MICROCHIMICA ACTA
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2024
·Vol. 191
·期 12
·1-10
·
IF 5.3
Ye Tai,Luo Zheng,Che Yueyue,Yuan Min,Cao Hui,Hao Liling,Zhang Qian,Xie Yongxin,Zhang Kaisen,Xu Fei
An inverted DNA tetrahedron–mediated modular DNA walker was developed for the determination of sulfadimethoxine. The inverted DNA tetrahedron scaffold raises several advantages of recognition module including appropriate lateral space, multiple recognition domains, and cost-effectiveness. The proposed inverted DNA tetrahedron-based recognition module exhibited better binding affinity and kinetics toward target antibiotic than that of other DNA tetrahedron counterparts. Upon specific binding with target, the released bipedal DNA walking strand hops to the signal amplification module and moves stochastically with assistant of nicking enzyme. By coupling these two modules, a good linear relationship between the fluorescence intensity of supernatant and the concentration of sulfadimethoxine was achieved in the range 0.1–100 nM, and the limit of detection was 64.7 pM. Furthermore, this modular DNA walker had also successfully applied to spiked honey and milk samples with satisfactory recoveries from 91.5 to 108.8%, demonstrating its practical sensing capability. Graphical
研究领域:
生物化学
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分子生物学
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分析化学
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PubMed
高影响因子
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.
研究领域:
分子生物学
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分析化学
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生物医学工程
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临床诊断
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高影响因子
RSC Advances
·
2020
·Vol. 10
·期 51
·31012-31021
·
IF 3.119
Shengmei Wang,Linqi Ouyang,Guiming Deng,Zhenzhen Deng,Shengfeng Wang
DNA functionalized nanomaterials have attracted tremendous attention for bioanalytical applications. Owing to exceptional fluorescence quenching ability, most DNA-based nanoprobes were designed with turn-on signals for target gene detection, while only a few of them could simultaneously achieve gene detection and regulation in one system. In this study, we explored the use of nanoscale zeolitic imidazolate framework-8 (ZIF-8) as a building block to construct a DNA-based nanoprobe. We found ZIF-8 could stably adsorb DNA to resist the dissociation by various biological ligands, enabling potential biological applications. However, ZIF-8 was not a nano-quencher to turn off the fluorophore labeling on the adsorbed DNA. We therefore designed a DNAzyme embedded molecular beacon (DMB) to functionalize ZIF-8. After endocytosis, ZIF-8 was disintegrated to release DMB for target mRNA detection, and the co-released Zn2+ acted as an effective cofactor to activate the embedded DNAzyme for mRNA regulation. This study provides a versatile nano-platform to realize multiple functions inside cells by using functional nucleic acids, which holds great promise for theranostic applications.
研究领域:
生物化学
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纳米技术
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分子生物学
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生物医学工程
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DOI
PubMed
高影响因子
IEEE SENSORS JOURNAL
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2024
·Vol. 24
·期 24
·40904-40911
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IF 4.3
Xuegang Li,Pengqi Gong,Xue Zhou
Deoxyribonucleic acid (DNA) detection represents an important direction of diagnosis and treatment of genetic diseases, which contains all the genetic information of the human body. The DNA sequence remains extremely challenging to detect, despite numerous previous studies that have achieved selective detection, due to the backward sensing scheme. For low-cost, high-sensitivity DNA hybridization detection, a probe-type highly sensitive DNA detection method based on surface plasmon resonance (SPR) is demonstrated in this article. First, low-cost refractive index (RI) tracking detection can be completed via optical fiber SPR. Then, the selective detection of complementary DNA (cDNA) is achieved by binding the probe DNA (pDNA) sequence to the optical fiber SPR sensor using polyethyleneimine (PEI). Compared with previous studies, the sensitivity [0.13 nm/(nmol/L)] is greatly upgraded, and the detection limit (DL) is reach to 4.87 nmol/L. This low-cost and high-performance optical fiber sensing method is conducive to the further development of DNA hybridization detection technology.
研究领域:
生物医学工程
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分子生物学
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高影响因子
BIOCONJUGATE CHEMISTRY
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2016
·
IF 4.5
Jianbo Li,Dawei Jiang,Baoliang Bao,Yulin He,Lei Liu,Xuemei Wang
Self-assembled DNA nanostructures, as a new type of nanocarriers, have shown great potential in molecular imaging probes. DNA bipyramid nanostructures (DBNs), as a classic kind of DNA nanostructure, can be precisely constructed through the unparalleled base-pairing precision of oligonucleotide strands. DBNs were prepared by self-assembly of six oligonucleotides with equal molar amounts in a single annealing step, and purified by high performance liquid chromatography (HPLC). DBNs were stable in 10% FBS as well as 80% mouse serum for at least 8 h. To prepare 99mTc-labeled DBNs, N-hydroxysuccinimidyl S-acetylmercaptoacetyl triglycinate (Sacetyl-MAG3-NHS ester) tagged single-stranded DNA (ssDNA) was first radiolabeled with Tc-99m, and DBNs with an overhang were assembled and then hybridized with 99mTc-ssDNA to prepare 99mTc-labeled DNA bipyramid nanostructures (99mTc-MAG3-DBNs). DBNs were radiolabeled, with the radiochemical purity being over 90%. The plasma half-life of 99mTc-MAG3-DBNs in normal KM mice was about 6 min. The biodistribution and SPECT/CT imaging were conducted with 99mTc-MAG3-DBNs in KM mice, and both showed that 99mTc-MAG3-DBNs mainly concentrated in the intestine, liver, and kidneys, and there was also prominent uptake in the gallbladder and bladder. We successfully obtained a new class of SPECT molecular probes based on this DNA polyhedron structure.
研究领域:
核医学
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分子影像
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生物化学
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放射学
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PubMed
高影响因子
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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2019
·Vol. 21
·期 6
·2919-2928
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IF 3.567
Kang-Tao Liu,Shi-Yong Ran
The metal ion–DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T–Hg2+–T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanism has not been fully understood. In the present study, we used magnetic tweezers to explore the interactions between λ-DNA and two metal ions, Hg2+ and Cd2+, at the single-molecule level. Both metal ions caused considerable DNA conformational changes. The resulting DNA compaction dynamics were related to the ion concentration and the exerted force. The increase in the ion concentration promoted DNA compaction, whereas exerting greater forces inhibited this process. Application of a high force generated two-stage dynamics of the Hg2+–DNA interaction. However, at a sufficiently high Hg2+ concentration, a lower force led to a three-stage process. In contrast, the curves of the binding of Cd2+ ions to DNA had a stepwise pattern. Both the AFM scanning results and the single-molecule measurements confirmed that Hg2+ influences the DNA conformation in a more pronounced manner than Cd2+. The multistage Hg2+–DNA interaction was considered to be a result of the different binding mechanisms, including the mismatched base-pair formation. A model was then proposed to explain the peculiar dynamics.
研究领域:
生物物理学
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分子生物学
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PubMed
高影响因子
Materials
·
2018
·Vol. 11
·期 2
·272
·
IF 2.467
Wenjuan Guo,Yanhong Wei,Zhao Dai,Guangping Chen,Yuanyuan Chu,Yifei Zhao
Based on the fluorescence resonance energy transfer (FRET) mechanism, fluorescent DNA probes were prepared with a novel DNA hairpin template method, with SiO2coated CdTe (CdTe/SiO2) core/shell nanoparticles used as the fluorescence energy donors and gold (Au) nanoparticles (AuNPs) as the energy acceptors. The nanostructure and energy donor/acceptor ratio in a probe were controlled with this method. The relationship between the nanostructure of the probes and FRET efficiency (quenching efficiency) were investigated. The results indicated that when the donor/acceptor ratios were 2:1, 1:1, and 1:2; the corresponding FRET efficiencies were about 33.6%, 57.5%, and 74.2%, respectively. The detection results indicated that the fluorescent recovery efficiency of the detecting system was linear when the concentration of the target DNA was about 0.0446–2.230 nmol/L. Moreover, the probes showed good sensitivity and stability in different buffer conditions with a low detection limit of about 0.106 nmol/L.Keywords:fluorescent DNA probes;CdTe/SiO2nanoparticles;Au nanoparticles;DNA hairpin template;nanostructure;quenching efficiency
研究领域:
生物化学
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纳米生物学
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PubMed
高影响因子
ANALYST
·
2021
·Vol. 146
·期 18
·5643-5649
·
IF 4.616
Li Tan,Jiangnan Lu,Xin Wang,Guang Liu,Xiaomei Mu,Kun Hu,Shulin Zhao,Jianniao Tian
Highly specific and ultrasensitive detection of uracil-DNA glycosylase (UDG) activity is of great significance for maintaining genomic integrity and medical research of related diseases. Here, we constructed a random DNA walking nanomachine based on a DNAzyme for UDG activity detection on the AuNP (Au nanoparticle) surface. When UDG is present, the U bases in the Y structure are removed, resulting in AP sites, which will be cleaved by Endo-IV to generate a 3′ concave end for Exo-III, causing the locking strand of the DNAzyme to be completely hydrolyzed by the Exo-III and release the walking strand to randomly pair with the substrate strand on the AuNP surface; then, the walking strand exerts its cleavage activity with the assistance of Mg2+ to cleave the substrate strand and keep the fluorophore 6-carboxyfluorescein (FAM) away from the surface of the AuNP, which restores the fluorescence signal of this system. In this way, sensitive detection of UDG can be realized, and the detection limit is as low as 3.69 × 10−6 U mL−1. In addition, we found that this method is highly specific to UDG and can be used to detect UDG specifically in complex samples, which has certain application prospects in biomedical research and clinical diagnosis related to UDG.
研究领域:
分子生物学
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纳米技术
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生物医学工程
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分析化学
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PubMed
高影响因子
BIOSENSORS & BIOELECTRONICS
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2018
·
IF 8.173
Xing-Pei Liu,Jing-Shuai Chen,Chang-jie Mao,He-Lin Niu,Ji-Ming Song,Bao-Kang Jin
A novel enhanced photoelectrochemical DNA sensor, based on a TiO 2 /Au hybrid electrode structure , was developed to detect target DNA. The sensor was developed by successively modifying fluorine-tin oxide (FTO) electrodes with TiO 2 nanoparticles , gold (Au) nanoparticles, hairpin DNA (DNA1), and CdSe-COOH quantum dots (QDs), which acted as signal amplification factors . In the absence of target DNA, the incubated DNA1 hairpin and the CdSe-COOH QDs were in close contact with the TiO 2 /Au electrode surface , leading to an enhanced photocurrent intensity due to the sensitization effect. After incubation of the modified electrode with the target DNA, the hairpin DNA changed into a double helix structure, and the CdSe QDs moved away from the TiO 2 /Au electrode surface, leading to a decreased sensitization effect and photoelectrochemical signal intensity. This novel DNA sensor exhibited stable, sensitive and reproducible detection of DNA from 0.1 μM to 10 fM, with a lower detection limit of 3 fM. It provided good specificity, reproducibility, stability and is a promising strategy for the detection of a variety of other DNA targets, for early clinical diagnosis of various diseases.
研究领域:
生物化学
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分析化学
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纳米技术
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生物医学工程
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PubMed
高影响因子
ADVANCED MATERIALS
·
2024
·
IF 27.4
Hongli Yang,Peihua Lin,Bo Zhang,Fangyuan Li,Daishun Ling
During fractionated radiotherapy, DNA damage repair intensifies in tumor cells, culminating in cancer radioresistance and subsequent radiotherapy failure. Despite the recent development of nanoradiosensitizers targeting specific DNA damage repair pathways, the persistence of repair mechanisms involving multiple pathways remains inevitable. To address this challenge, a nucleophilicity-engineered DNA ligation blockade nanoradiosensitizer (DLBN) comprising Au/CeO 2 heteronanostructure modified with trans-acting activator of transcription peptides is reported, which targets and inhibits the DNA ligation inside cancer cell nuclei via heterointerface-mediated dephosphorylation of DNA, a crucial step in overcoming cancer radioresistance. First, the Schottky-type heteronanostructure of cancer cell nucleus-targeting DLBN effectively intensifies radiation-induced DNA damage via catalase-mimetic activity and radiation-triggered catalytic reactions. Notably, by leveraging Au/CeO 2 heterointerface, DLBN spontaneously dissociates H 2 O to hydroxide, a nucleophile with higher nucleophilicity, thereby exhibiting remarkable dephosphorylation capability at DNA nicks through facilitated nucleophilic attack. This enables the blockade of DNA ligation, a pivotal step in all DNA damage repair pathways, effectively interrupting the repair process. Consequently, DLBN resensitizes radioresistant cells by overcoming therapy-induced radioresistance, leading to a substantial accumulation of unrepaired DNA damage. These findings offer insight into the dephosphorylation of DNA within nuclei, and underscore the potential of heteronanostructure-based nanoradiosensitizer to block DNA ligation against therapy-induced radioresistance.
研究领域:
癌症治疗
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纳米技术
·
放射生物学
·
分子生物学
·
材料科学
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PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
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2024
·
IF 3.1
Chu Cheng,Qingzhou Cheng,Wei Zhou,Yulong Chen,Pengfeng Xiao
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3’-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
研究领域:
分子生物学
·
遗传学
·
医学
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PubMed
高影响因子
SENSORS AND ACTUATORS B-CHEMICAL
·
2017
·
IF 5.401
Gonge Tang,Jie Gao,Caihong Wang,Hongliang Tan
Lanthanide coordination polymers (LnCPs) have aroused tremendous interest in recent years because of their unique structural and optical properties, but the construction of LnCPs-based fluorescent probe for sensing of biomacromolecules still remains a great challenge. In this work, a sensitive DNA fluorescent sensor was developed by integrating europium-containing coordination polymers (Eu/BTC CPs) with single-stranded DNA (ssDNA) probe labelled with dye. The Eu/BTC CPs is able to selectively absorb ssDNA probe due to π–π stacking interaction, and release it upon the introduction of complementary target DNA, leading to a fluorescence change of ssDNA probe labelled dye. However, the fluorescence of Eu/BTC CPs itself remains constantly along with the absorption and detachment of ssDNA probe on the surface of Eu/BTC CPs, which enables target DNA to be detected by naked-eyes. The presented DNA sensor not only showed high detection sensitivity, but also is capable of distinguishing complementary and single-base mismatched target DNA sequence with excellent selectivity. As a DNA sensing material, Eu/BTC CPs also possesses the features of simple preparation procedures and outstanding stability. Moreover, the presented sensor was successfully applied to determine the DNA levels in fetal bovine serum sample and showed a satisfactory result. We believe that the integration of LnCPs with ssDNA probe could find great potential applications for ultrasensitive fluorometric assays and biomedical imaging in the future.
研究领域:
生物化学
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分析化学
·
材料科学
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高影响因子
危险品化学品经营许可证（带存储）