学分析方法,并对DNA甲基化的研究前景进行了展望.     

Fluorescent Light‐up Probe for the Detection of Protein Aggregates

A fluorescent dye was decorated with water‐soluble pyridinium groups in order to be applied in the detection of cyclodextrins or DNA. The dye displays an enhancement of its emission intensity when the internal rotations are restricted due to the formation of an inclusion complex with cyclodextrins or upon interaction with DNA. In vivo, the fluorescent probe can stain protein aggregates with a selectivity comparable to the widely used Proteostat®.     

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (K_b = 2–7 × 10⁵ M⁻¹) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φ_fl < 0.01) that increases significantly upon binding to G4-DNA (Φ_fl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φ_fl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.     

Stimuli-Triggered Strand Displacement-Based Multifunctional Gene Detection Platform Controlled By A Multi-Input DNA Logic Gate

Highly sensitive detection of various cancer related genes is of great significance in a number of biomedical applications. Here we describe a logic-controlled multifunctional platform that is capable of detecting two kinds of gene sequences with a 2-aminopurine (2-AP) as a quencher-free fluorescent probe, the fluorescence of which dramatically increases when it loops out the DNA helices. This detection platform is assembled from the split ATP aptamer, G-quadruplex, and the antisense strands of the P53 and K-ras genes, together with their complementary components. It is selectively activated by ATP and K⁺ via the target-induced DNA strand displacement, enabling the exposure of two long toehold regions that allow the P53 and K-ras genes to trigger the next DNA strand displacements. A hairpin DNA containing a looped-out 2-AP in the stem is finally released, accompanying with a significant increase of fluorescence intensity. The whole process behaves as a four-input AND logic gate. Such a logic-controlled gene detection platform is able to convert the external stimulation of ions and biomolecules into a detectable fluorescence output and functions well in gene detection.     

一种新型咔唑类菁染料黏度荧光探针

合成了一种带有醛基的咔唑类菁染料KQ, 其自身的荧光量子产率较低, 对极性的敏感性小, 且荧光信号不受核酸等生物分子的干扰. KQ对环境黏度有很好的荧光响应, 相对荧光强度随着环境黏度的增大而增强, 并且在1×10^-3~1.3216 Pa·s黏度范围内, 染料的荧光强度与溶液的黏度呈良好的线性关系. 活细胞荧光成像实验结果表明, 染料KQ具有良好的细胞膜通透性, 并可对细胞内不同位置的黏度检测成像.     

Homogeneous Detection of Trypsin in Protein Mixtures Based on Fluorescence Resonance Energy Transfer between Anionic Conjugated Polymer and Fluorescent Probe

Herein we describe a novel and simple conjugated polymer‐fluorescent probe based platform for trypsin detection from protein mixtures in homogeneous solution. This platform takes advantage of specific interaction between the probe and the active site of trypsin and the electrostatic interaction between the polymer and the protein to mediate energy transfer between the polymer and the probe. This method does not require any separation steps, which should facilitate high‐throughput protease screening and drug discovery.

     

A New CoII Complex as a Bulge-Specific Probe for DNA

Bulge cleavage of two or three bases occurs when a DNA substrate is specifically cleaved oxidatively by [Co^II(tfa)₂(happ)] (see picture). Hydrogen peroxide is necessary for the activation of this octahedral complex, which suggests that hydroxyl radicals are the reactive species. The complex has no significant reactivity towards the corresponding sequence in a single-stranded DNA region, and it exhibits only a low affinity towards double-stranded DNA. happ=macrocyclic ligand based on 1,10-phenanthroline, tfa=trifluoroacetate.     

A Competitor-switched Electrochemical Sensor for Detection of DNA

A competitor‐switched electrochemical sensor based on a generic displacement strategy was designed for DNA detection. In this strategy, an unmodified single‐stranded DNA (cDNA) completely complementary to the target DNA served as the molecular recognition element, while a hairpin DNA (hDNA) labeled with a ferrocene (Fc) and a thiol group at its terminals served as both the competitor element and the probe. This electrochemical sensor was fabricated by self‐assembling a dsDNA onto a gold electrode surface. The dsDNA was pre‐formed through the hybridization of Fc‐labeled hDNA and cDNA with their part complementary sequences. Initially, the labeled ferrocene in the dsDNA was far from surface of the electrode, the electrochemical sensor exhibited a "switch‐off" mode due to unfavorable electron transfer of Fc label. However, in the presence of target DNA, cDNA was released from hDNA by target DNA, the hairpin‐open hDNA restored its original hairpin structure and the ferrocene approached onto the electrode surface, thus the electrochemical sensor exhibited a "switch‐on" mode accompanying with a change in the current response. The experimental results showed that as low as 4.4×10⁻¹⁰ mol/L target DNA could be distinguishingly detected, and this method had obvious advantages such as facile operation, low cost and reagentless procedure.     

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

DNA/银纳米簇荧光探针在检测Pb2+中的应用

基于DNA/银纳米簇的荧光特性报道了一种简单、灵敏、高选择性的荧光方法检测Pb²⁺.以茎部为富G结构,环状部分为聚C结构的发夹型DNA为模板合成具有稳定荧光的银纳米簇.当加入Pb²⁺后,发夹型DNA在Pb²⁺诱导下形成G-四链体结构,破坏了发夹型DNA的构型,极大地影响了合成银纳米簇的模板结构,导致银纳米簇的荧光强度降低.Pb²⁺存在和不存在时所产生荧光强度的差异与发夹型DNA的碱基序列和茎部配对碱基数有关.依据这一现象,在优化DNA碱基序列和茎部配对碱基数的基础上,可实现100 μmol/L至100 nmol/L范围内对Pb²⁺的定量检测,检出限为10 nmol/L.该方法对Pb²⁺的检测具有较好的选择性,并可应用于实际水样中Pb²⁺的检测.检测结果与原子吸收光谱进行比对,显示出较好的一致性.     

Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials

A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high‐speed AFM. The encapsulation of the DNA‐modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold‐containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.     

Detection of DNA and Protein Molecules Using an FET‐Type Biosensor with Gold as a Gate Metal

In this study, a field effect transistor (FET)‐type biosensor based on 0.5 μm standard complementary metal oxide semiconductor (CMOS) technology is proposed and its feasibility for detecting deoxyribonucleic acid (DNA) and protein molecules is investigated. Au, which has a chemical affinity with thiol by forming a self‐assembled monolayer (SAM), was used as the gate metal in order to immobilize DNA and protein molecules. A Pt pseudo‐reference electrode was employed for the detection of biomolecules. The sensor was fabricated as a p‐channel (P)MOSFET‐type because PMOSFET with positive surface potential is useful for detecting negatively charged biomolecules from the view point of its high sensitivity and fast response time. DNA and protein molecules were detected by measuring the variation of the drain current due to the variation of biomolecular charge and capacitance. DNA and protein molecules used in the experiment were 15mer–oligonucleotide probe and streptavidin‐biotin protein complexes, respectively. DNA was detected by both in situ and ex situ measurements. Additionally, to verify the interactions among SAM, streptavidin, and biotin, surface plasmon resonance (SPR) measurement was performed.     

A Signal‐Passing DNA‐Strand‐Exchange Mechanism for Active Self‐Assembly of DNA Nanostructures

DNA nanostructured tiles play an active role in their own self‐assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self‐assembly of tiles and enables local communication during the self‐assembly process. This localized signal‐passing mechanism provides a new element of control for autonomous self‐assembly of DNA nanostructures.     

A Novel Fluorescent Probe for ATP Detection Based on Synergetic Effect of Aggregation-induced Emission and Counterion Displacement

In this work,a fluorescent probe(TPEBe-I)was developed for adenosine triphosphate(ATP)detection based on the synergetic effect of aggregation-induced emission and counterion displacement.TPEBe-I gave weak emission in aqueous solution due to the heavy-atom effect of counter iodide ion.However,upon the addition of ATP,the new aggregate complex(TPEBe-ATP)was formed between the cationic unit of TPEBe-I and ATP through electrostatic interactions,which not only restricted the intramolecular motion of luminogen but also eliminated the quenching effect of iodide ion.As a result,the fluorescent light-up detection for ATP was successfully achieved.Moreover,TPEBe-I exhibited high selectivity towards ATP and showed a wide linear detection region towards the logarithm of ATP concentration(5—600μmol/L)with a detection limit of 1.0μmol/L,enabling TPEBe-I as a promising probe for ATP quantitative analysis.     

Versatile and Homogeneous DNA Tetraplex Platform for Constructing Label-Free Logic Devices: From Design to Application

The design of DNA-based logic circuits has become an active research field in DNA nanotechnology and holds great potential in intelligent bioanalysis. To date, although many DNA-based logic systems have been realized, the implementation of advanced logic functions is still challenging, especially with simple and homogeneous compositions. Herein, by integrating two DNA tetraplex structures (G-quadruplex and i-motif), a completely label-free logic platform with high scalability was established, with which a series of advanced functions were realized, including arithmetic (adders and subtractors) and nonarithmetic ones (majority and dual-transfer gates). Furthermore, the platform was also applied as an intelligent biosensor to coanalyze two cancer-related micro-RNAs with high sensitivities and specificities. Considering the excellent versatility, expandability, and biocompatibility, the platform may promote the development of DNA computing and hold great potential in multiparameter sensing and medical diagnosis.