TALANTA
·
2024
·
IF 5.6
Lifeng Zhang,Shihua Luo,Rui Fan,Ruixi Li,Wenbin Li,Siting Chen,Fei Lan,Yitong Zhu,Tingting Ji,Ye Zhang,Ling Li
APE1, an essential enzyme for DNA repair, is overexpressed in various cancers and has been identified as a potential biomarker for cancer diagnosis. However, detecting APE1 at low expression levels in the early stage of cancer presents a significant obstacle. Here, we introduced a novel localized Cas12a-based cascade amplification (LCas12a-CA) method. This method confined both the terminal deoxynucleotidyl transferase and the crRNA/Cas12a complex onto the surfaces of gold nanoparticles (AuNPs). This confinement not only boosts the stability of the multiple enzymes but also induces a substrate channeling effect. As a result, it significantly accelerates the reaction rate and enhances the sensitivity of APE1 detection. Upon the addition of APE1, the AP sites within the APE1 primer can be recognized and cleaved by APE1, exposing the 3′-OH ends. In the presence of LCas12a-CA, polyA sequences are generated at 3′-OH ends with the help of TdT and dATP. The sequences directly enter the Cas12a system, activating the trans -cleavage activity of Cas12a, thereby cutting the reporters on the surface of AuNPs and releasing fluorescence. Our platform demonstrates a detection limit (LOD) as low as 2.51 × 10 −6 U/mL, which is more than 60 times lower than that of free Cas12a-CA. Furthermore, the LCas12a-CA exhibits enhanced resistance ability in extreme environments and has been proven effective for the detection of APE1 in clinical samples. Overall, this work offers a promising platform for robust biosensing in cancer diagnosis and prognosis.
研究领域:
分子生物学
·
癌症研究
·
生物技术
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产品关联
DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2025
·
IF 6.7
Huimin Li,Xinru Yuan,Mei Ren,Jiajia Liu,Yixin Zheng,Ziyi Lin,Zixin Chen,Zhao Yang,Xin Su,Heyun Shen
Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/ref-1, APE1), a vital protein for DNA repair and cellular redox regulation, is frequently overexpressed in tumor cells, underscoring the importance of developing sensitive detection methods for early cancer diagnosis. However, the rapid detection and visualization of nuclear APE1 in tumor cells are still challenging. In this study, we successfully developed a novel DNA fluorescent nanoprobe based on polyamidoamine (PAMAM) for the rapid detection of cytoplasmic and nuclear APE1. The PAMAM surface was modified with arginine (Arg), named PR, and its hydrophobic core encapsulated the 1,6,7,12-tetrachloroperylene tetracarboxylic acid dianhydride (TA) dye to construct fluorescent nanoparticles (TPR). Furthermore, an APE1-responsive dsDNA (SP) was linked on the TPR surface, containing apurinic/apyrimidinic sites (AP sites) and the black hole quencher 2 (BHQ2) and ensuring that fluorescence remains off in the absence of APE1. TPR-SP exhibited a detection range of 0.125–25 U mL–1 and a detection limit as low as 0.03 U mL–1. Compared with the Arg-free nanoprobes (TP-SP), TPR-SP significantly accelerated endocytosis and nuclear penetration, reducing the APE1 detection time to one-quarter (from 2 to 0.5 h). Notably, the APE1 signal in the whole nucleus can also be significantly detected. Thus, the TPR nanoprobe achieves the rapid enrichment and amplification of fluorescence signals, leading to highly sensitive whole cellular APE1 detection. This innovative and efficient detection method greatly expands the technological means for early cancer detection.
研究领域:
生物化学
·
分子生物学
·
医学诊断
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
·
2024
·
IF 7.7
Mengxin Zhang,Yingyu Zhang,Qionglin Wang,Kangbo Liu,Lifeng Li,Zhidan Yu,Ligong Hou,Xianwei Zhang,Huan Zhao,Weyland Cheng,Wancun Zhang
In situ imaging of microRNA (miRNA) content and distribution is valuable for monitoring tumor progression. However, tumor specific in situ imaging remains a challenge due to low miRNA abundance, lack of biological compatibility, and poor specificity. In this study, we designed a DNA tetrahedral framework complex with hairpins (DTF-HP AP ) consisting of an apurinic/apyrimidinic site (AP site) that could be specifically recognized and cleaved by apurinic/apyrimidinic endonuclease 1 (APE1). Efficient and specific in situ imaging of miR-21 in tumors was thus achieved through catalytic hairpin assembly (CHA) reaction. In this study, DTF-HP AP was successfully constructed to trigger the cumulative amplification of fluorescence signal in situ . The specificity, sensitivity and serum stability of DTF-HP AP were verified in vitro , and DTF-HP AP could be easily taken up by cells, acting as a biosensor to detect tumors in mice. Furthermore, we verified the ability of DTF-HP AP to specifically image miR-21 in tumors, and demonstrated its capability for tumor-specific imaging in clinical samples.
研究领域:
分子生物学
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生物医学工程
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肿瘤学
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DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2025
·
IF 6.7
Junzhuo Shan,Yixiao Sheng,Lun Luo,Wenhai Wang,Xinjiang Liu,Yi Ma,Jufang Wang
Apurinic/apyrimidinic endonuclease 1 (APE1) is a key enzyme involved in DNA repair and cellular redox regulation, and is frequently overexpressed in tumor cells. This highlights the urgent need for a rapid and high-sensitive point-of-care testing (POCT) strategy for APE1 to facilitate early cancer diagnosis. Rolling circle amplification (RCA) is a widely used isothermal DNA amplification method; however, its application in APE1 detection remains rare. Here, we introduce a versatile RCA-Lock (Rlock) conversion platform that enables the transformation of RCA-based nucleic acid detection technologies into APE1-responsive assays. Building upon this platform, we further developed a novel POCT method for APE1 detection─Rlock-mediated, CRISPR/Cas12a-driven RCA cycle (RCRE)─which, for the first time, integrates CRISPR/Cas12a with RCA into a one-pot APE1 detection system. The RCRE assay achieves a limit of detection of 8.86 × 10–4 U/mL within 30 min, while requiring minimal equipment, low cost, and no complex handling procedures. This Rlock-based conversion strategy represents a transformative advance in the field of APE1 diagnostics and offers conceptual inspiration for the design of programmable nucleic acid–based biosensors. The resulting RCRE assay significantly broadens the technological landscape for early cancer detection and paves the way for future clinical translation.
研究领域:
分子诊断学
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生物化学
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生物技术
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癌症研究
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遗传学
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分析化学
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产品关联
DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2025
·
IF 6.7
Xiaofeng Bi,Jinyue Feng,Xiyuan Feng,Dianpeng Li,Yumin Wang,Shulin Zhao,Liangliang Zhang
The development of intelligent nanotheranostic technology that integrates diagnostic and therapeutic functions holds great promise for personalized nanomedicine. However, most of the nanotheranostic agents exhibit “always-on” properties and do not involve an amplification step, which may largely limit imaging contrast and restrict therapeutic efficacy. Herein, we construct a novel nanotheranostic platform (Hemin/DHPs/PDA@CuS nanocomposite) by assembling DNA hairpin probes (DHPs) and hemin on the surface of PDA@CuS nanosheets that enables amplified fluorescence imaging and activatable chemodynamic therapy (CDT) of tumors. The cancer-relevant APE1 triggers nucleic acid amplification with DHPs to generate activatable and amplified fluorescence signals for discriminating cancer cells from normal cells. Meanwhile, excessive G-quadruplex/hemin-based DNAzyme are also activated, and they function as Fenton-like catalysts to catalyze the production of highly toxic hydroxyl radicals (•OH) for CDT. Moreover, owing to the excellent photothermal conversion efficiency in the near-infrared-II (NIR-II) window, the PDA@CuS not only improves the catalytic performance of CDT but also furnishes PTT. A remarkable antitumor therapeutic effect is demonstrated both in vitro and in vivo. Therefore, the Hemin/DHPs/PDA@CuS nanocomposite is expected to provide a promising avenue for precise imaging-guided antitumor therapy.
研究领域:
生物医学工程
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肿瘤学
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纳米医学
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产品关联
DOI
PubMed
高影响因子
Analytical Methods
·
2025
·
IF 2.6
Changqing Du,Anran Li,Jinye Qiu,Jiarui Sun,Xiaokun Wang,Wei Xu,Maofeng Zhang,Dapeng Wang
Quantitative mRNA expression levels are essential for differential and clinical diagnoses. In this work, we present an apurinic/apyrimidinic endonuclease 1 (APE1)-assisted SERS sensing platform for rapid and ultrasensitive detection of TK1 mRNA. This platform utilizes a hairpin probe that contains a TK1 mRNA capture sequence along with an apurinic/apyrimidinic (AP) sites, which is specifically recognized and cleaved by APE1. Upon introduction of the target mRNA, hybridization occurs between the mRNA and the AP probe (HAP) within the hairpin structure, forming a doublestranded complex. APE1 then cleaves the HAP at the specific AP sites within the double-stranded complex, leading to a measurable change in the SERS intensity of the FAM-labeled HAP. Based on this principle, the developed SERS sensing platform demonstrates a highly linear response for TK1 mRNA detection across a wider range from 1 fM to 10 nM, with a detection limit (LOD) of 0.2 fM. Moreover, the SERS sensing platform shows great potential for the precise and quantitative detection of TK1 mRNA in human serum, which could be instrumental for mRNA-related research and the early clinical diagnosis of diseases.
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产品关联
DOI
PubMed
高影响因子
MICROCHEMICAL JOURNAL
·
2025
·
IF 5.1
Wentao Wang,Yingyu Zhang,Fei Zhang,Jing Gao,Zhidan Yu,Lifeng Li,Xianwei Zhang,Ligong Hou,Qiumei Zhou,Wancun Zhang
Sensitive, specific and simple quantitative and qualitative detection of nucleic acids is crucial for clinical diagnosis, especially in resource-limited settings. Therefore, in this study, an apurinic/apyrimidinic endonuclease 1 (APE1)-assisted cyclic amplification biosensor based on rolling circle amplification (RCA), referred to as A-RCA, was developed using molecular beacons as signal probes for highly sensitive and specific quantitative and qualitative detection of nucleic acids. The experimental results demonstrated that A-RCA exhibits exceptional sensitivity, with a detection limit of 19.5 aM and 14.3 aM for Mycoplasma pneumoniae ( M. pneumoniae ) DNA and M. pneumoniae RNA, respectively. In addition, A-RCA exhibits a broad linear range extending from 0.1 fM to 0.1 nM, and high specificity, enabling it to distinguish M. pneumoniae from other common respiratory pathogens. More importantly, a fluorescent test strip approach based on A-RCA (A-RCA-strip) was developed, enabling sensitive and specific point-of-care testing for the qualitative detection of nucleic acids. Similarly, the A-RCA-strip demonstrates high sensitivity, capable of detecting target signals as low as 0.1 fM, and exhibits high specificity in distinguishing M. pneumoniae from other common respiratory pathogenic microorganisms. Clinical detection showed that both A-RCA and A-RCA-strip could accurately identify M. pneumoniae , with 100 % concordance to established clinical methods. As a proof of concept, A-RCA and A-RCA-strip can detect other nucleic acid targets by simply changing the target sequence, providing a robust and versatile strategy for developing new clinical detection methods.
研究领域:
分子诊断
·
临床检验医学
·
分子生物学
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感染性疾病
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转化医学
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DOI
高影响因子
Biomolecules
·
2025
·Vol. 15
·期 9
·1275
·
IF 4.8
Yarong Zhang,Hongyan Ma,Zhenyao Gao,Miao Li,Fan Yang,Lingbo Sun,Yuecheng Zhang
Apurinic/apyrimidinic endonuclease 1 (APE1) selectively cleaves the apurinic/apyrimidinic site (AP site) in DNA, playing a critical role in base excision repair and genomic stability maintenance. Aberrant APE1 expression has been linked to numerous diseases, including cardiovascular disorders, neurological conditions, and various cancers. However, existing methods for detecting trace levels of APE1 remain suboptimal for certain applications. To address this limitation, we developed an innovative biosensing platform for ultrasensitive APE1 detection by integrating APE1-specific site recognition with hybridization chain reaction (HCR)-based signal amplification, enabling enzyme- and label-free bioassays. In this system, APE1 recognizes and cleaves the AP site-containing hairpin (HP) probe, releasing a single-stranded HCR initiator that triggers cascaded HCR amplification. Owing to the high efficiency of HCR, this method achieves ultrahigh sensitivity, with a calculated detection limit of 1.0 × 10−8U/mL. Furthermore, the biosensor demonstrates robust performance in cell lysates and is applicable for screening and evaluating APE1 inhibitors.
研究领域:
分子诊断
·
生物分析化学
·
癌症研究
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DNA修复机制
·
生物传感器开发
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产品关联
DOI
PubMed
高影响因子
Nature Communications
·
2024
·Vol. 15
·期 1
·1-23
·
IF 14.7
Yue Renye,Li Zhe,Liu Huiyi,Wang Youjuan,Li Yuhang,Yin Rui,Yin Baoli,Qian Haisheng,Kang Heemin,Zhang Xiaobing,Song Guosheng
Companion diagnostics using biomarkers have gained prominence in guiding radiotherapy. However, biopsy-based techniques fail to account for real-time variations in target response and tumor heterogeneity. Herein, we design an activated afterglow/MRI probe as a companion diagnostics tool for dynamically assessing biomarker apurinic/apyrimidinic endonuclease 1(APE1) during radiotherapy in vivo. We employ ultrabright afterglow nanoparticles and ultrasmall FeMnO x nanoparticles as dual contrast agents, significantly broadening signal change range and enhancing the sensitivity of APE1 imaging (limit of detection: 0.0092 U/mL in afterglow imaging and 0.16 U/mL in MRI). We devise longitudinally and transversely subtraction-enhanced imaging (L&T-SEI) strategy to markedly enhance MRI contrast and signal-to-noise ratio between tumor and normal tissue of living female mice. The combined afterglow and MRI facilitate both anatomical and functional imaging of APE1 activity. This probe enables correlation of afterglow and MRI signals with APE1 expression, radiation dosage, intratumor ROS, and DNA damage, enabling early prediction of radiotherapy outcomes (as early as 3 h), significantly preceding tumor size reduction (6 days). By monitoring APE1 levels, this probe allows for early and sensitive detection of liver organ injury, outperforming histopathological analysis. Furthermore, MRI evaluates APE1 expression in radiation-induced abscopal effects provides insights into underlying mechanisms, and supports the development of treatment protocols.
研究领域:
放射学
·
肿瘤学
·
医学影像
·
生物标志物研究
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治疗诊断学
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产品关联
DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2024
·
IF 6.7
Mengxin Zhang,Yingyu Zhang,Xianwei Zhang,Kangbo Liu,Lifeng Li,Zhidan Yu,Jingya Yuan,Wancun Zhang
Due to the potential off-tumor signal leakage and limited biomarker content, there is an urgent need for stimulus-responsive and amplification-based tumor molecular imaging strategies. Therefore, two tetrahedral framework DNA (tFNA-Hs), tFNA-H1AP, and tFNA-H2, were rationally engineered to form a polymeric tFNA network, termed an intelligent DNA network, in an AND-gated manner. The intelligent DNA network was designed for tumor-specific molecular imaging by leveraging the elevated expression of apurinic/apyrimidinic endonuclease 1 (APE1) in tumor cytoplasm instead of normal cells and the high expression of miRNA-21 in tumor cytoplasm. The activation of tFNA-H1AP can be achieved through specific recognition and cleavage by APE1, targeting the apurinic/apyrimidinic site (AP site) modified within the stem region of hairpin 1 (H1AP). Subsequently, miRNA-21 facilitates the hybridization of activated H1AP on tFNA-H1AP with hairpin 2 (H2) on tFNA-H2, triggering a catalytic hairpin assembly (CHA) reaction that opens the H1AP at the vertices of tFNA-H1AP to bind with H2 at the vertices of tFNA-H2 and generate fluorescence signals. Upon completion of hybridization, miRNA-21 is released, initiating the subsequent cycle of the CHA reaction. The AND-gated intelligent DNA network can achieve specific tumor molecular imaging in vivo and also enables risk stratification of neuroblastoma patients.
研究领域:
生物化学
·
分子生物学
·
医学影像学
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产品关联
DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2016
·Vol. 45
·期 6
·e45
·
IF 9.202
Zhai Junqiu,Liu Yibin,Huang Shan,Fang Simin,Zhao Meiping
Human apurinic/apyrimidinic endonuclease/redox effector factor 1 (APE1) is an essential DNA repair protein. Herein, we demonstrate that avidin-oriented abasic site-containing DNA strands (AP-DNA) on the surface of silica coated magnetic nanoparticles (SiMNP) can selectively respond to APE1 while resist the digestion by other nucleases. Mechanism studies have revealed that avidin may serve as an organizer protein and recruit APE1 to the DNA substrates on the nanoparticles via strong and specific interactions. Taking advantage of this newly disclosed property, we for the first time successfully displayed the intracellular activities of APE1 in living cells by fluorescence imaging. The avidin organized AP-DNA-SiMNP assembly holds great potential for enzyme-mediated release of drugs inside tumor cells which often contain higher levels of APE1 than normal cells.
研究领域:
分子生物学
·
医学
·
纳米技术
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产品关联
DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2025
·
IF 6.7
Junqiu Zhai,Han Zhang,Wenzhi Zhu,Jiewei Deng,Xinyan Li,Tiangang Luan
Simultaneous in situ monitoring of base excision repair (BER) correlated enzymes like apurinic/apyrimidinic endonuclease 1 (APE1) and flap endonuclease 1 (FEN1) in living cells offers valuable insights into their roles in disease development and cytotoxicity caused by pollutants, but comprehensive analysis is currently hindered by diverse enzyme functions and limited methods. In this study, we developed a dual-activatable DNA fluorescent probe (AP-FLAP) to simultaneously visualize APE1 and FEN1 activities, revealing the BER-related DNA damage caused by various environmental pollutants within living cells. The AP-FLAP probe was designed by ingeniously integrating a dumbbell structure containing a 5′ flap and a hairpin structure containing AP sites into a single oligonucleotide probe. APE1 specifically hydrolyzed the AP sites, releasing a 5-carboxy-X-rhodamine (ROX) signal, while FEN1 recognized and cleaved the 5′ flap, releasing a 6-carboxyfluorescein (FAM) signal. The probe allowed for independent determination of APE1 and FEN1 activities with good specificity and sensitivity. Subsequently, we applied the AP-FLAP probe to investigate base damage induced by 1-methylphenanthrene (1-MP) and 6-chlorobenzo[a]pyrene (6-Cl-BaP) in human umbilical vein endothelial cells (HUVECs). Significant base damage by 1-MP and 6-Cl-BaP exposure was revealed, with a positive correlation of damage degree with different exposure concentrations from 0.1 to 100 μM. Notably, 6-Cl-BaP caused significant damage even at 0.1 μM, in a concentration-dependent manner. Our work provides a powerful tool for elucidating BER molecular mechanisms and DNA damage repair under environmental exposure and opens new avenues for developing multifunctional nucleic acid probes for a wide range of applications in chemical biology and biomedical research.
研究领域:
分子生物学
·
细胞生物学
·
环境毒理学
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DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）