TALANTA
·
2022
·
IF 6.556
Junyang Chen,Mengke Wang,Chenyu Zhou,Jiabao Zhang,Xingguang Su
Specific and cost-effective methodologies for human papillomavirus (HPV) gene detection are significant for clinical diagnosis and cancer control. Herein, a label-free and fluorimetric/colorimetric dual-mode sensing strategy was developed for the quantitative determination of HPV DNA based on the integration of fluorescent DNA-silver nanoclusters (DNA/AgNCs) and G-quadruplex/hemin DNAzyme. The fluorimetric sensing strategy was based on the phenomena that the fluorescence enhancement of DNA/AgNCs obtained in proximity of guanine-rich DNA sequences and the photoinduced electron transfer (PET) effect between the electron donor (DNA/AgNCs) and electron receptor (G-quadruplex/hemin). The colorimetric sensing strategy was relied on the peroxidase-like activity of G-quadruplex/hemin DNAzyme. By integrating DNA/AgNCs and DNAzyme, this dual-mode strategy could produce two independent signals to improve the analytical diversity and accuracy. Under optimized conditions, the fluorimetry and colorimetry of the strategy displayed a linear range of 0.01–4 and 0.02–4 nM, with the low detection limit of 2.3 and 5.2 pM, respectively. Additionally, this dual-mode strategy has been successfully applied to HPV DNA analysis in different real samples with excellent results. Moreover, the sensing platform could be developed for different HPVs DNA assay by only adjusting the recognition sequence, which provided a universal strategy for various kinds of virus analysis.
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ANALYTICAL CHEMISTRY
·
2015
·
IF 5.636
Nannan Liu,Zekun Yang,Xiaoding Lou,Benmei Wei,Juntao Zhang,Pengcheng Gao,Ruizuo Hou,Fan Xia
Almost all of the important functions of DNA are realized by proteins which interact with specific DNA, which actually happens in a limited space. However, most of the studies about the protein–DNA binding are in an unconfined space. Here, we propose a new method, nanopore-based DNA-probe sequence-evolution (NDPSE), which includes up to 6 different DNA-probe systems successively designed in a nanoscale confined space which unveil the more realistic characteristics of protein–DNA binding phenomena. There are several features; for example, first, the edge-hindrance and core-hindrance contribute differently for the binding events, and second, there is an equilibrium between protein–DNA binding and DNA–DNA hybridization.
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SENSORS AND ACTUATORS B-CHEMICAL
·
2017
·
IF 5.401
Xiao Fang Zhang,Na Li,Cui Ye,Jia Yu Liang,Nian Bing Li,Hong Qun Luo
Uracil-DNA glycosylase (UDG), one of the base-excision repair enzymes, is closely relevant for the diseases of the organism. Here, we proposed a resonance Rayleigh scattering (RRS) strategy for sensitively detecting the active UDG based on a dual amplification DNA machine without label under the catalysis of exonuclease III (Exo III). In our study, a double-stranded DNA complex S1-S2 containing triggers and peculiar uracil bases was employed. To achieve the dual amplification strategy, we adopted hairpin probes HP1 and HP2. The unique hairpin probes can partially hybridize with S1 and S2, respectively. With the excision reaction of UDG, the uracil bases were excised from S2 in double-stranded S1-S2, resulting in a lower melting temperature of the S1-S2. Then, the S1-S2 was dissociated to single-stranded S1 and S2 with abasic sites. Subsequently, the liberated strands separately hybridized with hairpins to initiate the Exo III-catalyzed dual amplification. In the presence of K + , countless c-myc sequences which were produced by the amplification reaction formed G-quadruplex structures. Finally, with the addition of Mg 2+ , long and continuous G-wire structures were obtained, causing an obvious enhancement of RRS intensity. The proposed RRS DNA machine obtained the limit of detection as low as 1.0 × 10 −5 U/mL for the active UDG assay. Moreover, qualitative analysis of the active UDG was successfully achieved in HeLa cells lysate. The DNA machine is a potential tool to be used in UDG clinical diagnosis or functional study.
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BIOSENSORS & BIOELECTRONICS
·
2016
·
IF 7.476
Siqi Zhang,Kun Wang,Kai-Bin Li,Wei Shi,Wen-Ping Jia,Xiaoying Chen,Ting Sun,De-Man Han
A silver nanoclusters (AgNCs)/graphene oxide (GO)-based fluorescence sensor was developed for label-free DNA detection through hybridization chain reaction (HCR). A DNA sequence associated with the human immunodeficiency virus (HIV) was selected as a model target. Two DNA probes , hairpin probe 1 (H 1 ) and hairpin probe 2 (H 2 ), were partially complementary. GO was used as an adsorption material to capture the hairpin probes and a selective fluorescence quencher was used to reduce the background signal. Upon addition of AgNO 3 and NaBH 4 , the AgNCs were synthesized at the terminals of the H 1 and H 2 probes. In the absence of target DNA (T HIV ), hybridization chain reaction (HCR) could not be triggered due to the stability of H 1 and H 2 probes. The hairpin probe-protected AgNCs attached to the GO surface, efficiently quenching fluorescence of the AgNCs. Therefore, the system showed very low background. In presence of T HIV , the target triggered the chain-like assembly of H 1 and H 2 through HCR, generating a long chain of H 1 and H 2 complexes. The HCR product (AgNCs nanowires) could not be adsorbed on the surface of GO; hence, it generated a strong fluorescent signal based on the concentration of the target. Under the optimized conditions, the detection limit of the fluorescence sensor was 1.18 nM, and hence it can be applied to clinical samples.
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ANALYTICA CHIMICA ACTA
·
2016
·
IF 4.712
Pei Liu,Kexin Zhang,Ranran Zhang,Huanshun Yin,Yunlei Zhou,Shiyun Ai
Abnormal level of DNA methyltransferase (MTase) – mediated DNA methylation is closely related with cancer and bacterial diseases. Herein, a novel strategy based on the keypad lock of duplex DNA modified meso-SiO 2 @Fe 3 O 4 was developed for colorimetric assay of Dam MTase activity. When the Dam MTase was introduced, the duplex DNA can be methylated at a palindrome sequence of 5′-GATC-3′ and cleaved by the methylation-sensitive restriction endonuclease Dpn I. Due to the instability of the newly formed DNA fragment, the hybrid will separated into a single-stranded DNA. Then the keypad lock will open, and the catalytic reaction of TMB and H 2 O 2 can be initiated through the pores of meso-SiO 2 @Fe 3 O 4 , and a high color signal can be clearly observed by the naked eye. Contrarily, without Dam MTase, the catalytic reaction will not be initiated, and result no color signal. The proposed method exhibited a wide dynamic range with a low detection limit of 0.73 U/mL. Additionally, this way can be performed in human serum with satisfying recovery. And the inhibition of Dam MTase can also be well demonstrated by using paclitaxel as a model. Therefore, the designed way not only provides a platform for monitoring Dam MTase activity, but also useful for further application in disease diagnosis and drug discovery.
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ANALYST
·
2016
·Vol. 141
·期 20
·5829-5834
·
IF 4.033
Xiangmin Miao,Zongbing Li,Liansheng Ling
An ultrasensitive fluorescent platform for sequence-specific recognition of double-stranded DNA (dsDNA) based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe was developed. The target dsDNA could hybridize with the loop portion of the molecular beacon (MB) to form a triplex DNA structure and opened the “stem–loop” structure of the MB; such triplex DNA was used as an assistant probe (AP). Meanwhile, a fluorophore labeled DNA-AuNP probe that contained a specific enzyme cleavage site was introduced and its fluorescence signal was efficiently quenched due to the vicinity of the fluorophore to the AuNP surface. Such a DNA-AuNP probe could hybridize with the 5′ stem portion of the MB in the AP to form duplex DNA strands that contained a specific enzyme cleavage site for the nicking enzyme assisted cleavage reaction, and resulted in the release of the fluorophore from the AuNP surface and the recovery of the fluorescence signal. Because the AP remains intact during such a cleavage process, it could be reused to hybridize with the next DNA-AuNP probe and trigger the nicking nuclease assisted signal amplification. Under optimal conditions, a low detection limit of 3.8 pM was obtained for dsDNA detection, and the assay has high sequence specificity for dsDNA detection.
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Journal of Biomedical Nanotechnology
·
2018
·Vol. 14
·期 1
·150-160
·
IF 5.068
Li Taotao,Yi Huan,Liu Yuan,Wang Zunliang,Liu Shiquan,He Nongyue,Liu Hongna,Deng Yan
DNA strands have been used as templates to form different sized silver nanoclusters. Although DNA templated silver nanoclusters (NCs) probes which show outstanding fluorescence properties have been widely applied in chemical sensing and cellular imaging, synthesis of DNA template Au–Ag
bimetallic nanoclusters remains a challenge. A facile one-step synthesis method was thus developed in this study to form Au–Ag NCs using C4-ATAT-C4 as template. C4-ATAT-C4 acted as a stabilizer for preventing aggregation of the Au–Ag NCs. The obtained Au–Ag NCs stabilized
by C4-ATAT-C4 showed bright fluorescence and high stability. A series of experiments showed that temperature, citrate-citric acid buffer, sequence and concentration of DNA played an important role in the synthesis of fluorescent Au–Ag NCs. In addition, a ratiometric fluorescence probe
was designed through combining the nucleotide sequence (C4-ATAT-C4) and hybridization sequence in the presence of the double-strand-chelating dye Super SYBR Green (SG). The combination of prepared Au–Ag NCs, Super SG, and perfectly matched DNA emitted fluorescence at 500 and 590 nm,
respectively, when the composite was excited at 290 nm. A gastric cancer gene was also selectively detected by our developed ratiometric fluorescence probe.
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ELECTROCHIMICA ACTA
·
2012
·
IF 3.832
Xiaomeng Meng,Minrong Xu,Jianying Zhu,Huanshun Yin,Shiyun Ai
In this paper, a novel sensitive biosensor was fabricated for DNA detection based on gold nanoparticles (AuNPs) locked nucleic acid modified hairpin DNA probe (LNA-m-HpDNA) and enzymatic signal amplification. LNA-m-HpDNA dually labeled with 3′-thiol and 5′-biotin was efficiently assembled on the electrode via the interaction of thiol and gold. The stem-loop structure of LNA-m-HpDNA was unfolded after hybridization with target DNA, which forced biotin away from the electrode surface. Streptavidin-labeled horseradish peroxidase (Streptavidin-HRP) was subsequently immobilized on the electrode surface via the specific conjugation of biotin and streptavidin. Thereafter, the resulting HRP/target DNA–LNA-m-HpDNA (cDNA–LNA)/AuNPs modified Au electrode was successfully assembled for the construction of the DNA biosensor. Cyclic voltammetry and electrochemical impedance spectroscopy were carried out for the characterization of modified electrodes. Electrochemical reduction signal of benzoquinone was investigated in this work to indirectly analyze DNA hybridization via chronoamperometry. Under optimum conditions, the biosensor showed a good linear relationship between the current value and logarithm of the target DNA concentration ranging from 10 to 1000 pM with a low detection limit of 6.0 pM (S/N = 3). Furthermore, the DNA biosensor exhibited excellent discrimination ability to detect single-base mismatched DNA, three-base mismatched DNA and non-complementary DNA sequence. This strategy could provide a new platform for disease diagnose with high sensitivity.
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SENSORS
·
2024
·Vol. 24
·期 3
·773
·
IF 3.4
Hong Liu,Weiwei Wei,Jiajun Song,Jin Hu,Zhezhe Wang,Peng Lin
In this work, we report a new concept of upconversion-powered photoelectrochemical (PEC) bioanalysis. The proof-of-concept involves a PEC bionanosystem comprising a NaYF4:Yb,Tm@NaYF4upconversion nanoparticles (UCNPs) reporter, which is confined by DNA hybridization on a CdS quantum dots (QDs)/indium tin oxide (ITO) photoelectrode. The CdS QD-modified ITO electrode was powered by upconversion absorption together with energy transfer effect through UCNPs for a stable photocurrent generation. By measuring the photocurrent change, the target DNA could be detected in a specific and sensitive way with a wide linear range from 10 pM to 1 μM and a low detection limit of 0.1 pM. This work exploited the use of UCNPs as signal reporters and realized upconversion-powered PEC bioanalysis. Given the diversity of UCNPs, we believe it will offer a new perspective for the development of advanced upconversion-powered PEC bioanalysis.Keywords:photoelectrochemical biosensors;upconversion nanoparticles;energy transfer;photo reabsorption
研究领域:
生物分析学
·
纳米技术
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Nature Communications
·
2026
·
IF 18.1
Zhong Rui,Fu Yanjie,Jiang Shubao,Wang Shan,Yue Liang,Tan Weihong
Multistable systems, ideally, could stabilize at any desired, switchable state within a continuous spectrum. However, conventional systems, constrained by signal-mediated mutual activation or inhibition, are limited to a finite set of discrete steady states. Here, we propose a rational framework for achieving continuously tunable multistability through reversible displacement reaction-mediated competition between positive autoregulatory DNA polymerization/nicking modules. This framework harnesses the chemical energy of dNTP hydrolysis to suppress spontaneous interconversion between modules for stabilizing at any target state along a continuous compositional gradient. With unparalleled tunability, the framework enables continuous, orthogonal state transitions and concentration-adaptive molecular memory in response to transient stimuli. Moreover, the single-stranded DNAs generated by polymerization/nicking reactions can be customized with predefined structures and functions, enabling continuously multistable control over downstream processes, e.g., biocatalysis and RNA transcription, while maintaining multistability. This framework establishes a versatile and robust platform for developing chemical and material systems with continuously tunable multistability.
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Nature Protocols
·
2021
·Vol. 16
·期 12
·5460-5483
·
IF 13.491
Yao Chi,Zhang Rui,Tang Jianpu,Yang Dayong
DNA hydrogels have unique properties, including sequence programmability, precise molecular recognition, stimuli-responsiveness, biocompatibility and biodegradability, that have enabled their use in diverse applications ranging from material science to biomedicine. Here, we describe a rolling circle amplification (RCA)-based synthesis of 3D DNA hydrogels with rationally programmed sequences and tunable physical, chemical and biological properties. RCA is a simple and highly efficient isothermal enzymatic amplification strategy to synthesize ultralong single-stranded DNA that benefits from mild reaction conditions, and stability and efficiency in complex biological environments. Other available methods for synthesis of DNA hydrogels include hybridization chain reactions, which need a large amount of hairpin strands to produce DNA chains, and PCR, which requires temperature cycling. In contrast, the RCA process is conducted at a constant temperature and requires a small amount of circular DNA template. In this protocol, the polymerase phi29 catalyzes the elongation and displacement of DNA chains to amplify DNA, which subsequently forms a 3D hydrogel network via various cross-linking strategies, including entanglement of DNA chains, multi-primed chain amplification, hybridization between DNA chains, and hybridization with functional moieties. We also describe how to use the protocol for isolation of bone marrow mesenchymal stem cells and cell delivery. The whole protocol takes ~2 d to complete, including hydrogel synthesis and applications in cell isolation and cell delivery.
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Scientific Reports
·
2017
·Vol. 7
·期 1
·1-5
·
IF 4.259
Shi Chao,Wang Yifan,Zhang Menghua,Ma Cuiping
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis. We found that 20% PEG 200 could significantly catalyze DNA self-assembly and increase the reaction efficiency, such as linear hybridization chain reaction (HCR) and exponential hairpin assembly (EHA). Therefore, we foresee that a fast and efficient DNA self-assembly in structural DNA nanotechnology will be desirable.
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