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Song SF, Zhang XW, Chen S, Shu Y, Yu YL, Wang JH. CRISPR-based dual-aptamer proximity ligation coupled hybridization chain reaction for precise detection of tumor extracellular vesicles and cancer diagnosis. Talanta 2024; 280:126780. [PMID: 39191105 DOI: 10.1016/j.talanta.2024.126780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/16/2024] [Accepted: 08/24/2024] [Indexed: 08/29/2024]
Abstract
Tumor cell-derived extracellular vesicles (TEVs) contain numerous cellular molecules and are considered potential biomarkers for non-invasive liquid biopsy. However, due to the low abundance of TEVs secreted by tumor cells and their phenotypic heterogeneity, there is a lack of sensitive and specific methods to quantify TEVs. Here, we developed a dual-aptamer proximity ligation-coupled hybridization chain reaction (HCR) method for tracing TEVs, exploiting CRISPR to achieve highly sensitive detection. Taking advantage of the high binding affinity of aptamers, the two aptamers (AptEpCAM, AptHER2) exhibited the high selectivity for TEVs recognition. HCR generated long-repeated sequence containing multiple crRNA targetable barcodes, and the signals were further amplified by CRISPR upon recognizing the HCR sequences, thereby enhancing the sensitivity. Under optimal conditions, the developed method demonstrated a favorable linear relationship in the range of 2 × 103-107 particles/μL, with a limit of detection (LOD) of 3.3 × 102 particles/μL. We directly applied our assay to clinical plasma analysis, achieving 100 % accuracy in cancer diagnosis, thus demonstrating the potential clinical applications of TEVs. Due to its simplicity and rapidity, excellent sensitivity and specificity, this method has broad applications in clinical medicine.
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Affiliation(s)
- Shi-Fan Song
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Xue-Wei Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yang Shu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
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2
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Li L, Li M. Modular Engineering of Aptamer-Based Nanobiotechnology for Conditional Control of ATP Sensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2302972. [PMID: 38009471 DOI: 10.1002/adma.202302972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/24/2023] [Indexed: 11/29/2023]
Abstract
Dynamic changes of intracellular, extracellular, and subcellular adenosine triphosphates (ATPs) have fundamental interdependence with the physio-pathological states of cells. Spatially selective in situ imaging of such ATP dynamics offers valuable mechanistic insights into the related biological activities. Despite significant advances in the design of aptamer sensors for ATP detection, the dearth of methods that enable precise ATP imaging in specific cellular locations remains a challenge in this field. This review focuses on the modular engineering of regulatable sensing technology via the integration of aptamer probe designs with advanced functional nanomaterials, allowing conditional control of ATP sensing and imaging with high spatial precision from subcellular organelles to living animals. Highlighting the recent advances in the design of photo-triggered nanosensors for spatiotemporally controlled ATP imaging, endogenously-triggered ATP sensing in a cell-selective manner, and spatially-controlled nanodevices for ATP imaging in specific organelles and extracellular microenvironments. Emphasis will be put on elucidating the principles of how nanotechnology can be applied to regulate the spatial precision of aptamer-based ATP sensing activities. The authors envision that this perspective provides insights into the engineering of aptamer-based nanobiotechnology for opening new frontiers in precise molecular sensing and other bio-applications.
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Affiliation(s)
- Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, 100083, China
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3
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Feng R, Yu S, Qian Z, Wang Y, Xie G, Li B, Chen J, Wu YX, Tang K. A DNA octahedral amplifier for endogenous circRNA detection and bioimaging in living cells and its biomarker study. Analyst 2024; 149:807-814. [PMID: 38116839 DOI: 10.1039/d3an01803b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The discovery of reliable biomarkers is essential for early diagnosis, treatment, and prognosis assessment of diseases. Many research studies have shown that circRNA is a potential biomarker for diagnosis and prognosis of diseases. However, in situ monitoring circRNA in live cells is still a challenge at present, which brings a major limitation to the development and verification of circRNA as a disease biomarker. In this study, a catalytic hairpin assembly (CHA) reaction-based DNA octahedral amplifier (DOA) was developed for fluorescence resonance energy transfer (FRET) detection and bioimaging of circRNA in living cells. The DOA was first produced by self-assembling a DNA octahedron with six customized single-stranded DNAs, and two hairpins H1 (Cy3) and H2 (Cy5) were then hybridized to four vertices of the DNA octahedron. Idiopathic pulmonary fibrosis (IPF)-related circHIPK3 was used as the target. Once the CHA reaction from H1 and H2 on DOA was activated by a sequence-specific back-splice junction (BSJ) of circHIPK3, a significant FRET signal can be obtained from Cy3 to Cy5. The circHIPK3 was subsequently released to cause the next CHA reaction. Because the DOA has the advantages of the spatial-confinement effect, resistance to nuclease degradation and easy penetration into cells, rapid and excellent signal amplification FRET detection and bioimaging of endogenous circHIPK3 can be achieved in various cells. This study provides a high-precision assay platform to explore the possibility of using circRNA as a biomarker, and it is valuable for circRNA-related early diagnosis and treatment of diseases.
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Affiliation(s)
- Rong Feng
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Shengrong Yu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Zhiling Qian
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yiming Wang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Gege Xie
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Bingqian Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Jingwen Chen
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yong-Xiang Wu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass spectrometry and Clinical Application, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
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4
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He S, Shang J, He Y, Wang F. Enzyme-Free Dynamic DNA Reaction Networks for On-Demand Bioanalysis and Bioimaging. Acc Chem Res 2024. [PMID: 38271669 DOI: 10.1021/acs.accounts.3c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
ConspectusThe pursuit of in-depth studying the nature and law of life activity has been dominating current research fields, ranging from fundamental biological studies to applications that concern synthetic biology, bioanalysis, and clinical diagnosis. Motivated by this intention, the spatiotemporally controlled and in situ analysis of living cells has been a prospective branch by virtue of high-sensitivity imaging of key biomolecules, such as biomarkers. The past decades have attested that deoxyribonucleic acid (DNA), with biocompatibility, programmability, and customizable features, is a competitive biomaterial for constructing high-performance molecular sensing tools. To conquer the complexity of the wide extracellular-intracellular distribution of biomarkers, it is a meaningful breakthrough to explore high-efficiently amplified DNA circuits, which excel at operating complex yet captivating dynamic reaction networks for various bioapplications. In parallel, the multidimensional performance improvements of nucleic acid circuits, including the availability, detection sensitivity, and reliability, are critical parameters for realizing accurate imaging and cell regulation in bioanalysis.In this Account, we summarize our recent work on enzyme-free dynamic DNA reaction networks for bioanalysis from three main aspects: DNA circuitry functional extension of molecular recognition for epigenetic analysis and regulation, DNA circuitry amplification ability improvement for sensitive biomarker detection, and site-specific activation of DNA circuitry systems for reliable and accurate cell imaging. In the first part, we have designed an epigenetically responsive deoxyribozyme (DNAzyme) circuitry system for intracellular imaging and gene regulation, which enriches the possible analyzed species by chemically modifying conventional DNAzyme. For example, an exquisite N6-methyladenine (m6A)-caged DNAzyme was built for achieving the precise FTO (fat mass and obesity-associated protein)-directed gene regulation. In addition, varieties of DNAzyme-based nanoplatforms with self-sufficient cofactor suppliers were assembled, which subdued the speed-limiting hardness of DNAzyme cofactors in live-cell applications. In the second part, we have developed a series of hierarchically assembled DNA circuitry systems to improve the signal transduction ability of traditional DNA circuits. First, the amplification ability of the DNAzyme circuit has been significantly enhanced via several heterogeneously or homogeneously concatenated circuitry models. Furthermore, a feedback reaction pathway was integrated into these concatenated circuits, thus dramatically increasing the amplification efficiency. Second, considering the complex cellular environment, we have simplified the redundancy of multicomponents or reaction procedures of traditional cascaded circuits, relying on the minimal component complexity and merely one modular catalytic reaction, which guaranteed high cell-delivering uniformity while fostering reaction kinetics and analysis reliability. In the third part, we have constructed in-cell-selective endogenous-stimulated DNA circuitry systems via the multiply guaranteed molecular recognitions, which could not only eliminate the signal leakage, but could also retain its on-site and multiplex signal amplification. Based on the site-specific activation strategy, more circuitry availability in cellular scenarios has been acquired for reliable and precise biological sensing and regulation. These enzyme-free dynamic DNA reaction networks demonstrate the purpose-to-concreteness engineering for tailored multimolecule recognition and multiple signal amplification, achieving high-gain signal transduction and high-reliability targeted imaging in bioanalysis. We envision that the enzyme-free dynamic DNA reaction network can contribute to more bioanalytical layouts, which will facilitate the progression of clinical diagnosis and prognosis.
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Affiliation(s)
- Shizhen He
- College of Chemistry and Molecular Sciences, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, People's Republic of China
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5
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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6
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Chen J, Yu S, Qian Z, He K, Li B, Cao Y, Tang K, Yu S, Wu YX. Target-triggered enzyme-free amplification for highly efficient AND-gated bioimaging in living cells. Analyst 2023; 148:5963-5971. [PMID: 37867382 DOI: 10.1039/d3an01157g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Rapid, simultaneous, and sensitive detection of biomolecules has important application prospects in disease diagnosis and biomedical research. However, because the content of intracellular endogenous target biomolecules is usually very low, traditional detection methods can't be used for effective detection and imaging, and to enhance the detection sensitivity, signal amplification strategies are frequently required. The hybridization chain reaction (HCR) has been used to detect many disease biomarkers because of its simple operation, good reproducibility, and no enzyme involvement. Although HCR signal amplification methods have been employed to detect and image intracellular biomolecules, there are still false positive signals. Therefore, a target-triggered enzyme-free amplification system (GHCR system) was developed, as a fluorescent AND-gated sensing platform for intracellular target probing. The false positive signals can be well avoided and the accuracy of detection and imaging can be improved by using the design of the AND gate. Two cancer markers, GSH and miR-1246, were used as two orthogonal inputs for the AND gated probe. The AND-gated probe only works when GSH and miR-1246 are the inputs at the same time, and FRET signals can be the output. In addition to the use of AND-gated imaging, FRET-based high-precision ratiometric fluorescence imaging was employed. FRET-based ratiometric fluorescent probes have a higher ability to resist interference from the intracellular environment, they can avoid false positive signals well, and they are expected to have good specificity. Due to the advantages of HCR, AND-gated, and FRET fluorescent probes, the GHCR system exhibited highly efficient AND-gated FRET bioimaging for intracellular endogenous miRNAs with a lower detection limit of 18 pM, which benefits the applications of ratiometric intracellular biosensing and bioimaging and offers a novel concept for advancing the diagnosis and therapeutic strategies in the field of cancer.
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Affiliation(s)
- Jia Chen
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shengrong Yu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Zhiling Qian
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Kangdi He
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Bingqian Li
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yuting Cao
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Keqi Tang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Shengjia Yu
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yong-Xiang Wu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
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7
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Li QN, Wang DX, Han GM, Liu B, Tang AN, Kong DM. Low-Background CRISPR/Cas12a Sensors for Versatile Live-Cell Biosensing. Anal Chem 2023; 95:15725-15735. [PMID: 37819747 DOI: 10.1021/acs.analchem.3c03131] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The trans-cleavage activity of CRISPR/Cas12a has been widely used in biosensing. However, many CRISPR/Cas12a-based biosensors, especially those that work in "on-off-on" mode, usually suffer from high background and thus impossible intracellular application. Herein, this problem is efficiently overcome by elaborately designing the activator strand (AS) of CRISPR/Cas12a using the "RESET" effect found by our group. The activation ability of the as-designed AS to CRISPR/Cas12a can be easily inhibited, thus assuring a low background for subsequent biosensing applications, which not only benefits the detection sensitivity improvement of CRISPR/Cas12a-based biosensors but also promotes their applications in live cells as well as makes it possible to design high-performance biosensors with greatly improved flexibility, thus achieving the analysis of a wide range of targets. As examples, by using different strategies such as strand displacement, strand cleavage, and aptamer-substrate interaction to reactivate the inhibited enzyme activity, several CRISPR/Cas12a-based biosensing systems are developed for the sensitive and specific detection of different targets, including nucleic acid (miR-21), biological small molecules (ATP), and enzymes (hOGG1), giving the detection limits of 0.96 pM, 8.6 μM, and 8.3 × 10-5 U/mL, respectively. Thanks to the low background, these biosensors are demonstrated to work well for the accurate imaging analysis of different biomolecules in live cells. Moreover, we also demonstrate that these sensing systems can be easily combined with lateral flow assay (LFA), thus holding great potential in point-of-care testing, especially in poorly equipped or nonlaboratory environments.
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Affiliation(s)
- Qing-Nan Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Gui-Mei Han
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Wei K, He M, Zhang J, Zhao C, Nie C, Zhang T, Liu Y, Chen T, Jiang J, Chu X. A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo. Angew Chem Int Ed Engl 2023; 62:e202307025. [PMID: 37615278 DOI: 10.1002/anie.202307025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.
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Affiliation(s)
- Kaiji Wei
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Chuan Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tong Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yi Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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9
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Huang X, Chen M, Huang Z, Zhang Y, Shen T, Shi Y, Tong Y, Zou X, Liu SY, Guo J, Dai Z. On-Site-Activated Transmembrane Logic DNA Nanodevice Enables Highly Specific Imaging of Cancer Cells by Targeting Tumor-Related Nucleolin and Intracellular MicroRNA. Anal Chem 2023; 95:14746-14753. [PMID: 37723832 DOI: 10.1021/acs.analchem.3c02868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
The ability to specifically image cancer cells is essential for cancer diagnosis; however, this ability is limited by the false positive associated with single-biomarker sensors and off-site activation of "always active" nucleic acid probes. Herein, we propose an on-site, activatable, transmembrane logic DNA (TLD) nanodevice that enables dual-biomarker sensing of tumor-related nucleolin and intracellular microRNA for highly specific cancer cell imaging. The TLD nanodevice is constructed by assembling a tetrahedral DNA nanostructure containing a linker (L)-blocker (B)-DNAzyme (D)-substrate (S) unit. AS-apt, a DNA strand containing an elongated segment and the AS1411 aptamer, is pre-anchored to nucleolin protein, which is specifically expressed on the membrane of cancer cells. Initially, the TLD nanodevice is firmly sealed by the blocker containing an AS-apt recognition zone, which prevents off-site activation. When the nanodevice encounters a target cancer cell, AS-apt (input 1) binds to the blocker and unlocks the sensing ability of the nanodevice for miR-21 (input 2). The TLD nanodevice achieves dual-biomarker sensing from the cell membrane to the cytoplasm, thereby ensuring cancer cell-specific imaging. This TLD nanodevice represents a promising strategy for the highly reliable analysis of intracellular biomarkers and a promising platform for cancer diagnosis and related biomedical applications.
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Affiliation(s)
- Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Meng Chen
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhan Huang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Taorong Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Yanli Tong
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jianhe Guo
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
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10
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Chai Q, Chen J, Zeng S, Zhu T, Chen J, Qi C, Mao G, Liu Y. Closed Cyclic DNA Machine for Sensitive Logic Operation and APE1 Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207736. [PMID: 36916696 DOI: 10.1002/smll.202207736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/16/2023] [Indexed: 06/08/2023]
Abstract
DNA self-assembly has been developed as a kind of robust signal amplification strategy, but most of reported assembly pathways are programmed to amplify signal in one direction. Herein, based on mutual-activated cascade cycle of hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA), a closed cycle circuit (CCC) based DNA machine is developed for sensitive logic operation and molecular recognition. Benefiting from the synergistically accelerated signal amplification, the closed cyclic DNA machine enabled the logic computing with strong and significant output signals even at weak input signals. The typical logic operations such as OR, YES, AND, INHIBIT, NOR, and NAND gate, are conveniently and clearly executed with this DNA machine through rational design of the input and computing elements. Moreover, by integrating the target recognition module with the CCC module, the proposed DNA machine is further employed in the homogeneous detection of apurinic/apyrimidinic endonuclease 1 (APE1). The precise recognition and exponential signal amplification facilitated the highly selective and sensitive detection of APE1 with limit of detection (LOD) of 7.8 × 10-5 U mL-1 . Besides, the normal cells and tumor cells are distinguished unambiguously by this method according to the detected concentration difference of cellular APE1, which indicates the robustness and practicability of this method.
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Affiliation(s)
- Qingli Chai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jinyang Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Shasha Zeng
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Ting Zhu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jintao Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Chunjiao Qi
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Guobin Mao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Yucheng Liu
- Core Facility of Wuhan University, Wuhan, Hubei, 430072, China
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11
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Liu L, Xiong M, Rong Q, Zhang M, Zhang X. Nucleic acid sensors in vivo: challenges and opportunities. VIEW 2023. [DOI: 10.1002/viw.20220064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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12
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Liu JX, Xin MK, Sun X, Liu D, Li CY. NIR Photocontrolled Fluorescent Nanosensor under a Six-Branched DNA Nanowheel-Induced Nucleic Acid Confinement Effect for High-Performance Bioimaging. ACS APPLIED MATERIALS & INTERFACES 2023; 15:10529-10540. [PMID: 36802484 DOI: 10.1021/acsami.2c23165] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although DNA nanotechnology is a promising option for fluorescent biosensors to perform bioimaging, the uncontrollable target identification during biological delivery and the spatially free molecular collision of nucleic acids may cause unsatisfactory imaging precision and sensitivity, respectively. Aiming at solving these challenges, we herein integrate some productive notions. On the one hand, the target recognition component is inserted with a photocleavage bond and a core-shell structured upconversion nanoparticle with a low thermal effect is further employed to act as the ultraviolet light generation source, under which a precise near-infrared photocontrolled sensing is achieved through a simple external 808 nm light irradiation. On the other hand, the collision of all of the hairpin nucleic acid reactants is confined by a DNA linker to form a six-branched DNA nanowheel, after which their local reaction concentrations are vastly enhanced (∼27.48 times) to induce a special nucleic acid confinement effect to guarantee highly sensitive detection. By selecting a lung cancer-associated short noncoding microRNA sequence (miRNA-155) as a model low-abundance analyte, it is demonstrated that the newly established fluorescent nanosensor not only presents good in vitro assay performance but also exhibits a high-performance bioimaging competence in live biosystems including cells and mouse body, propelling the progress of DNA nanotechnology in the biosensing field.
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Affiliation(s)
- Jun-Xian Liu
- School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Meng-Kun Xin
- School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
| | - Xiaoming Sun
- School of Basic Medical Sciences, Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, P. R. China
| | - Da Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Cheng-Yu Li
- School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, P. R. China
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13
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Chen Y, Xing Y, Wang Z, Li L, Wang H, Tang S, Cai K, Zhang J. Dual factor coactivatable fluorescent nanosensor with boosted cytoplasmic biomarker accessibility toward selective tumor imaging. Biosens Bioelectron 2023; 223:115026. [PMID: 36565544 DOI: 10.1016/j.bios.2022.115026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Fluorescent nanosensor-based tumor imaging holds great promise in cancer diagnosis and treatment assistance, yet the signal contrast is heavily hampered by the unspecific/unwanted activation at microscopic regions with a highly restricted local abundance of biomarkers. Herein, we developed an activation boosting strategy by the integration and manipulation of dual-factor coactivation of sensing and lysosome escape facilitated the rise of cytosolic biomarker accessibility. By employing hybrid DNA probes on gold nanoquenchers, ATP sensing initiated conformation switch of the corresponding aptamer units triggered the exposure of a hidden toehold in a loop structure. Sequentially, miRNA-21 sensing was triggered by toehold-mediated strand displacement and detachment of the binding complexes. The application of lysosomotropic agent chloroquine at optimized time interval facilitated the release of nanosensors into the cytosol and a ∼10.5-fold increment of intracellular fluorescence in vitro, while coactivation improved the cancer-to-normal cell signal ratio by ∼5.9 times. The synergy effects led to a high tumor-to-normal tissue ratio value of ∼7.9 in the in vivo imaging results. This strategy establishes a new paradigm of fluorescent nanosensors for selective and specific tumor imaging.
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Affiliation(s)
- Yuhua Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Yuxin Xing
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Zhenqiang Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Lin Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Hailing Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Shuqi Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China
| | - Jixi Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing, 400044, PR China.
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14
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Zhou C, Song Y, Jin X, Li B, Pang C. Construction of a scalable DNA computing nano-system for large-scale and complex logical operations. NANOSCALE HORIZONS 2023; 8:176-184. [PMID: 36524605 DOI: 10.1039/d2nh00525e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The predictability of Watson-Crick base pairing provides unique structural programmability to DNA, facilitating the development and application of biomolecules in biocomputing. However, in DNA-based biocomputing, the scale of operation that can be achieved by an existing reaction system is very limited. How to expand the operation range of a logic circuit and realize the integration and extensibility of circuits is always the key problem to be solved in this field. In this work, by designing a multifunctional DNA-nanostructure-based reaction platform, which can realize an output of up to 2n scalable fluorescence signals, combined with the construction of an input "library" and a modular distribution strategy of output signals, for the first time, we successfully performed the calculation of both square roots and cube roots of consecutive integers within a decimal number of "10" and in each result of the operation, two digits after the decimal point are preserved (). We believe that the design concept presented in this work can help effectively solve the urgent problems of biological computing in terms of computational scaling, integration and scalability, and can open up new horizons for the design of new functional devices and complex computing circuits.
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Affiliation(s)
- Chunyang Zhou
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Yiwei Song
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Xiuyan Jin
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Bei Li
- Changchun Institute of Optics, Precision Machinery and Physics, Chinese Academy of Sciences, Changchun, 130031, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Pang
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
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15
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Cascaded molecular logic gates using antibiotics as inputs based on exonuclease III and DNAzyme. Talanta 2023; 252:123832. [DOI: 10.1016/j.talanta.2022.123832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 11/18/2022]
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16
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Qi M, Shi P, Zhang X, Cui S, Liu Y, Zhou S, Zhang Q. Reconfigurable DNA triplex structure for pH responsive logic gates †. RSC Adv 2023; 13:9864-9870. [PMID: 36998523 PMCID: PMC10043996 DOI: 10.1039/d3ra00536d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C+ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks. We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.![]()
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Affiliation(s)
- Mingxuan Qi
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
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17
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Gong S, Wang X, Zhou P, Pan W, Li N, Tang B. AND Logic-Gate-Based CRISPR/Cas12a Biosensing Platform for the Sensitive Colorimetric Detection of Dual miRNAs. Anal Chem 2022; 94:15839-15846. [DOI: 10.1021/acs.analchem.2c03666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shaohua Gong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Xi Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Ping Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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18
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He S, Yu S, Li R, Chen Y, Wang Q, He Y, Liu X, Wang F. On‐Site Non‐enzymatic Orthogonal Activation of a Catalytic DNA Circuit for Self‐Reinforced In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202206529. [DOI: 10.1002/anie.202206529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
- Department of Gastrointestinal Surgery Zhongnan Hospital of Wuhan University Wuhan P. R. China
- Research Centre for Infectious Diseases and Cancer Chinese Academy of Medical Sciences Wuhan P. R. China
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19
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Zhao J, Di Z, Li L. Spatiotemporally Selective Molecular Imaging via Upconversion Luminescence‐Controlled, DNA‐Based Biosensor Technology. Angew Chem Int Ed Engl 2022; 61:e202204277. [DOI: 10.1002/anie.202204277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
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20
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He S, Yu S, Li R, Chen Y, Wang Q, He Y, Liu X, Wang F. On‐Site Nonenzymatic Orthogonal Activation of a Catalytic DNA Circuit for Self‐Reinforced In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | - Yuqiu He
- Wuhan University Chemistry CHINA
| | | | - Fuan Wang
- Wuhan University College of Chemistry and Molecular Sciences Bayi Road 299 430072 Wuhan CHINA
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21
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Zhao J, Di Z, Li L. Spatiotemporally Selective Molecular Imaging via Upconversion Luminescence‐Controlled, DNA‐Based Biosensor Technology. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jian Zhao
- NCNST: National Center for Nanoscience and Technology CAS key Lab CHINA
| | - Zhenghan Di
- NCNST: National Center for Nanoscience and Technology CAS key Lab CHINA
| | - Lele Li
- National Center for Nanoscience and Technology CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety 11 ZhongGuanCun BeiYiTiao, Haidian District 100190 Beijing CHINA
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22
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Chen J, Fu S, Zhang C, Liu H, Su X. DNA Logic Circuits for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108008. [PMID: 35254723 DOI: 10.1002/smll.202108008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.
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Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chunyi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huiyu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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23
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A high-integrated DNA biocomputing platform for MicroRNA sensing in living cells. Biosens Bioelectron 2022; 207:114183. [PMID: 35303538 DOI: 10.1016/j.bios.2022.114183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/31/2022]
Abstract
DNA logic computing has captured increasing interest due to its ability to assemble programmable DNA computing elements for disease diagnosis, gene regulation, and targeted therapy. In this work, we developed an aptamer-equipped high-integrated DNA biocomputing platform (HIDBP-A) with a dual-recognition function that enabled cancer cell targeting. Dual microRNAs were the input signals and can perform AND logic operations. Compared to the free DNA biocomputing platform (FDBP), the integration of all computing elements into the same DNA tetrahedron greatly improved logic computing speed and efficiency owing to the confinement effect reflected by the high local concentration of computing elements. As a proof of concept, the utilization of microRNA as the input signal was beneficial for improving the scalability and flexibility of the sequence design of the logic nano-platform. Given that the different microRNAs were over-expressed in cancer cells, this new HIDBP-A has great promise in accurate diagnosis and logic-controlled disease treatment.
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24
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Wang DD, Zhang J, Yu QQ, Zhang K, Chen TT, Chu X. Biomineralized Zeolitic Imidazolate Framework-8 Nanoparticles Enable Polymerase-Driven DNA Biocomputing for Reliable Cell Identification. Anal Chem 2022; 94:4794-4802. [PMID: 35266710 DOI: 10.1021/acs.analchem.1c05605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Investigating multiple miRNA expression patterns in living cells by DNA logic biocomputing is a valuable strategy for diagnosis and biomedical studies. The introduction of protein enzymes in DNA logic biocomputing circuits not only expands the toolbox of nucleic acid assembly techniques, but also further improves the specificity of recognizing and processing of DNA input. Herein, a polymerase-driven primer exchange reaction, acting as the sensing module, is introduced into the biocomputing system and transduces the multiple miRNAs sensing event into the intermediate triggers for activating the subsequent processing module, which further performs signal readout through DNAzyme catalytic substrate cleavage reaction. By using biomineralized zeolitic imidazolate framework-8 nanoparticles (ZIF-8 NPs) to deliver all the components of the biocomputing system, including polymerase and DNA probes, we realized polymerase-driven DNA biocomputing operations in living cells, including AND and OR gates. The results exhibited that biomineralized ZIF-8 NPs can protect the loaded cargoes against the external environment and deliver them efficiently to the cytoplasm. The polymerase-driven DNA biocomputing system based on multiple miRNAs sensing can be used for reliable cell identification and may provide a promising platform for more accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Dan-Dan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qiao-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ke Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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25
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Lv WY, Li CH, Yang FF, Li YF, Zhen SJ, Huang CZ. Sensitive Logic Nanodevices with Strong Response for Weak Inputs. Angew Chem Int Ed Engl 2022; 61:e202115561. [PMID: 34989066 DOI: 10.1002/anie.202115561] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 02/04/2023]
Abstract
Sensitive sensing is critical when developing new calculation systems with weak input signals (ISs). In this work, a "weak-inputs-strong-outputs" strategy was proposed to guide the construction of sensitive logic nanodevices by coupling an input-induced reversible DNA computing platform with a hybridization chain reaction-based signal amplifier. By rational design of the sequence of computing elements (CEs) so as to avoid cross-talking between ISs and signal amplifier, the newly formed logic nanodevices have good sensitivity to the weak ISs even at low concentrations of CEs, and are able to perform YES, OR, NAND, NOR, INHIBIT, INHIBIT-OR and number classifier operation, showing that the DNA calculation proceeds in dilute solution medium that greatly improves the calculation proficiency of logic nanodevices without the confinement of the lithography process in nanotechnology.
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Affiliation(s)
- Wen Yi Lv
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Chun Hong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Fei Fan Yang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
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26
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Pan J, Deng F, Liu Z, Shi G, Chen J. Toehold-Mediated Cascade Catalytic Assembly for Mycotoxin Detection and Its Logic Applications. Anal Chem 2022; 94:3693-3700. [PMID: 35176850 DOI: 10.1021/acs.analchem.1c05485] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this work, an enzyme-free biosensor is reported for mycotoxin detection based on a toehold-mediated catalytic hairpin assembly (CHA) and a DNAzyme-cascaded hydrolysis reaction. In the presence of a mycotoxin, the recognition between an aptamer and the mycotoxin releases the trigger DNA. The trigger DNA initiates the toehold-mediated CHA, generating large amounts of partial duplex B/C with four toeholds, which can be used to assemble the DNAzyme-cascaded hydrolysis reaction. Furthermore, through a collaborative autoassembly reaction among the B/C duplex, DNA1, and DNA2, supramolecular nanostructures corresponding to Mg2+-dependent DNAzymes can be formed. With the incubation of Mg2+, the dual-modified (TAMRA/BHQ2) substrate strand DNA2 will be cleaved into two fragments, yielding a high TAMRA fluorescence signal for mycotoxin testing. Under optimal conditions, the sensing system was ultrasensitive and showed low detection limits of 0.2 pM for ochratoxin A (OTA), 0.13 pM for aflatoxin B1 (AFB1), and 0.17 pM for zearalenone (ZEN). The mycotoxin aptasensor also exhibited high selectivity and was successfully applied for the quantitative analysis of OTA, AFB1, and ZEN in wine samples. Due to the advantages of flexibility and versatility, this mycotoxin platform was used to fabricate several concatenated logic gates including "AND-INHIBIT", "INHIBIT-OR", "OR-AND", and "OR-INHIBIT" logic biocomputings. Such multiple functions of the logic system provided a universal sensing strategy for the intelligent detection of multiplex mycotoxins, demonstrating considerable potential in food safety and environmental monitoring.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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27
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Lv WY, Li CH, Yang FF, Li YF, Zhen SJ, Huang CZ. Sensitive Logic Nanodevices with Strong Response for Weak Inputs. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Wen Yi Lv
- Southwest University College of Pharmaceutical Sciences CHINA
| | - Chun Hong Li
- Southwest University College of Pharmaceutical Sciences CHINA
| | - Fei Fan Yang
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Yuan Fang Li
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Shu Jun Zhen
- Southwest University College of Chemistry and Chemical Engineering Tiansheng Road, BeiBei 400715 Chongqing CHINA
| | - Cheng Zhi Huang
- Southwest University College of Pharmaceutical Sciences CHINA
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28
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Liu Q, Wu B, Li M, Huang Y, Li L. Heterostructures Made of Upconversion Nanoparticles and Metal-Organic Frameworks for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103911. [PMID: 34791801 PMCID: PMC8787403 DOI: 10.1002/advs.202103911] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/08/2021] [Indexed: 05/02/2023]
Abstract
Heterostructure nanoparticles (NPs), constructed by two single-component NPs with distinct nature and multifunctional properties, have attracted intensive interest in the past few years. Among them, heterostructures made of upconversion NPs (UCNPs) and metal-organic frameworks (MOFs) can not only integrate the advantageous characteristics (e.g., porosity, structural regularity) of MOFs with unique upconverted optical features of UCNPs, but also induce cooperative properties not observed either for single component due to their special optical or electronic communications. Recently, diverse UCNP-MOF heterostructures are designed and synthesized via different strategies and have demonstrated appealing potential for applications in biosensing and imaging, drug delivery, and photodynamic therapy (PDT). In this review, the synthesis strategies of UCNP-MOF heterostructures are first summarized, then the authors focus mainly on discussion of their biomedical applications, particularly as PDT agents for cancer treatment. Finally, the authors briefly outlook the current challenges and future perspectives of UCNP-MOF hybrid nanocomposites. The authors believe that this review will provide comprehensive understanding and inspirations toward recent advances of UCNP-MOF heterostructures.
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Affiliation(s)
- Qing Liu
- School of Life ScienceInstitute of Engineering MedicineKey Laboratory of Molecular Medicine and BiotherapyBeijing Institute of TechnologyBeijing100081China
| | - Bo Wu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and TechnologyBeijing100190China
| | - Mengyuan Li
- School of Chemistry and Biological EngineeringUniversity of Science and Technology BeijingBeijing100083China
| | - Yuanyu Huang
- School of Life ScienceInstitute of Engineering MedicineKey Laboratory of Molecular Medicine and BiotherapyBeijing Institute of TechnologyBeijing100081China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and TechnologyBeijing100190China
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29
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Cai Z, Fu Y, Qiu Z, Wang Y, Wang W, Gu W, Li Z, Wu S, Gao F. Multitarget Reaction Programmable Automatic Diagnosis and Treatment Logic Device. ACS NANO 2021; 15:19150-19164. [PMID: 34698495 DOI: 10.1021/acsnano.1c07307] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate diagnosis and precise and effective treatment are currently the two magic weapons for dealing with cancer. However, a single marker is often associated with multiple cellular events, which is not conducive to accurate diagnosis, and overly mild treatment methods often make the treatment effect unsatisfactory. In this paper, we construct a Au/Pd octopus nanoparticle-DNA nanomachine (Au/Pd ONP-DNA nanomachine) as a fully automatic diagnosis and treatment logic system. In this system, multiple DNA components are targeting detection units, Au/Pd ONPs act as carriers, and Au/Pd ONPs with an 808 nm laser is the treatment unit. In order to achieve the purpose of precise treatment, we will detect two secondary markers under the premise of detecting one major tumor marker. When all of the designated targets are detected (the logic system input is (1, 1, 1), and the output is (1, 1)), the 808 nm laser can be programmed to automatically radiate tumors and perform photothermal therapy and photodynamic therapy. In vivo and in vitro experiments show that this logic system not only can accurately identify tumor cells but also has considerable therapeutic effects.
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Affiliation(s)
- Zhiheng Cai
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Yingqiang Fu
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, People's Republic of China
| | - Zhili Qiu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Ying Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Wandong Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Wenxiang Gu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Zheng Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Shengyue Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221002, People's Republic of China
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30
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Li LL, Lv WY, Wang Y, Li YF, Li CM, Huang CZ. DNA Logic Nanodevices for Real-Time Monitoring of ATP in Lysosomes. Anal Chem 2021; 93:15331-15339. [PMID: 34756034 DOI: 10.1021/acs.analchem.1c02829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA logic nanodevices have prospects in molecular recognitions but still face challenges in achieving DNA computation-controlled regulation in specific compartments of living cells. By incorporating the i-motif sequence and ATP aptamers into a Y-shaped DNA (Y-DNA) structure, and applying gold nanoparticles (AuNPs) as the transporting carrier, herein we present a new type of DNA logic nanodevices to monitor the ATP levels in lysosomes of living cells. Triple energy transfers including dual fluorescent resonance energy transfers (FRETs) and a nanometal surface energy transfer (NSET) occurred in the DNA logic nanodevices. It was identified that the proposed nanodevices perform an AND logic operation to output FRET signals only when an endogenous proton and ATP simultaneously exist in the cellular microenvironment. Owing to the use of the i-motif sequence, the nanodevices have lysosome-recognizing capacity without causing alkalization of the acidic organelle, making DNA computation-controlled regulation at the level of cellular organelles achievable. These DNA logic nanodevices show high application prospects in lysosome-related cellular function and disease treatment.
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Affiliation(s)
- Li Li Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Wen Yi Lv
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yao Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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31
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Zhang J, Fu H, Chu X. Metal-Organic Framework Nanoparticles Power DNAzyme Logic Circuits for Aberrant MicroRNA Imaging. Anal Chem 2021; 93:14675-14684. [PMID: 34696580 DOI: 10.1021/acs.analchem.1c02878] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
At the molecular level, a large number of studies exist on the use of dynamic DNA molecular circuits for disease diagnosis and biomedicine. However, how to design programmable molecular circuit devices to autonomously and accurately diagnose multiple low-abundance biomolecules in complex cellular environments remains a challenge. Here, we constructed DNAzyme logic circuits for the analysis and imaging of multiple microRNAs in living cells using Cu/ZIF-8 NPs as a nanocarrier of the logic gate modules and the Cu2+ cofactor of the Cu2+-dependent DNAzyme. The logic gate modules of the logic operation system were adsorbed on the surface of Cu/ZIF-8 NPs via electrostatic interaction. After internalization, pH-responsive Cu/ZIF-8 NPs could efficiently release the logic gate modules and Cu2+, which allowed us to realize multiple logic computations initiated by endogenous miRNA, including one YES logic gate and two binary logic gates (OR and AND) in different living cells. Cu2+-DNAzyme logic circuits could quickly respond to multiple endogenous miRNAs in the complex cell environment, which also provided a new research method for the application of DNA biocomputing circuits in living cells.
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Affiliation(s)
- Juan Zhang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637009, P. R. China.,State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hongquan Fu
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637009, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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32
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Zhang Y, Chen W, Fang Y, Zhang X, Liu Y, Ju H. Activating a DNA Nanomachine via Computation across Cancer Cell Membranes for Precise Therapy of Solid Tumors. J Am Chem Soc 2021; 143:15233-15242. [PMID: 34514797 DOI: 10.1021/jacs.1c06361] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Taking advantage of cancer cells' endogenous characters, the responsive activation of DNA nanomachines has achieved great success in tumor therapy. Combining with extra stimuli such as external light irradiation provided spatiotemporal control of DNA nanomachine activation. However, specific activation at the cellular level is still challenging considering the macroscopic-scale exposure area of usual light sources. DNA logic gates located at the cell membrane contributed to cellular specificity, but the free diffusion of input DNA strands during the operation process would impair efficiency and result in side effects to circumjacent normal cells in solid tumors. Here we design a transmembrane DNA logical computation strategy to activate a DNA nanomachine only in cancer cells from a complex solid tumor microenvironment. The DNA nanomachine multishell UCNPs-DNA is prepared by modifying DNA strands on upconversion nanoparticles. LA-apt, a DNA strand anchoring to a cancer cell membrane overexpressed receptor, and intracellular miRNA-21 served as inputs 1 and 2, respectively. Hybridization with input 1 at the cell membrane not only exposes the miRNA-21 recognition region at the DNA nanomachine, but also delivers it into cancer cells. The cascade hybridization with intracellular input 2 completes the "AND" gate operation and releases a DNA strand L2 as output. L2 acts as the trigger to operate the DNA nanomachine and correspondingly activates the photosensitizer Rose Bengal for reactive oxygen species generation. Through the "AND" gate operation of the DNA nanomachine across the cancer cell membrane, highly precise therapy only to cancer cells is achieved in a complex solid tumor microenvironment, which could become a promising modality for precise therapy of solid tumors.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weiwei Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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33
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Hao M, Miao P, Wang Y, Wang W, Ge S, Yu X, Hu XX, Ding B, Zhang J, Yan M. Near-Infrared Light-Initiated Photoelectrochemical Biosensor Based on Upconversion Nanorods for Immobilization-Free miRNA Detection with Double Signal Amplification. Anal Chem 2021; 93:11251-11258. [PMID: 34369163 DOI: 10.1021/acs.analchem.1c02160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Photoelectrochemical (PEC) sensors are relatively new sensing platforms with high detection sensitivity and low cost. However, the current PEC biosensors dependent on ultraviolet or visible light as the exciting resource cause injuries to biological samples and systems, which restrains the applications in complicated matrixes. Herein, a near-infrared light (NIR)-initiated PEC biosensor based on NaYF4:Yb,Tm@NaYF4@TiO2@CdS (csUCNRs@TiO2@CdS) was constructed for sensitive detection of acute myocardial infarction (AMI)-related miRNA-133a in an immobilization-free format coupled with a hybridization chain reaction and a redox circle signal amplification strategy. A low-energy 980 nm NIR incident laser was converted to 300-480 nm light to excite the adjacent TiO2@CdS photosensitive shell to generate photocurrent by NaYF4:Yb,Tm@NaYF4 upconversion nanorods. Also, magnetic beads were employed for the homogeneous determination of target miRNA-133a to reduce the recognition steric hindrance and improve the detection sensitivity. The photocurrent response was positively correlated with the level of ascorbic acid as the energy donor to consume photoacoustic holes produced on the surface of csUCNRs@TiO2@CdS, which was generated by alkaline phosphatase catalyzation and regenerated by tris(2-carboxyethyl) phosphine reduction upon the appearance of miRNA-133a. Exerting a NIR-light-driven and immobilization-free strategy, the as-constructed biosensor displayed linearly sensitive and selective determination of miRNA-133a with a detection limit of 36.12 aM. More significantly, the assay method provided a new concept of the PEC sensing strategy driven by NIR light to detect diverse biomarkers with pronounced sensitivity, light stability, and low photodamage.
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Affiliation(s)
- Mengjiao Hao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Pei Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yan Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Wenshou Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, China
| | - Xinyan Yu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Xiao-Xiao Hu
- College of Life Sciences, Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Biyan Ding
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jing Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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