MICROCHIMICA ACTA
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2024
·Vol. 191
·期 7
·1-13
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IF 5.3
Zhao Tangtang,Xiao Ruilin,Li Yueqi,Ren Jierong,Niu Liyun,Chang Bingmei
With their regulated Boolean logic operations in vitro and in vivo, DNA logic circuits have shown great promise for target recognition and disease diagnosis. However, significant obstacles must be overcome to improve their operational efficiency and broaden their range of applications. In this study, we propose an Exo III-powered closed-loop DNA circuit (ECDC) architecture that integrates four highly efficient AND logic gates. The ECDC utilizes Exo III as the sole enzyme-activated actuator, simplifying the circuit design and ensuring optimal performance. Moreover, the use of Exo III enables a self-feedback (autocatalytic) mechanism in the dynamic switching between AND logic gates within this circulating logic circuit. After validating the signal flow and examining the impact of each AND logic gate on the regulation of the circuit, we demonstrate the intelligent determination of miR-21 using the carefully designed ECDC architecture in vitro. The proposed ECDC exhibits a linear detection range for miR-21 from 0 to 300 nM, with a limit of detection (LOD) of approximately 0.01 nM, surpassing most reported methods. It also shows excellent selectivity for miR-21 detection and holds potential for identifying and imaging live cancer cells. This study presents a practical and efficient strategy for monitoring various nucleic acid-based biomarkers in vitro and in vivo through specific sequence modifications, offering significant potential for early cancer diagnosis, bioanalysis, and prognostic clinical applications. Graphical abstract
研究领域:
分子生物学
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生物医学工程
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诊断学
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DOI
PubMed
高影响因子
Sensing and Bio-Sensing Research
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2025
·
IF 4.9
Baolin Li,Yaxin Huang,Zixin Zhu,Min Zhong,Guangrong Li,Jinbo Liu
Adenosine triphosphate (ATP) plays a critical role in cellular energy metabolism, acting as the energy source for many biological reactions. Abnormal fluctuations in ATP levels are directly linked to various diseases such as malignancies, bacterial infections, and cardiovascular disorders, making early-stage disease detection through rapid, highly sensitive ATP measurement essential. The current methods for ATP detection suffer from drawbacks such as complex procedures, reliance on expensive instruments, and prolonged reaction times. To this end, we have developed a novel biosensor named ATP Output Sensor Activated by CRISPR (AOSAC).This biosensor employs aptamer-based specific recognition combined with a dual-enzyme, amplification-free system involving Exo III and CRISPR-Cas12a for ATP detection. This sensor operates through an aptamer in a closed duplex structure, upon binding ATP, releases a trigger strand. This strand displaces an activation chain, which in turn interacts with Cas12a's crRNA, initiating trans-cleavage activity that cleaves a single-stranded DNA probe to produce a fluorescent signal. Concurrently, the activation chain's release sites are targeted by Exo III, enhancing signal amplification without the need for complex nucleic acid amplification, thus providing a highly selective, rapid detection method. This technique offers a linear detection range from 0 nM to 20 μM with a detection limit of 44.2 nM, presenting a novel strategy for signal amplification and high specificity in distinguishing ATP from its analogues.
研究领域:
分子生物学
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生物化学
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医学检测
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DOI
高影响因子
TALANTA
·
2019
·
IF 4.916
Tingting Wang,Huanshun Yin,Yuting Zhang,Linkui Wang,Yue Du,Yuping Zhuge,Shiyun Ai
A simple and sensitive electrochemical method was developed for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards endonuclease DpnII activity. Without ampicillin, DNA aptamer firstly hybridizes with the capture probe to form double strand DNA (dsDNA) structure. Then, dsDNA is cleaved by DpnII restriction endonuclease to form two dsDNA fragments. In which, one fragment is released from electrode surface and the other fragment is kept on electrode surface. Then, the dsDNA fragment kept on electrode surface is further digested by Exo III, which leads to the release of the dsDNA fragment from electrode surface. Thus, the electrochemical signal increases due to the decrease of the interface electron transfer resistance causing by the release of dsDNA from electrode surface. However, the formation of dsDNA is blocked when forming aptamer-ampicillin conjugate, which makes the obstruction of the digestion of DpnII and Exo III towards capture probe. Thus, a weak electrochemical signal is achieved due to the increase of the interface electron transfer resistance causing by the dsDNA on the electrode surface. Based on the relationship between ampicillin concentration and the decrease of the electrochemical signal, antibiotic is detected with low detection limit of 32 pM under optimal conditions, which is lower than the mandated maximum residue limit of European Union (9.93 nM). The developed method also presents good detection selectivity . Moreover, the applicability is confirmed by detecting antibiotic in milk and water samples with satisfactory results.
研究领域:
分析化学
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生物化学
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分子生物学
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DOI
PubMed
高影响因子
Small
·
2018
·Vol. 14
·期 10
·1703858
·
IF 9.598
Keying Zhang,Lin Yang,Feng Lu,Xingcai Wu,Jun-Jie Zhu
Here, a sensitive and universal noncoding RNA (ncRNA) upconversion sensing nanoplatform is developed. Gold nanoparticles bearing one hairpin DNA (Hp) molecule are conjugated to the linker DNA modified NaYF 4 :Yb, Er@NaYF 4 upconversion nanoparticles by DNA hybridization, leading to quenching of the upconversion emission through fluorescence resonance energy transfer. A signal DNA (SDNA) sequence is designed to open Hp, recovering the upconversion emission. To achieve universality and high sensitivity of the nanoprobe, an exonuclease III (Exo III)-assisted cycling amplification strategy is introduced. A multifunctional hairpin DNA (mHp) containing ncRNA recognition sequence and SDNA sequence is designed to recognize ncRNA and trigger Exo III as a biocatalyst to stepwise disintegrate itself, releasing both ncRNA and SDNA. The released ncRNA can be reused to release more SDNA, which greatly improves the sensing sensitivity. By changing the recognition portion of mHp, various ncRNA can be detected. The sensitive detection of both homeobox (HOX) transcript antisense RNA segment and miR-21 is achieved with this novel strategy, even in human serum, indicating the universality and sensitivity of the proposed strategy. Additionally, the expression level of miR-21 in human breast cancer cell (MCF-7) lysate is successfully measured, suggesting its potential in clinical diagnosis.
研究领域:
生物技术
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纳米技术
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癌症诊断
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分子生物学
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DOI
PubMed
高影响因子
ANALYST
·
2019
·Vol. 144
·期 9
·3023-3029
·
IF 4.019
Qianqian Pei,Xiaolei Song,Su Liu,Jingfeng Wang,Xueqi Leng,Xuejun Cui,Jinghua Yu,Yu Wang,Jiadong Huang
A facile signal-on electrochemical DNA biosensor has been developed for ultrasensitive detection of pathogenic bacteria using an Exo III-assisted autonomous multiple-cycle amplification strategy. The strategy relies on pathogens and aptamer binding-initiated release of a trigger, which combines with the 3′-protruding terminus of the hairpin probe 1, leading to the formation of double-stranded DNA with a blunt 3′ terminus which starts the Exo III-assisted multiple signal amplification reaction. In addition, hairpin probe 2 labeled with an electroactive reporter at the middle of the loop region is ingeniously designed to contain a short hairpin-embedded segment, which can fold into a hairpin structure via an Exo III-assisted cleavage reaction, thus bringing the redox molecule in proximity to the electrode surface for “signal-on” sensing. Under optimal conditions, this biosensor exhibits a very low detection limit as low as 8 cfu mL−1 and a wide linear range from 1.0 × 101 to 1.0 × 107 cfu mL−1 of target pathogenic bacteria. As far as we know, this is the first time that the Exo III-assisted autonomous multiple-cycle amplification strategy has been used for signal-on electrochemical sensing of pathogenic bacteria. In addition, the proposed sensor can also be used for highly sensitive detection of other targets by changing the aptamer sequence, such as nucleic acids, proteins and small molecules. Therefore, the proposed signal-on electrochemical sensing strategy might provide a simple and practical new platform for detection of pathogenic bacteria and related biological analysis, food safety inspection and environmental monitoring.
研究领域:
生物化学
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电化学
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分析化学
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微生物学
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DOI
PubMed
高影响因子
MOLECULES
·
2023
·Vol. 28
·期 5
·2208
·
IF 4.6
Moli Zhang,Yang Yang,Lingyi Xin,Hua Zhang,Lun Wu,Jun Zhu,Jing Zhu,Shiyun Liu,Zhaohui Wang,Qinhua Chen,Guangyi Yang
Recently, miRNAs have become a promising biomarker for disease diagnostics. miRNA-145 is closely related to strokes. The accuracy determination of miRNA-145 (miR-145) in stroke patients still remains challenging due to its heterogeneity and low abundance, as well as the complexity of the blood matrix. In this work, we developed a novel electrochemical miRNA-145 biosensor via subtly coupling the cascade strand displacement reaction (CSDR), exonuclease III (Exo III), and magnetic nanoparticles (MNPs). The developed electrochemical biosensor can quantitatively detect miRNA-145 ranging from 1 × 102to 1 × 106aM with a detection limit as low down as 100 aM. This biosensor also exhibits excellent specificity to distinguish similar miRNA sequences even with single-base differences. It has been successfully applied to distinguish healthy people from stroke patients. The results of this biosensor are consistent with the results of the reverse transcription quantitative polymerase chain reaction (RT-qPCR). The proposed electrochemical biosensor has great potential applications for biomedical research on and clinical diagnosis of strokes.Keywords:electrochemistry;miRNA-145;stroke;CSDR;Exo III;MNPs
研究领域:
生物医学工程
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分子诊断学
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DOI
PubMed
高影响因子
ANALYST
·
2024
·
IF 3.6
Fengyao Yu,Longyue Qin,Hua Zhang,Longshua Qin,Hao Fan
In this study, we innovatively synthesized bipyridine ruthenium cluster nanosheets (RuMOFNCs), a novel metal–organic framework material that exhibits both fluorescence and electrochemiluminescence. Gold nanoparticles (AuNPs) were anchored onto RuMOFNCs via bipyridine chelation, enhancing optical signals and creating sites for attaching biologically functional probes. We employed tetraferrocene-modified DNA probes, linked via gold–sulfur (Au–S) bonds, to construct a dual-mode fluorescence–electrochemiluminescence biosensor. This sensor, exploiting exonuclease III (Exo III)-mediated cyclic amplification, inhibits the electron transfer from RuMOFNC to tetraferrocene, resulting in amplified fluorescence and electrochemiluminescence signals. The sensor demonstrates exceptional sensitivity for detecting the BRAF gene, with fluorescence and electrochemiluminescence detection limits of 10.3 aM (range: 0.1 fM to 1 nM) and 3.1 aM (range: 1 aM to 10 pM), respectively. These capabilities are attributed to RuMOFNCs’ luminescence properties, tetraferrocene's quenching effect, and the specificity of base pairing. This study's findings hold substantial promise for biomedical research and clinical diagnostics, particularly in precision medicine and early disease detection.
研究领域:
生物医学工程
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分子诊断
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纳米技术
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产品关联
DOI
PubMed
高影响因子
ANALYST
·
2019
·Vol. 145
·期 2
·445-452
·
IF 4.019
Yanfang Cui,Haiwang Wang,Su Liu,Yu Wang,Jiadong Huang
The self-assembly of plasmonic nanoparticles provides a powerful approach to generate surface-enhanced Raman scattering (SERS), which promotes the actual applications in chemical and biomolecular analyses. Herein, we developed a facile SERS sensing strategy for an ATP assay with a 3-D DNA nanomachine that walks by the Exo III cleavage, leading to the formation of AuNP aggregates, which resulted in the enhancement of the electromagnetic field. Depending on the target-activated Exo III cleavage, the 3-D nanomachine can walk along the 3-D track on the surface of AuNPs and generate self-assembled hot-spots to enhance the SERS signal of a Raman dye, allowing a homogenous assay of the ATP concentration with high sensitivity and reproducibility. Under optimized experimental conditions, the biosensor detected ATP with a widened dynamic range from 1 pM to 1 × 105 pM with a limit of detection of up to 0.29 pM. Hence, the novel strategy provides a useful and practical platform for the SERS assay of ATP with high sensitivity and repeatability. Besides, this platform shows great potential for applications in high-throughput assays for drug screening and clinical diagnostics.
研究领域:
生物化学
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纳米生物学
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分析化学
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DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
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2017
·
IF 6.32
Chunxiang Li,Weisen Lu,Ming Zhu,Bo Tang
The performance of the photoelectrochemical (PEC) bioanalysis relies closely on the properties of the used photoactive species. In this study, a visible-light induced PEC active species, [(C6)2Ir(dcbpy)]+PF6– (C6 = coumarin 6, dcbpy = 2,2′-bipyridine-4,4′-dicarboxylic acid) was prepared based on C6 with the stronger absorbance in the visible region. The as-prepared complex was characterized by 1H NMR, UV–visible absorption and cyclic voltammetry. It exhibits intense absorption in visible region at 480 nm with a molar extinction coefficient (ε) of more 40000 M–1 cm–1, which is approximately twice that of Ru(bpy)32+. The PEC behaviors of the iridium(III) complex were investigated through covalently attaching to the ITO electrode. Induced by visible light, a large and stable cathodic photocurrent can be observed when dissolved O2 is served as a sacrificial electron acceptor. Also probable mechanisms of photocurrent generation are deduced. Employing [(C6)2Ir(dcbpy)]+PF6– as signal reporter, the Au NPs-based nanoprobe was constructed and successfully applied to assembly PEC platform based on the Exo III-assisted recycling amplification for bioanalysis. With thrombin as a model analyte, the PEC platform was found to be logarithmically proportional to thrombin concentrations across the range from 20 fM to 10 pM with fine selectivity, indicating excellent PEC properties of the synthesized Ir(III) complex and enormous potential for PEC bioanalysis.
研究领域:
分析化学
·
生物医学工程
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DOI
PubMed
高影响因子
ANALYTICA CHIMICA ACTA
·
2017
·
IF 4.95
Lei Xu,Xin Shen,Bingzhi Li,Chunhong Zhu,Xuemin Zhou
Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine. The strategy employed two unlabeled hairpin DNA oligonucleotides (HP1 and HP2), where HP1 contained the aptamer towards adenosine and HP2 embedded the guanine-rich sequence (GRS). In the presence of adenosine, hairpin HP1 could form specific binding with adenosine and trigger the unfolding of HP1's hairpin structure. The resulting adenosine-HP1 complex could hybridize with HP2, generating the Exo III recognition site. After Exo III-assisted degradation, the GRS was released from HP2, and the adenosine-HP1 was released back to the solution to combine another HP2, inducing the cycling amplification. After multiple circulations, the released ample GRSs were induced to form G-quadruplex, further catalyzing the oxidation of TMB, yielding a color change which was finally mirrored in the absorbance change. On the contrary, the absence of adenosine failed to unfold HP1, remaining color unchanged eventually. Thanks to the amplification strategy, the limit of detection was lowered to 17 nM with a broad linear range from 50 nM to 6 μM. The proposed method was successfully applied to the detection of adenosine in biological samples and satisfying recoveries were acquired.
研究领域:
生物化学
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分析化学
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分子生物学
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DOI
PubMed
高影响因子
NEW JOURNAL OF CHEMISTRY
·
2017
·Vol. 41
·期 15
·7613-7620
·
IF 3.269
Qianqian Pei,Yu Wang,Su Liu,Yifei Qin,Xueqi Leng,Xuejun Cui,Jiadong Huang
In this study, a novel electrochemical biosensor based on exonuclease III (Exo III)-aided autonomous cascade signal amplification for ultrasensitive and highly specific detection of Salmonella typhimurium (S. typhimurium) has been reported. Herein, two duplex DNA probes were ingeniously designed. An Ap–Pr duplex probe was constructed as a recognition element by hybridizing an S. typhimurium aptamer (Ap) with a primer (Pr). A P–S duplex probe has been designed to contain a protruding DNA fragment at 5′-termini that has an identical sequence with Pr (the secondary Pr), a complementary duplex DNA that is used for blocking a signal-triggered probe (S), and an overhung nucleic acid segment at 3′-end that can anneal with Pr and form double-stranded DNA with a blunt 3′-terminus, thus initiating Exo III-aided amplification reaction. Upon sensing of the target S. typhimurium, the specific recognition of S. typhimurium and aptamer releases Pr, which anneals with the P–S duplex and triggers the Exo III cleavage reaction, accompanied by release of Pr, S, and secondary Pr. After this, the released Pr and secondary Pr anneal with other P–S duplex, which in turn triggers the Exo III-assisted cycling cleavage. Thus, large amounts of S are liberated, which hybrids with S* (DNA probe complementary to S); thereby, 5′-methylene blue (MB)-labelled DNA probe (MBP) folds into a hairpin structure with 5′-terminus close to electrode surface for efficient electronic transfer. Moreover, the S–S* hybrid duplex is specifically hydrolyzed by Exo III to liberate S, which accordingly results in the cycling cleavage of S*. Therefore, numerous MBP transform into a hairpin structure with electroactive MB close to the electrode surface; this generates significantly amplified electrochemical signal towards S. typhimurium detection. The present developed strategy exhibited high sensitivity towards S. typhimurium with a detection limit of 2.8 × 10 cfu mL−1. Furthermore, the proposed autonomous cascade signal amplification strategy can be easily extended for detection towards a wide spectrum of analytes including nucleic acid, proteins, and small molecules possessing their corresponding aptamers. Therefore, the developed Exo III-aided autonomous cascade signal amplification strategy might indeed provide a facile and universal tool for bioanalysis and clinical diagnosis.
研究领域:
生物传感技术
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分子诊断
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分析化学
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DOI
高影响因子
MICROCHEMICAL JOURNAL
·
2025
·
IF 5.1
Dianbo Yu,WenZhao Zhang,Jiahou Xu,Yuanxun Gong,Jiayi Zhang,Jihua Wei,Kai Zhang,Xianjiu Liao
Nuclear factor kappa B (NF-κB) p50 is a critical transcription factor that regulates immune responses, inflammation, and cell proliferation. Precise detection of NF-κB p50 at ultralow concentrations is of paramount importance for early disease diagnosis and mechanistic studies. Here, we report an electrochemical biosensor integrating double-crossover DNA tiles and entropy-driven strand displacement, amplified by Exonuclease III (Exo III) digestion. By designing a self-assembled DNA tile scaffold on a gold electrode and employing a DNA tetrahedron architecture, the sensor achieves a highly ordered surface configuration, minimizing background noise and enhancing specificity. In the absence of NF-κB p50, Exo III selectively digests a double-stranded DNA substrate, releasing single-stranded triggers that undergo an entropy-driven reaction to form a Y-shaped scaffold on the electrode. This assembly effectively hinders redox probe access, lowering the differential pulse voltammetry (DPV) signal. Conversely, NF-κB p50 binding protects the DNA substrate from digestion, preserving a higher current output. Under optimized conditions—30 nM DNA tiles, 2 U μL −1 Exo III, 30 min cleavage, and 100 nM DNA3/DNA4/DNA5—the biosensor exhibits an ultralow detection limit of 2.65 aM and excellent specificity, as confirmed by negligible cross-reactivity with other proteins. Furthermore, the method shows robust anti-interference performance in complex matrices (e.g., diluted cell lysates). These findings underscore the potential of this DNA tile-based biosensor for clinical diagnostics and fundamental research on NF-κB p50–mediated pathways.
研究领域:
生物传感器
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分子诊断
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生物电子学
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核酸纳米技术
·
转录因子
✓ 已验证
产品关联
DOI
高影响因子
危险品化学品经营许可证（带存储）