Locked nucleic acid/DNA chimeric aptamer probe for tumor diagnosis with improved serum stability and extended imaging window in vivo

As promising molecular probes for in vivo tumor imaging, aptamers without modification remain problematic due to insufficient serum stability and unabiding imaging window. To address this problem, a novel locked nucleic acid (LNA)/DNA chimeric aptamer probe was developed through proper LNA incorporation and supplemented 3′-3′-thymidine (3′-3′-T) capping. TD05, a DNA aptamer against lymphoma Ramos cells, being used as the model, a series of modification strategies were designed and optimized with different positions, numbers and combinations. It was revealed that the combined use of LNA and 3′-3′-T had a synergistic effect, and with the increase of LNA substitution in stem region, the serum stability of TD05 was gradually enhanced while its affinity and specificity were perfectly maintained to Ramos cells. Particularly, TD05.6 with 7-base pair-LNA substitution exhibited the significantly elevated detection stability half-life from ∼0.5 h of TD05 to 5–6 h of TD05.6 for target cells in serum. Moreover, a much slower clearance rate in tumor-bearing mice was also observed for TD05.6, thus leading to the greatly extended tumor imaging window from <150 min of TD05 to >600 min of TD05.6. This strategy might be of great potentials to generate more aptamer probes that are stable and nuclease-resistant for tumor diagnosis in real biological systems.     

A pH-responsive activatable aptamer probe for targeted cancer imaging based on i-motif-driven conformation alteration

We present here a p H-responsive activatable aptamer probe for targeted cancer imaging based on i-motif-driven conformation alteration. This p H-responsive activatable aptamer probe is composed of two single-stranded DNA. One was used for target recognition, containing a central, target specific aptamer sequence at the 3′-end and an extension sequence at the 5′-end with 5-carboxytetramethylrhodamine(TAMRA) label(denoted as strand A). The other(strand I), being competent to work on the formation of i-motif structure, contained four stretches of the cytosine(C) rich domain and was labeled with a Black Hole Quencher 2(BHQ2) at the 3′-end. At neutral or slightly alkaline p H, strand I was hybridized to the extension sequence of strand A to form a double-stranded DNA probe, termed i-motif-based activatable aptamer probe(I-AAP). Because of proximityinduced energy transfer, the I-AAP was in a "signal off" state. The slightly acidic p H enforced the strand I to form an intramolecular i-motif and then initiated the dehybridization of I-AAP, leading to fluorescence readout in the target recognition. As a demonstration, AS1411 aptamer was used for MCF-7 cells imaging. It was displayed that the I-AAP could be carried out for target cancer cells imaging after being activated in slightly acidic environment. The applicability of I-AAP for tumor tissues imaging has been also investigated by using the isolated MCF-7 tumor tissues. These results implied the I-AAP strategy is promising as a novel approach for cancer imaging.     

In vivo Fluorescence Imaging of Tumors using Molecular Aptamers Generated by Cell‐SELEX

Poor sensitivity and low specificity of current molecular imaging probes limit their application in clinical settings. To address these challenges, we used a process known as cell‐SELEX to develop unique molecular probes termed aptamers with the high binding affinity, sensitivity, and specificity needed for in vivo molecular imaging inside living animals. Importantly, aptamers can be selected by cell‐SELEX to recognize target cells, or even surface membrane proteins, without requiring prior molecular signature information. As a result, we are able to present the first report of aptamers molecularly engineered with signaling molecules and optimized for the fluorescence imaging of specific tumor cells inside a mouse. Using a Cy5‐labeled aptamer TD05 (Cy5‐TD05) as the probe, the in vivo efficacy of aptamer‐based molecular imaging in Ramos (B‐cell lymphoma) xenograft nude mice was tested. After intravenous injection of Cy5‐TD05 into mice bearing grafted tumors, noninvasive, whole‐body fluorescence imaging then allowed the spatial and temporal distribution to be directly monitored. Our results demonstrate that the aptamers could effectively recognize tumors with high sensitivity and specificity, thus establishing the efficacy of these fluorescent aptamers for diagnostic applications and in vivo studies requiring real‐time molecular imaging.     

Detection of FRET efficiency in imaging systems by photo-bleaching acceptors

Fluorescence resonance energy transfer (FRET) is widely used to obtain the distance between a donor and an acceptor in biological research. However, the detection of FRET efficiencies with fluorescence microscopy imaging systems remains a great challenge due to the difficulties of transferring gray scales of the images into fluorescence intensities, and the absence of exact quantum yields of donors and acceptors. Herein, we presented a new method to detect the FRET efficiency in imaging systems by analyzing the photo-bleaching-induced changes in fluorescent intensities of quantum dots (QDs, donors) and Cy5 dyes (acceptors). Our method is different from the previous acceptor-photo-bleaching studies in imaging systems by theoretically analyzing the bleaching process, and bringing forward a new parameter which is universal for samples of the same kind. It is convenient for calculating FRET efficiencies. There is hardly any spectral crosstalk between 605QD and Cy5, thus the FRET result is more accurate than that of many other common FRET pairs. The lengths of single-stranded and double-stranded DNA fragments in solution were determined via the analysis of FRET efficiency values. This technique provides a reliable approach to study biomacromolecules in living cells through fluorescent imaging and in situ measurements.     

Green Synthesis of Red‐Emitting Carbon Nanodots as a Novel “Turn‐on” Nanothermometer in Living Cells

Temperature measurements in biology and medical diagnostics, along with sensitive temperature probing of living cells, is of great importance; however, it still faces significant challenges. Herein, a novel “turn‐on” carbon‐dot‐based fluorescent nanothermometry device for spatially resolved temperature measurements in living cells is presented. The carbon nanodots (CNDs) are prepared by a green microwave‐assisted method and exhibit red fluorescence (λ_em=615 nm) with high quantum yields (15 %). Then, an on–off fluorescent probe is prepared for detecting glutathione (GSH) based on aggregation‐induced fluorescence quenching. Interestingly, the quenched fluorescence could be recovered by increasing temperature and the CNDs–GSH mixture could behave as an off–on fluorescent probe for temperature. Thus, red‐emitting CNDs can be utilized for “turn‐on” fluorescent nanothermometry through the fluorescence quenching and recovery processes, respectively. We employ MC3T3‐E1 cells as an example model to demonstrate the red‐emitting CNDs can function as “non‐contact” tools for the accurate measurement of temperature and its gradient inside a living cell.     

A Native‐Chemical‐Ligation‐Mechanism‐Based Ratiometric Fluorescent Probe for Aminothiols

Thiol‐containing amino acids (aminothiols) such as cysteine (Cys) and homocysteine (Hcy) play a key role in various biological processes including maintaining the homeostasis of biological thiols. However, abnormal levels of aminothiols are associated with a variety of diseases. The native chemical ligation (NCL) reaction has attracted great attention in the fields of chemistry and biology. NCL of peptide segments involves cascade reactions between a peptide‐α‐thioester and an N‐terminal cysteine peptide. In this work, we employed the NCL reaction mechanism to formulate a Förster resonance energy transfer (FRET) strategy for the design of ratiometric fluorescent probes that were selective toward aminothiols. On the basis of this new strategy, the ratiometric fluorescent probe 1 for aminothiols was judiciously designed. The new probe is highly selective toward aminothiols over other thiols and exhibits a very large variation (up to 160‐fold) in its fluorescence ratio (I₄₅₈/I₆₀₃). The new fluorescent probe is capable of ratiometric detection of aminothiols in newborn calf and human serum samples and is also suitable for ratiometric fluorescent imaging of aminothiols in living cells.     

Aptamer switch probe based on intramolecular displacement

A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design utilizes both a fluorophore and a quencher which are respectively modified at the two termini of the ASP. In the absence of the target molecule, the short DNA will hybridize with the aptamer, keeping the fluorophore and quencher in close proximity, thus switching off the fluorescence. However, when the ASP meets its target, the binding between the aptamer and the target molecule will disturb the intramolecular DNA hybridization, move the quencher away from the fluorophore, and, in effect, switch on the fluorescence. Both ATP and human alpha-thrombin aptamers were engineered to demonstrate this design, and both showed that fluorescence enhancement could be quantitatively mediated by the addition of various amounts of target molecules. Both of these ASPs presented excellent selectivity and prompt response toward their targets. With intrinsic advantages resulting from its intramolecular signal transduction architecture, the ASP design holds promising potential for future applications, such as biochip and in situ imaging, which require reusability, excellent stability, prompt response, and high sensitivity.     

基于磁性辅助的杂交链反应放大检测三磷酸腺苷

本文提出了一种基于磁性辅助的杂交链反应放大检测三磷酸腺苷(ATP)的传感策略。磁性纳米粒子表面易于修饰,而且操作方便,具有很好的分离效果,能够提高生物传感的选择性。首先,利用生物素与链霉亲和素之间的亲和力作用,将生物素标记的ATP核酸适配体连接到链霉亲和素修饰的磁性纳米粒子表面,加入与ATP核酸适配体互补的一段DNA进行杂交,通过磁性分离除去未杂交上的DNA,加入靶向ATP,ATP与其适配体特异性结合将适配体的互补链通过磁性分离出来,磁性分离出的信号DNA继续用于下一步的杂交链反应,将信号放大,最后利用氧化石墨烯(GO)对荧光的猝灭效应降低背景荧光,达到高灵敏度、高选择性检测靶向ATP。其中,ATP的最低检测浓度为0.1nmol/L。     

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.     

新型荧光/EPR双功能次氯酸探针的构建及性能

构建了一种新型香豆素-萘酰亚胺荧光/电子顺磁共振双功能探针CNNOH,并结合荧光光谱、电子顺磁共振(EPR)波谱和紫外-可见吸收光谱对其性能进行了研究.结果表明,该探针可结合荧光光谱的灵敏性和EPR波谱的特异性进行次氯酸的检测;由于香豆素与萘酰亚胺之间存在荧光共振能量转移(FRET)效应,探针分子具有较大的Stokes位移(135 nm),可有效避免由激发光导致的杂散光对检测的干扰.该双功能探针具有检出限低(0.214μmol/L)、反应速度快(~10 s)、检测范围宽(0~5 mmol/L)、选择性好及在生理条件下稳定的特点,预期在活体细胞检测方面有良好的应用前景.     

Highly Sensitive Bioluminescent Probe for Thiol Detection in Living Cells

The sensitive detection of thiols including glutathione and cysteine is desirable owing to their roles as indispensable biomolecules in maintaining intracellular biological redox homeostasis. Herein, we report the design and synthesis of SEluc‐1 (s ulfinate e ster luc iferin), a chemoselective probe exhibiting a ratiometric and turn‐on response towards thiols selectively in fluorescence and bioluminescence, respectively. The probe, which was designed based on the “caged” luciferin strategy, displays excellent selectivity, high signal/noise ratio (>240 in the case of bioluminescence), and a biologically relevant limit of detection (LOD, 80 nm for cysteine), which are all desirable traits for a sensitive bioluminescent sensor. SEluc‐1 was further applied to fluorescence imaging of thiol activity in living human cervical cancer HeLa cell cultures, and was successfully able to detect fluctuations in thiol concentrations induced by oxidative stress in a bioluminescent assay utilizing African green monkey fibroblast COS‐7 cells and human breast adenocarcinoma MCF‐7 cells.     

肿瘤乏氧靶向响应的罗丹明荧光探针及其成像介导手术治疗

基于罗丹明的良好荧光性能, 经化学偶联反应制备并表征了一个偶氮乏氧特异响应的“Off-On”型荧光成像探针(FY-4). 从分子层面证实了其荧光“Off-On”性能和响应机制; 在L02正常细胞及4T1, HeLa和A549肿瘤细胞层面考察了其对受试细胞株的毒性和不同乏氧时间的荧光成像性能; 再利用4T1肿瘤模型, 分别以肿瘤原位注射和尾静脉注射的方式考察了其荧光成像性能, 并探究了其荧光成像介导切除肿瘤性能, 最后还考察了FY-4的生物安全性. 结果表明, FY-4有高的肿瘤乏氧靶向特异“关-开”响应的荧光成像差异显影及荧光成像介导切除肿瘤的潜能, 结合其良好的光物理性能、 生物安全性和明晰的给药时间等特性, 有望为生物医学荧光成像介导肿瘤切除提供新的研究工具.     

High-intensity fluorescence imaging and sensitive electrochemical detection of cancer cells by using an extracellular supramolecular reticular DNA-quantum dot sheath

Acting as a cage-type cellular probe, an extracellular supramolecular reticular DNA-quantum dot (QD) sheath has been developed for high-intensity fluorescence microscopy imaging and the sensitive electrochemical detection of Ramos cells. The extracellular supramolecular reticular DNA-QD sheath is constructed from layer-by-layer self-assembly of DNA-CdTe QD probes and DNA nanowire frameworks functionalized with a Ramos cell-binding aptamer. The DNA-QD sheath forms specifically and quickly on the surface of Ramos cells at physiological temperature, and the assembly of large numbers of DNA-CdTe QD probes on the surface of Ramos cells produces exceedingly high fluorescence intensity. Using the extracellular supramolecular reticular DNA-QD sheath as the cellular probe, Ramos cells can be clearly observed and easily distinguished from a mixture of multiple cancer cells by fluorescence microscopy imaging. Using the new cage-type cellular probe, a sensitive sandwich-type electrochemical strategy has also been developed to achieve accurate quantitative analysis of Ramos cells. Under the optimized conditions, Ramos cells can be detected quantitatively in a range from 10 to 1000 cells with a detection limit of 10 cells. This strategy presents a promising platform for highly sensitive and convenient evaluation of cancer cell levels.     

Optimization of pairings and detection conditions for measurement of FRET between cyan and yellow fluorescent proteins.

Detection of F?rster resonance energy transfer (FRET) between cyan and yellow fluorescent proteins is a key method for quantifying dynamic processes inside living cells. To compare the different cyan and yellow fluorescent proteins, FRET efficiencies were measured for a set of the possible donor:acceptor pairs. FRET between monomeric Cerulean and Venus is more efficient than the ECFP:EYFP pair and has a 10% greater F?rster distance. We also compared several live cell microscopy methods for measuring FRET. The greatest contrast for changes in intramolecular FRET is obtained using a combination of ratiometric and spectral imaging. However, this method is not appropriate for establishing the presence of FRET without extra controls. Accurate FRET efficiencies are obtained by fluorescence lifetime imaging microscopy, but these measurements are difficult to collect and analyze. Acceptor photobleaching is a common and simple method for measuring FRET efficiencies. However, when applied to cyan to yellow fluorescent protein FRET, this method becomes prone to an artifact that leads to overestimation of FRET efficiency and false positive signals. FRET was also detected by measuring the acceptor fluorescence anisotropy. Although difficult to quantify, this method is exceptional for screening purposes, because it provides high contrast for discriminating FRET.     

A new method for the detection of ATP using a quantum-dot-tagged aptamer

Fluorescence resonance energy transfer (FRET) between a quantum dot as donor and an organic fluorophore as acceptor has been widely used for detection of nucleic acids and proteins. In this paper, we developed a new method, characterized by 605-nm quantum dot (605QD) fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease, to detect adenosine triphosphate (ATP). The new method involved the use of three different oligonucleotides: 3′-biotin-modified DNA that binds to streptavidin-conjugated 605QD; 3′-Cy5-labelled DNA; and a capture DNA consisting of an ATP aptamer and a sequence which could hybridize with both 3′-biotin-modified DNA and 3′-Cy5-labelled DNA. In the absence of the target ATP, the capture DNA binds to 3′-biotin-modified DNA and 3′-Cy5-labelled DNA, bringing quantum dot and Cy5 into close proximity for greater FRET efficiency. When ATP is introduced, the release of the 3′-Cy5-labelled DNA from the hybridization complex took place, triggering 605QD fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease. Taken together, the virtue of FRET pair 605QD/Cy5 and the property of aptamer-specific conformation change caused by aptamer–ATP interaction, combined with the fluorescence intensity change of both 605QD and Cy5, provide prerequisites for simple and convenient ATP detection. Zhang Chen and Guang Li contributed equally to this work.     

A FRET-based fluorescent probe for imaging H2S in living cells

A FRET-based fluorescence probe was developed for selective detection of H₂S in aqueous buffer and inside living cells. For this probe, the FRET probe could be cleaved by H₂S, and the fluorescence of FRET donor is released. The probe is highly selective to H₂S over other biologically relevant species to give color change for naked eye observation. Confocal imaging indicated that the probe could monitor intracellular H₂S level changes.     

Fluorescence detection of potassium ion using the G-quadruplex structure

Oligonucleotides with sequences of human telomere DNA or thrombin binding aptamer (TBA) are known to form tetraplex structures upon binding the K(+) ion. Structural changes associated with the formation of tetraplex assemblies led to the development of potassium-sensing oligonucleotide (PSO) probes, in which two fluorescent dyes were attached to both termini of particular oligonucleotide. The combination of dyes included fluorescence resonance energy transfer (FRET) and excimer emission approaches, and the structural changes upon binding K(+) ion could be monitored by a fluorescence technique. These systems showed a very high preference for K(+) over Na(+) ion, which was suitable for fluorescence imaging of the potassium concentration gradient in a living cell. In the case of human telomere DNA, it was also possible to follow the polymorphism of its tetraplex structures.     

Single-Sided Competitive Axial Coordination of G-Quadruplex/Hemin as Molecular Switch for Imaging Intracellular Nitric Oxide

Axial coordination is a crucial biological process to regulate biomolecules’ functions in natural enzymes. However, it is a great challenge to determine the single or dual axial interaction between the metal center of enzymes and the ligand. In this work, a controllable axial coordination system was developed based on G-quadruplex/hemin complex by designing a series of fluorescent derivatives. The mechanism on axial coordination of G-quadruplex/hemin with coumarin-imidazole ligands was proposed to be single-sided, and led to fluorescence quenching of ligands. Upon addition of nitric oxide, the fluorescence of ligands was recovered through competitive axial coordination, providing a “signal on” strategy for signal transduction. More significantly, the fluorescent imaging of intracellular nitric oxide was achieved after conjugating with gold nanoparticles. Also, the proposed protocol provided a smart strategy to monitor the relationship between nitric oxide and p53 protein activity in living cells.     

Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays

A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity.     

Fluorescent Detection of Hypochlorous Acid from Turn‐On to FRET‐Based Ratiometry by a HOCl‐Mediated Cyclization Reaction

Hypochlorous acid (HOCl), a reactive oxygen species (ROS), plays a significant biological role in living systems. However, abnormal levels of HOCl are implicated in many inflammation‐associated diseases. Therefore, the detection of HOCl is of great importance. In this work, we describe the HOCl‐promoted cyclization of rhodamine‐thiosemicarbazides to rhodamine‐oxadiazoles, which is then exploited as a novel design strategy for the development of a new fluorescence turn‐on HOCl probe 2 . On the basis of the fluorescence resonance energy transfer (FRET) signaling mechanism, 2 was further converted into 1 a and 1 b , which represent the first paradigm of FRET‐based ratiometric fluorescent HOCl probes. The outstanding features of 1 a and 1 b include well‐resolved emission peaks, high sensitivity, high selectivity, good functionality at physiological pH, rapid response, low cytotoxicity, and good cell‐membrane permeability. Furthermore, these excellent attributes enable us to demonstrate, for the first time, the ratiometric imaging of endogenously produced HOCl in living cells by using these novel ratiometric probes. We expect that 1 a and 1 b will be useful molecular tools for studies of HOCl biology. In addition, the HOCl‐promoted cyclization reaction of rhodamine‐thiosemicarbazides to rhodamine‐oxadiazoles should be widely applicable for the development of different types of fluorescent HOCl probes.