SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2026
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IF 4.8
Dechan Lu,Rubing Bai,Jingwen Lin,Tao Wang,Chaofan Lv,Rongmao Qiu
Lung cancer mortality remains high due to the difficulty in accurately distinguishing early-stage lung cancer (LC) from benign lung disease (BLD) via conventional diagnostic approaches, and DNA methylation serves as an ideal early epigenetic marker for LC diagnosis while lacking efficient detection technologies. Herein, we developed a multi-pH fused surface-enhanced Raman scattering (SERS) strategy for label-free DNA methylation detection, enabling preliminary discrimination potential between early-stage LC and BLD. We first identified pH-dependent methylation-associated spectral markers by investigating SERS characteristics of cytosine/5-methylcytosine and methylated/unmethylated DNA standards under acidic (pH 3), neutral (pH 7) and alkaline (pH 9) conditions, and validated the specificity and universality of these markers at cellular level (A549/BEAS-2B cells). For clinical formalin-fixed paraffin-embedded (FFPE) samples, we quantified the pH-responsive intensity variations of core methylation-associated peaks in LC and BLD DNA, and further constructed a principal component analysis-linear discriminant analysis (PCA-LDA) model to compare the diagnostic efficacy of single-pH and multi-pH fused SERS spectra. Single-pH SERS detection showed limitations with low diagnostic performance, while the multi-pH spectral fusion strategy integrated complementary methylation feature information across different pH conditions, achieving a diagnostic accuracy of 0.93 for LC-BLD discrimination in clinical FFPE samples, with excellent sensitivity and specificity. This study presents a multi-pH fused SERS method for DNA methylation-associated spectral analysis, which improves the capture of complementary spectral information compared with single-pH detection and provides a label-free exploratory approach for differentiating early-stage LC from BLD.
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INFRARED PHYSICS & TECHNOLOGY
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2026
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IF 3.8
Lu Chen,Xili Jing,Tianli Huo,Dongfang Li,Mingshi Song,Shuguang Li
Currently, the high-precision quantification of disease-related complementary DNA (cDNA) remains difficult, owing to the complex procedures of existing nucleic acid detection methods and their susceptibility to temperature fluctuations. Therefore, a dual-film-modulated fiber-optic surface plasmon resonance (SPR) biosensor with self-temperature compensation was proposed in this work, enabling high-precision detection of cDNA concentration through real-time temperature readout for in-situ temperature correction to improve the controllability of the measurement process. A low-loss no-core fiber (NCF) was used as the sensing platform, with an Ag film as the SPR excitation layer. A CeF 3 film was introduced into the DNA channel to enhance the interfacial response, while a TiO 2 layer was introduced into the temperature channel to regulate the resonance band and enable thermal readout. Simulations verified the sensitization effect of CeF 3 and the resonance wavelength modulation effect of TiO 2 . Further single-channel calibration and cascaded tests showed that the two channels operated independently with negligible crosstalk. The experimental results demonstrated that, over a cDNA concentration range of 0-90 nM, the DNA probe exhibited a maximum sensitivity of 0.412 nm/nM, an average sensitivity of 0.294 nm/nM, and a limit of detection (LOD) of 1.62 nM. Compared with conventional single-layer Au/Ag fiber-optic SPR nucleic acid sensors, the proposed sensor, with the synergistic integration of a CeF 3 sensitization layer and temperature compensation, achieves more accurate DNA quantification and a more competitive LOD. Its low cost and streamlined fabrication process further enhance its value for large-scale deployment, underscoring its strong potential in biomedical applications such as disease monitoring.
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Cell Reports
·
2025
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IF 6.9
Xihui Xu,Yue Dou,Shangjun Zhao,Chunfang Zhao,Yahua Chen,Mingyi Jiang,Zhenguo Shen,Chen Chen
Plants deploy a “cry-for-help” strategy to recruit beneficial microbes, thereby enhancing stress resistance and expanding their ecological niches in harsh environments. However, the molecular mechanisms driving this plant-microbe communication remain poorly understood. To uncover the underlying dialogue, we explore interactions between two plant-growth-promoting bacteria (PGPBs) and their host plants, rice and Solanum nigrum , under heavy metal (HM) stress. We identify an interkingdom signaling pathway, characterized by “root reactive oxygen species (ROS)-microbial indole-3-acetic acid (IAA)-root DNA methylation,” which mediates plant-PGPB interactions. Under HM stress, root-derived ROS triggers IAA synthesis in PGPBs, which subsequently suppresses ROS production in the roots, thereby mitigating HM damage in plants. Furthermore, PGPB-derived IAA induces root DNA methylation modifications via ROS-dependent pathways, establishing a cross-kingdom signaling mechanism that links microbial metabolism to plant DNA methylation. This interkingdom signaling pathway is widely observed in the rhizosphere, providing insights into plant-microbe interactions in adverse environments.
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Nature Communications
·
2023
·Vol. 14
·期 1
·1-17
·
IF 16.6
Zhang Weina,Wang Mingzhu,Song Zhiwei,Fu Qianzheng,Chen Jiayu,Zhang Weitao,Gao Shuai,Sun Xiaoxiang,Yang Guang,Zhang Qiang,Yang Jiaqing,Tang Huanyin,Wang Haiyan,Kou Xiaochen,Wang Hong,Mao Zhiyong,Xu Xiaojun,Gao Shaorong,Jiang Ying
Farrerol, a natural flavanone, promotes homologous recombination (HR) repair to improve genome-editing efficiency, but the specific protein that farrerol directly targets to regulate HR repair and the underlying molecular mechanisms have not been determined. Here, we find that the deubiquitinase UCHL3 is the direct target of farrerol. Mechanistically, farrerol enhanced the deubiquitinase activity of UCHL3 to promote RAD51 deubiquitination, thereby improving HR repair. Importantly, we find that embryos of somatic cell nuclear transfer (SCNT) exhibited defective HR repair, increased genomic instability and aneuploidy, and that the farrerol treatment post nuclear transfer enhances HR repair, restores transcriptional and epigenetic network, and promotes SCNT embryo development. Ablating UCHL3 significantly attenuates farrerol-mediated stimulation in HR and SCNT embryo development. In summary, we identify farrerol as an activator of the deubiquitinase UCHL3, highlighted the importance of HR and epigenetic changes in SCNT reprogramming and provide a feasible method to promote SCNT efficiency.
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Journal of Environmental Chemical Engineering
·
2023
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IF 7.7
Qingbin Yuan,Shangjie Wang,Yuying Chen,Xiaohan Li,Yisi Xu,Ruiqing Li,Yi Wang,Yi Luo
Extracellular antibiotic resistance genes (exARGs) constitute a significant type of antibiotic resistance genes. However, current exARGs studies are restricted due to the lack of efficient extraction methods for extracellular DNA (exDNA), which are laborious, dependent on extra experimental agents, and prone to interference by coexisting substances. In this study, we have developed an ultra-selective exDNA extraction method based on molecular imprinting technology . The resulting guanine imprinted beads are micron grade spheres with high capacity (384.6 mg/g) and speed (90% adsorption in 10 min) for DNA adsorption at variable lengths, including ultra-short DNA (<100 bp)， without requiring extra agents. The guanine-imprinted beads demonstrated exclusive DNA adsorption capabilities and avoided interference by other competing substances. Furthermore, guanine imprinted beads effectively extracted DNA at ideal recovery efficiencies (81%∼109%) from diverse environments, such as soil, air, river water and vegetable. Higher abundance of exARGs was obtained by using guanine imprinted beads than currently used commercial magnetic beads. In addition to exDNA extraction quality, a higher diversity of exDNA-releasing bacteria was acquired by guanine imprinted beads. This contributes to 1.2-fold increase in ARG-genera (172 v.s. 150) and 3.6-fold increase in ARG-pathogen associations (96 v.s. 27), indicating a greater number of bacterial hosts of ARGs. This study provides a simple and robust method for advanced exDNA studies, such as discovering novel exARGs and identifying hosts of exARGs.
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BIOSENSORS & BIOELECTRONICS
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2023
·
IF 12.6
Gu Shi,Chong Yan,Junhua Chen
Sensitive and reliable detection of antibiotics is of great significance for environmental and food safety due to its high risk in trace concentrations. Herein, we developed a fluorescence sensing system for chloramphenicol (CAP) detection based on dumbbell DNA-mediated signal amplification . Two hairpin dimers (2H1 and 2H2) were employed as the building blocks to construct the sensing scaffolds. The CAP-aptamer binding in another hairpin H0 can liberate the trigger DNA , which then activates the cyclic assembly reaction between 2H1 and 2H2. The separation of FAM and BHQ in the formed product of cascaded DNA ladder yields a high fluorescence signal for CAP monitoring. Compared with the monomer hairpin assembly between H1 and H2, the dimer hairpin assembly between 2H1 and 2H2 exhibits enhanced signal amplification efficiency and reduced reaction time. The developed CAP sensor showed a wide linear range from 10 fM to 10 nM with a detection limit of 2 fM. Importantly, this sensing platform has been successfully applied to the determination of CAP in fish, milk, and water samples with satisfactory recovery and accuracy. With the advantages of high sensitivity, mix-and-read pattern, and robustness, our proposed CAP sensor can be used as a simple and routine tool for the detection of trace amounts of antibiotic residues.
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MICROCHIMICA ACTA
·
2023
·Vol. 190
·期 3
·1-10
·
IF 5.7
Tang Juan,Liu Liping,Wang Haiyang,Cheng HongLi,Qin Jiao,Zeng Zhiyao,Lin Youxiu,Tang Dianping,Pu Shouzhi
A flexible photoelectrochemical (PEC) biosensor is proposed for the sensitive detection of ochratoxin A (OTA) based on glucose oxidase (GOx)-encapsulated target-responsive hydrogel, using Fenton reaction-mediated in situ formation of polyaniline (PANI) as signal amplified strategy. The target-responsive DNA hydrogels with high loading capacity can carry a large amount of GOx, which not only avoids laborious labeling process but also enhances the analytical performance. Upon introduction of target molecules, the hydrogel can be opened, and multiple GOx was released, thus producing lots of H 2 O 2 via catalytic reduction of glucose. As a component of the Fenton reagent, H 2 O 2 can react with the Fe 2+ on the graphene oxidase-PAMAM-Fe 2+ (GO-PAMAM-Fe 2+ ) to generate Fe 3+ and ·OH. This in turn can oxidize aniline and generate polyaniline (PANI), resulting in the enhancement of the photocurrent signal of GO-MoS 2 -CdS photoelectrode. The GO-PAMAM-Fe 2+ as the neighborhood component of GO-MoS 2 -CdS-based photoactive material not only can increase the loading amount of Fe 2+ , but also can inhibit the decrease of photocurrent of GO-MoS 2 -CdS by direct modification of Fe 2+ on the photoactive material. Moreover, the high loading capacity of DNA hydrogel can efficiently promote the performance of the PEC biosensor. The PEC biosensor exhibited satisfactory analytical performance for OTA with a linear range of 0.0001–0.1 ng/mL and a low detection limit of 0.05 pg/mL. It presents recommendable specificity, stability, and practical applications. Importantly, the PEC biosensor provides a new concept for construction of PEC biosensing platform. Graphical abstract
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CHEMICAL ENGINEERING JOURNAL
·
2023
·
IF 15.1
Longfei Tang,Jingyi Yang,Ziting Liu,Qin Mi,Lili Niu,Juan Zhang
A new nanoprobe (DTAAT) has been well designed based on DNA tetrahedron supported hybridization chain reaction (HCR) and further applied for in situ analysis of bacteria. Antibody-aptamer conjugate (AA) has been coupled with DNA tetrahedron (DT) followed by the linkage of trigger strand (A). Bacteria can be preciously recognized by dual binding of both antibody and aptamer in DTAAT, to release trigger strand which is complementary with aptamer. By virtue of proximity effect, the released trigger strand can further efficiently induce the simultaneous occurrence of arrays of HCR at three vertices of DT, with rapid reaction rate of 359.29 min −1 in comparison with that of 212.60 min −1 for free HCR. DTAAT can be served for in situ imaging of bacteria by confocal laser scanning microscopy and single-cell characterization by flow cytometry. Moreover, using DTAAT as probe, the quantitative analysis of bacteria can be realized with high specificity and anti-interference capability. In a word, the developed DTAAT nanoprobe has a great potential for accurate and sensitive in situ analysis of bacteria.
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ANALYST
·
2023
·Vol. 148
·期 4
·799-805
·
IF 4.2
Shixin Cai,Xin Chen,Haohan Chen,Yuting Zhang,Xiaoli Wang,Nandi Zhou
The development of sensitive adenosine triphosphate (ATP) sensors is imperative due to the tight relationship between the physiological conditions and ATP levels in vivo. Herein, a fluorescent aptasensor for ATP is presented, which adopts a strategy that combines a split aptamer and a DNAzyme/walker with terminal deoxynucleotidyl transferase (TDT)-assisted formation of DNA-AgNCs to realize fluorescence detection of ATP. A multifunctional oligonucleotide sequence is rationally designed, which integrates a split aptamer, a DNAzyme and a DNA walker. Both multifunctional oligonucleotide and its substrate strand are connected to the surface of Fe3O4@Au nanoparticles via Au–S bonds. The existence of ATP can induce the formation of the complete aptamer, and then activate the DNAzyme to circularly cleave the substrate strand, leaving 2′,3′-cyclophosphate at the 3′end of the strand. This blocks the polymerization of dCTP to form poly(C) even in the presence of TDT and dCTP, due to the lack of free 3′-OH. In contrast, when ATP is absent, the DNAzyme/walker cannot work and then TDT catalyzes the formation of poly(C) at the free 3′-OH of the substrate strand, which is subsequently utilized as the template to prepare DNA-AgNCs. The fluorescence response derived from AgNCs thus reflects the ATP concentration. Under the optimum conditions, the aptasensor shows a linear response range from 5 nM to 10 000 nM, with a detection limit of 0.27 nM. The level of ATP in human serum can be effectively measured by the aptasensor with good recovery, indicating its application potential in medical samples.
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Journal of Materials Chemistry B
·
2022
·Vol. 11
·期 1
·99-108
·
IF 7.571
Yongtao Wang,Nana Wang,Yazhou Chen,Yingjun Yang
Breast cancer is considered as a worldwide disease due to its high incidence and malignant metastasis. Although numerous techniques have been developed well to conduct breast cancer therapy, the influence of micropattern-induced interfacial heterogeneity on the molecular mechanism and nuclear signalling transduction of carcinogenesis is rarely announced. In this study, PDMS stencil-assisted micropatterns were fabricated on tissue culture plates to manage cell clustering colony by adjusting initial cell seeding density and the size of microholes. The curvature of each microholes was controlled to construct the interfacial heterogeneity of MDA-MB231 cancer cells at the periphery of micropatterned colony. The distinguished focal adhesion (FA) and cytoskeleton distribution at the central and peripheral regions of the cell colony were regulated by heterogeneous properties. The interfacial heterogeneity of FA and cytoskeleton would induce the biased tension force to encourage more ezrin expression at the periphery and further promote DNA synthesis, therefore disclosing a stem-like phenotype in heterogeneous cells. This study will provide a value source of information for the development of micropattern-induced heterogeneity and the interpretation of metastatic mechanism in malignant breast cancer cells.
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CHEMICAL ENGINEERING JOURNAL
·
2022
·
IF 16.744
Xiaoyang Liang,Ping Liu,Wen Li,Long Binh Vong,Tingting Wang,Lujing Geng,Yue Zhou,Siyu Wang,Qiang Lu,Fengping Tan,Xinxing Wang,Nan Li
Reactive oxygen species (ROS)-mediated cell cycle arrest mechanism shows distinguished potential for the inhibiting of cancer cells. However, poly ADP-ribose polymerase (PARP), an enzyme which can contribute to the repair of single-strand DNA nicks, largely limited the efficiency in cell cycle arrest. Here, polydopamine (PDA)/hyaluronic acid (HA) decorated and protein translation inhibitor homoharringtonine (HHT) loaded tellurium (Te)-prussian blue (PB) nanorods ( [email protected] @PDA-HA/HHT NRs) were synthesized for boosted G2 cell cycle arrest to realize tumor ablation. Under NIR-II irradiation, Te and Fe elements can collectively generate ROS and deplete GSH due to the fenton-like reaction and metal-reducing reaction under tumor microenvironment (TME), thus disturbing the DNA structure to induce cell cycle arrest. More importantly, HHT suppresses PARP production to induce DNA repair dysfunction, thereby boosting DNA oxidative damage. Remarkably, this nanoplatform degrades into ionic form under acid condition, illustrating inherently TME-responsive biodegradability. The anti-tumor evaluation illustrated that [email protected] @PDA-HA/HHT NRs could notably destroy tumor cells in both cellular experiments and mouse models. This study made a successful attempt in boosted cell cycle arrest and encouraged more biological explorations on biodegradation nanomaterials, especially in combating cancers.
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BIOSENSORS & BIOELECTRONICS
·
2022
·
IF 12.545
Lina Wang,Duo Yi,Youfu Geng,Tingting Duan,Zhifeng Tong,Shaolan Chen,Zhiyao Ning,Yu Du,Xueming Hong,Xuejin Li
The rapid and efficient detection of deafness gene DNA plays an important role in the clinical diagnosis of deafness diseases. This study demonstrates the ultrasensitive detection of complementary DNA (cDNA) by employing a nanointerface-sensitized fiber optic biosensor. The sensor consists of SMF-TNCF-MMF-SMF (abbreviated as STMS) structure with lateral offset. Besides, it is functionalized with a nanointerface of black phosphorus (BP) to enhance the light-matter interaction and eventually improve the sensing performances. Relying on this nanointerface-sensitized sensor, we successfully realize the in-situ detection of cDNA at concentrations ranging from 1 pM to 1 μM, with a sensitivity of 0.719 nm/lgM. The limit of detection (LOD) is as low as 0.24 pM, which is at least two orders of magnitude lower than those of existing methods. The sensor exhibits the advantages of simple operation, fast response, label-free measurement, excellent repeatability, and high selectivity. Our contribution suggests a convenient approach for deafness gene DNA detection and can be extended for general ultra-low concentration DNA detection applications.
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