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Dong X, Qiu Z, Wang Z, Li J, Qin W, Dang J, Zhou W, Jia G, Chen Y, Wang C. Efficient Silver(I)-Containing I-Motif DNA Hybrid Catalyst for Enantioselective Diels-Alder Reactions. Angew Chem Int Ed Engl 2024; 63:e202407838. [PMID: 38860437 DOI: 10.1002/anie.202407838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/12/2024]
Abstract
The inherent chiral structures of DNA serve as attractive scaffolds to construct DNA hybrid catalysts for valuable enantioselective transformations. Duplex and G-quadruplex DNA-based enantioselective catalysis has made great progress, yet novel design strategies of DNA hybrid catalysts are highly demanding and atomistic analysis of active centers is still challenging. DNA i-motif structures could be finely tuned by different cytosine-cytosine base pairs, providing a new platform to design DNA catalysts. Herein, we found that a human telomeric i-motif DNA containing cytosine-silver(I)-cytosine (C-Ag+-C) base pairs interacting with Cu(II) ions (i-motif DNA(Ag+)/Cu2+) could catalyze Diels-Alder reactions with full conversions and up to 95 % enantiomeric excess. As characterized by various physicochemical techniques, the presence of Ag+ is proved to replace the protons in hemiprotonated cytosine-cytosine (C : C+) base pairs and stabilize the DNA i-motif to allow the acceptance of Cu(II) ions. The i-motif DNA(Ag+)/Cu2+ catalyst shows about 8-fold rate acceleration compared with DNA and Cu2+. Based on DNA mutation experiments, thermodynamic studies and density function theory calculations, the catalytic center of Cu(II) ion is proposed to be located in a specific loop region via binding to one nitrogen-7 atom of an unpaired adenine and two phosphate-oxygen atoms from nearby deoxythymidine monophosphate and deoxyadenosine monophosphate, respectively.
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Affiliation(s)
- Xingchen Dong
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Ziyang Qiu
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Zixiao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jiaqi Li
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Weijun Qin
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Wenqin Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yashao Chen
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changhao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (MOE), Xi'an Key Laboratory of Organometallic Material Chemistry, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
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2
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Fu R, Hou J, Wang Z, Xianyu Y. DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles. ACS NANO 2024; 18:14754-14763. [PMID: 38781600 DOI: 10.1021/acsnano.4c04265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
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3
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Wang Q, Jin D, Liu C, Shi L, Li T. A Tumor-Specific Cascade-Activating Smart Prodrug System for Enhanced Targeted Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309482. [PMID: 38150668 DOI: 10.1002/smll.202309482] [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: 10/19/2023] [Revised: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Developing intelligently targeted drugs with low side effects is urgent for cancer treatment. Toward this goal, a tumor-specific cascade-activating smart prodrug system consisting of a G-quadruplex(G4)-modulated tumor-targeted DNA vehicle and a well-designed cellular stimuli-responsive ligand-drug conjugates (LDCs) is proposed. An original "donor-acceptor" binary fluorescent ligand, with ultrahigh affinity, brightness, and photostability, is engineered to tightly bind G4 structures and significantly improve the nuclease resistance of the DNA vehicle, which serves as a bridge contributing to the construction of the prodrug system, named ApG4/LDCs. Sodium nitroprusside and doxorubicin are loaded into ApG4/LDCs in one pot and generate nitric oxide and superoxide anion in response to cancer cellular environments, which in cascade generates peroxynitrite to cause DNA damage while promoting the self-monitored drug release to achieve enhanced targeted therapy. Such a cascade activation and self-reinforcement process is executed only when the prodrug system targets the tumor tissue followed by cell uptake, showing significant antitumor efficacy and greatly weakening the damage to normal tissues. Given the unique features, the innovative strategy for prodrug design may open a new door to precision disease treatment.
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Affiliation(s)
- Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Duo Jin
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Chengbin Liu
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Lili Shi
- Department of Chemistry, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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4
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Tholen HM, Ambulo CP, Lee KM, Buskohl PR, Harne RL. Optomechanical computing in liquid crystal elastomers. SOFT MATTER 2023; 19:6978-6986. [PMID: 37665593 DOI: 10.1039/d3sm00819c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Embodied decision-making in soft, engineered matter has sparked recent interest towards the development of intelligent materials. Such decision-making capabilities can be realized in soft materials via digital information processing with combinational logic operations. Although previous research has explored soft material actuators and embedded logic in soft materials, achieving a high degree of autonomy in these material systems remains a challenge. Light is an ideal stimulus to trigger information processing in soft materials due to its low thermal effect and remote use. Thus, one approach for developing soft, autonomous materials is to integrate optomechanical computing capabilities in photoresponsive materials. Here, we establish a methodology to embed combinational logic circuitry in a photoresponsive liquid crystal elastomer (LCE) film. These LCEs are designed with embedded switches and integrated circuitry using liquid metal-based conductive traces. The resulting optomechanical computing LCEs can effectively process optical information via light, thermal, and mechanical energy conversion. The methods introduced in this work to fabricate a material capable of optical information processing can facilitate the implementation of a sense of sight in soft robotic systems and other compliant devices.
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Affiliation(s)
- Haley M Tholen
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, USA.
| | - Cedric P Ambulo
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, USA
- Azimuth Corporation, Fairborn, OH, USA
| | - Kyung Min Lee
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, USA
- Azimuth Corporation, Fairborn, OH, USA
| | - Philip R Buskohl
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH, USA
| | - Ryan L Harne
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA, USA.
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5
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Liu LS, Leung HM, Morville C, Chu HC, Tee JY, Specht A, Bolze F, Lo PK. Wavelength-Dependent, Orthogonal Photoregulation of DNA Liberation for Logic Operations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:1944-1957. [PMID: 36573551 DOI: 10.1021/acsami.2c20757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this study, we synthesized two phosphoramidites based on 2,7-bis-{4-nitro-8-[3-(2-propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene (BNSF) and 4,4'-bis-{8-[4-nitro-3-(2-propyl)-styryl]}-3,3'-di-methoxybiphenyl (BNSMB) structures as visible light-cleavable linkers for oligonucleotide conjugation. In addition to the commercial ultraviolet (UV) photocleavable (PC) linker, the BNSMB linker was further applied as a building component to construct photoregulated DNA devices as duplex structures, which are functionalized with fluorophores and quenchers. Selective cleavage of PC and BNSMB is achieved in response to ultraviolet (UV) and visible light irradiations as two inputs, respectively. This leads to controllable dissociation of pieces of DNA fragments, which is followed by changes of fluorescence emission as signal outputs of the system. By tuning the number and position of the photocleavable molecules, fluorophores, and quenchers, various DNA devices were developed, which mimic the functions of Boolean logic gates and achieve logic operations in AND, OR, NOR, and NAND gates in response to two different wavelengths of light inputs. By sequence design, the photolysis products can be precisely programmed in DNA devices and triggered to release in a selective and/or sequential manner. Thus, this photoregulated DNA device shows potential as a wavelength-dependent drug delivery system for selective control over the release of multiple individual therapeutic oligonucleotide-based drugs. We believe that our work not only enriches the library of photocleavable phosphoramidites available for bioconjugation but also paves the way for developing spatiotemporal-controlled, orthogonal-regulated DNA-based logic devices for a range of applications in materials science, polymers, chemistry, and biology.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Hoi Man Leung
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Clément Morville
- Conception et Applications des Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, Illkirch 67401, France
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Jing Yi Tee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Alexandre Specht
- Conception et Applications des Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, Illkirch 67401, France
| | - Frédéric Bolze
- Conception et Applications des Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, Illkirch 67401, France
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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Chen B, Ma W, Long X, Cheng H, Sun H, Huang J, Jia R, He X, Wang K. Membrane Protein and Extracellular Acid Heterogeneity-Driven Amplified DNA Logic Gate Enables Accurate and Sensitive Identification of Cancer Cells. Anal Chem 2022; 94:2502-2509. [PMID: 35089704 DOI: 10.1021/acs.analchem.1c04347] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA logic gates, as a class of smart molecular devices with excellent biocompatibility and convenient information processing mode, have been widely used for identification of cancer cells based on logic analysis of cancer biomarkers. However, most of the developed DNA logic gates for identification of cancer cells are mainly driven by homogeneous biomarkers such as membrane proteins or RNAs, which may suffer from insufficient accuracy. Herein, we reported a membrane protein and extracellular acid heterogeneity-driven amplified DNA logic gate (HDLG) for accurate and sensitive identification of cancer cells by combining the superior signal amplification characteristics of the hybridization chain reaction (HCR) and the precise computation ability of the logic operation. In this strategy, a DNA aptamer was employed for membrane protein recognition, and a split i-motif was used for the response of the extracellular acid. Only when the two heterogeneous biomarkers existed simultaneously, the DNA logic gate could be driven to perform the "AND" logic operation and induce the formation of an intact trigger to initiate a HCR process on the cell surface, generating an amplified "ON" fluorescence signal. Benefiting from the design of heterogeneity-driven and signal amplification, this DNA logic gate could not only autonomously perform high-resolution fluorescence imaging on the surface of target cancer cells, but also perform sensitive analysis of target cancer cells with a cell number of 70 detected in 200 μL of buffer and desirable accuracy in differentiating target cancer cells from complicated cell mixtures. We anticipate that this novel HDLG is expected to be applied in precise disease diagnosis.
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Affiliation(s)
- Biao Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Wenjie Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xu Long
- The Guangdong Technion-Israel Institute of Technology, Shantou 515000, China
| | - Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Huanhuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Ruichen Jia
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
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7
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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8
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Chen H, Sun H, Zhang W, Zhang Q, Ma J, Li Q, Guo X, Xu K, Tang Y. Chelerythrine as a fluorescent light-up ligand for an i-motif DNA structure. NEW J CHEM 2021. [DOI: 10.1039/d0nj04863a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A fluorescent light-up ligand for an i-motif structure has been reported in this study.
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Affiliation(s)
- Hongbo Chen
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Hongxia Sun
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Wende Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qin Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Jun Ma
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qian Li
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Xiaomeng Guo
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Kanyan Xu
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Yalin Tang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
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9
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Zhao D, Tang H, Wang H, Yang C, Li Y. Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores. ACS Sens 2020; 5:2177-2183. [PMID: 32588619 DOI: 10.1021/acssensors.0c00798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag+), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.
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Affiliation(s)
- Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
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10
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Huang D, Guo C, Miao J, Zhang Y, Lin X, Chen D, Yang S, Yang Q, Tang Y. Construction of a novel DNA-based comparator and its application in intelligent analysis. NANOSCALE 2019; 11:16241-16244. [PMID: 31454010 DOI: 10.1039/c9nr05270d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a novel and general comparator was constructed based on cascaded strand displacement reactions and DNA hybridization and its potential in intelligently weighing the quantitative predominance of two targets was explored in a complex biological matrix, which not only enriches the information processing mode of DNA computation but also provides an instructive way to deal with quantitative analyzing tasks in further DNA-based logic sensors.
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Affiliation(s)
- Dan Huang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Chen Guo
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Jiarong Miao
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yi Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Xiao Lin
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Die Chen
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Shu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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11
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Direct detection of potassium and lead (II) ions based on assembly-disassembly of a chiral cyanine dye /TBA complex. Talanta 2019; 201:490-495. [PMID: 31122455 DOI: 10.1016/j.talanta.2019.04.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 11/24/2022]
Abstract
A highly selective and sensitive direct detection of potassium (K+) and lead (Pb2+) ions was developed by using the assembly and disassembly of a chiral cyanine dye/TBA complex. The dye DMSB (3-ethyl-2-[3-(3-ethyl-3H-benzoselenazol-2-ylidene)-2-methylprop-1-enyl] benzoselenazolium bromide) loses the ability of self-assembly, but it can be activated by thrombin-binding aptamer (TBA) G-quadruplex structure. And only the TBA G-quadruplex formed in the presence of K+, can strongly induce J-aggregate signals of DMSB. Because the Pb2+ ions can bind and stabilize the TBA G-quadruplex with much higher efficiency than K+, the J-aggregate signals of DMSB falls sharply when the Pb2+ is present. As a result, the assembly and disassembly of DMSB allows the selective detection of 10 μM K+ and 20 nM Pb2+ respectively, even the competitive sodium ion (Na+) was as high as 145 mM. The linear correlation existed between the J-aggregate intensity and the concentration of K+ and Pb2+ over the range of 0.5-5.0 mM and 200-2000 nM, respectively. Moreover, the concentration of K+ (∼3 mM) and Pb2+ (below 20 nM) in human blood serum samples were determined by the present method, which agreed well with inductively coupled plasma mass spectrometry (ICP-MS). This work not only opens a door for the further development of G-quadruplex-based aptasensor in complex real system, but also provides a simple and versatile sensing platform for ion detection in clinic.
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12
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Tam DY, Zhuang X, Wong SW, Lo PK. Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805481. [PMID: 30861628 DOI: 10.1002/smll.201805481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/30/2019] [Indexed: 05/23/2023]
Abstract
Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xinyu Zhuang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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13
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Huang D, Yang C, Yao Y, Li J, Guo C, Chen J, Zhang Y, Yang S, Yang Q, Tang Y. Versatile and Homogeneous DNA Tetraplex Platform for Constructing Label‐Free Logic Devices: From Design to Application. Chemistry 2019; 25:6996-7003. [PMID: 30933378 DOI: 10.1002/chem.201900734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Huang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chunrong Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Ye Yao
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jicheng Li
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chen Guo
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jianchi Chen
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yi Zhang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Shu Yang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Qianfan Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yalin Tang
- National Laboratory for Molecular SciencesCentre for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable, and Stable SpeciesInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P.R. China
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14
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Cao Y, Kuang Y, Yang L, Ding P, Pei R. Construction of One- and Two-Dimensional Nanostructures by the Sequential Assembly of Quadruplex DNA Scaffolds. Biomacromolecules 2019; 20:2207-2217. [DOI: 10.1021/acs.biomac.9b00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ye Kuang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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15
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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16
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Satpathi S, Sappati S, Das K, Hazra P. Structural characteristics requisite for the ligand-based selective detection of i-motif DNA. Org Biomol Chem 2019; 17:5392-5399. [DOI: 10.1039/c9ob01020c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new approach has been explored to detect i-motif DNA structures over its complementary GQ DNA based on the hemi-protonated cytosine–cytosine (C+–C) base pairing recognition. This approach also shows its versatility by detecting various i-motif DNA structures with different chain lengths, molecularity and sizes, etc.
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Affiliation(s)
- Sagar Satpathi
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Subrahmanyam Sappati
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Konoya Das
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Partha Hazra
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
- Centre for Energy Science
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17
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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18
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Shi J, Zhou M. Probing the conformational switch of I-motif DNA using tunable resistive pulse sensing. Biochim Biophys Acta Gen Subj 2018; 1862:2564-2569. [PMID: 30048743 DOI: 10.1016/j.bbagen.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 02/04/2023]
Abstract
I-motif DNA, which can fold and unfold reversibly in various environments, plays a significant role in DNA nanotechnology and biological functions. Thus, it is of fundamental importance to identify the different conformations of i-motif DNA. Here, we demonstrate that distinct structures of i-motif DNA conjugated to polystyrene spheres can be distinguished through tunable resistive pulse sensing technique. When dispersed in acidic buffer, i-motif DNA coating on polystyrene spheres would fold into quadruplex structure and subsequently induce an apparent increase in the translocation duration time upon passing through a nanopore due to the shielding effect of the surface charge of the nanospheres. However, if the DNA strands don't have conformational changes in acidic buffer, little shift can be observed in the translocation duration time of the DNA functionalized polystyrene spheres. A before-and-after assay was also performed to illustrate the fast speed of i-motif DNA folding using this technique. The successful implementation of tunable resistive pulse sensing to monitor the conformational transition of i-motif DNA provides a potential tool to detect the structural changes of DNA and an alternative approach to study the function of DNA structures.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Ming Zhou
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China.
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19
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Lippert B, Sanz Miguel PJ. Merging Metal–Nucleobase Chemistry With Supramolecular Chemistry. ADVANCES IN INORGANIC CHEMISTRY 2018. [DOI: 10.1016/bs.adioch.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Abou Assi H, Lin YC, Serrano I, González C, Damha MJ. Probing Synergistic Effects of DNA Methylation and 2′-β-Fluorination on i-Motif Stability. Chemistry 2017; 24:471-477. [PMID: 29096420 DOI: 10.1002/chem.201704591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Hala Abou Assi
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Yu Chen Lin
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
| | - Israel Serrano
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”; CSIC; Serrano 119 28006 Madrid Spain
| | - Masad J. Damha
- Department of Chemistry; McGill University; 801 Sherbrooke St. West Montreal QC H3A 0B8 Canada
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21
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Dai Z, Leung HM, Lo PK. Stimuli-Responsive Self-Assembled DNA Nanomaterials for Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602881. [PMID: 28005298 DOI: 10.1002/smll.201602881] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/31/2016] [Indexed: 05/23/2023]
Abstract
Stimuli-responsive DNA-based materials represent a major class of remarkable functional nanomaterials for nano-biotechnological applications. In this review, recent progress in the development of stimuli-responsive systems based on self-assembled DNA nanostructures is introduced and classified. Representative examples are presented in terms of their design, working principles and mechanisms to trigger the response of the stimuli-responsive DNA system upon expose to a large variety of stimuli including pH, metal ions, oligonucleotides, small molecules, enzymes, heat, and light. Substantial in vitro studies have clearly revealed the advantages of the use of stimuli-responsive DNA nanomaterials in different biomedical applications, particularly for biosensing, drug delivery, therapy and diagnostic purposes in addition to bio-computing. Some of the challenges faced and suggestions for further development are also highlighted.
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Affiliation(s)
- Ziwen Dai
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Hoi Man Leung
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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22
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Day HA, Wright EP, MacDonald CJ, Gates AJ, Waller ZAE. Reversible DNA i-motif to hairpin switching induced by copper(II) cations. Chem Commun (Camb) 2016; 51:14099-102. [PMID: 26252811 PMCID: PMC4563791 DOI: 10.1039/c5cc05111h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
i-Motif DNA structures have previously been utilised for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Herein we describe how copper(II) cations can alter the conformation of i-motif DNA into an alternative hairpin structure which is reversible by chelation with EDTA.
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Affiliation(s)
- Henry Albert Day
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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23
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Dembska A. The analytical and biomedical potential of cytosine-rich oligonucleotides: A review. Anal Chim Acta 2016; 930:1-12. [PMID: 27265899 DOI: 10.1016/j.aca.2016.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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24
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Kang BH, Gao ZF, Li N, Shi Y, Li NB, Luo HQ. Thiazole orange as a fluorescent probe: Label-free and selective detection of silver ions based on the structural change of i-motif DNA at neutral pH. Talanta 2016; 156-157:141-146. [PMID: 27260446 DOI: 10.1016/j.talanta.2016.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/27/2016] [Accepted: 05/01/2016] [Indexed: 02/05/2023]
Abstract
Silver ions have been widely applied to many fields and have harmful effects on environments and human health. Herein, a label-free optical sensor for Ag(+) detection is constructed based on thiazole orange (TO) as a fluorescent probe for the recognition of i-motif DNA structure change at neutral pH. Ag(+) can fold a C-rich single stranded DNA sequence into i-motif DNA structure at neutral pH and that folding is reversible by chelation with cysteine (Cys). The DNA folding process can be indicated by the fluorescence change of TO, which is non-fluorescent in free molecule state and emits strong fluorescence after the incorporation with i-motif DNA. Thus, a rapid, sensitive, and selective method for the detection of Ag(+) and Cys is developed with a detection limit of 17 and 280nM, respectively. It is worth noting that the mechanism underlying the increase of the fluorescence of thiazole orange in the presence of i-motif structure is explained. Moreover, a fluorescent DNA logic gate is successfully designed based on the Ag(+)/Cys-mediated reversible fluorescence changes. The proposed detection strategy is label-free and economical. In addition, this system shows a great promise for i-motif/TO complex to analyze Ag(+) in the real samples.
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Affiliation(s)
- Bei Hua Kang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhong Feng Gao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Na Li
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yan Shi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Nian Bing Li
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Hong Qun Luo
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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25
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Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. Chem Commun (Camb) 2016; 52:179-82. [DOI: 10.1039/c5cc08242k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Liya Ji
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
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26
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Xu L, Wang J, Sun N, Liu M, Cao Y, Wang Z, Pei R. Neutral red as a specific light-up fluorescent probe for i-motif DNA. Chem Commun (Camb) 2016; 52:14330-14333. [DOI: 10.1039/c6cc07674b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neutral red as the first specific light-up fluorescent probe for i-motif DNA is presented.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Min Liu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Yi Cao
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Zhili Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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27
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015; 55:164-8. [DOI: 10.1002/anie.201507249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/15/2015] [Indexed: 12/21/2022]
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28
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Zhang Y, Liu W, Zhang W, Yu S, Yue X, Zhu W, Zhang D, Wang Y, Wang J. DNA-mediated gold nanoparticle signal transducers for combinatorial logic operations and heavy metal ions sensing. Biosens Bioelectron 2015; 72:218-24. [DOI: 10.1016/j.bios.2015.05.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 04/29/2015] [Accepted: 05/07/2015] [Indexed: 01/25/2023]
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30
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Lannes L, Halder S, Krishnan Y, Schwalbe H. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem 2015; 16:1647-56. [PMID: 26032298 DOI: 10.1002/cbic.201500182] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/19/2022]
Abstract
Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.
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Affiliation(s)
- Laurie Lannes
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany)
| | - Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India)
| | - Yamuna Krishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).,Department of Chemistry, University of Chicago, E305, GCIS, 929 E, 57th Street, Chicago, IL 60637 (USA)
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany).
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31
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G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch. Sci Rep 2015; 5:10479. [PMID: 25990684 PMCID: PMC4438431 DOI: 10.1038/srep10479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/15/2015] [Indexed: 12/30/2022] Open
Abstract
Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and 1H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.
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Qi H, Huang G, Han Y, Zhang X, Li Y, Pingguan-Murphy B, Lu TJ, Xu F, Wang L. Engineering artificial machines from designable DNA materials for biomedical applications. TISSUE ENGINEERING PART B-REVIEWS 2015; 21:288-97. [PMID: 25547514 DOI: 10.1089/ten.teb.2014.0494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.
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Affiliation(s)
- Hao Qi
- 1Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, P.R. China.,2School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Guoyou Huang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yulong Han
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiaohui Zhang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuhui Li
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Belinda Pingguan-Murphy
- 5Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur, Malaysia
| | - Tian Jian Lu
- 4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Xu
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Lin Wang
- 3MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.,4Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P.R. China
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Lu L, Wang M, Liu LJ, Wong CY, Leung CH, Ma DL. A luminescence switch-on probe for terminal deoxynucleotidyl transferase (TdT) activity detection by using an iridium(iii)-based i-motif probe. Chem Commun (Camb) 2015; 51:9953-6. [DOI: 10.1039/c5cc02790j] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An iridium(iii) complex exhibiting higher responce towards i-motif DNA over dsDNA and ssDNA was employed for the construction of a TdT activity detection platform. The limit of detection for TdT was 0.25 U ML−1.
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Affiliation(s)
- Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Modi Wang
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Chun-Yuen Wong
- Department of Biology and Chemistry
- City University of Hong Kong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
- Partner State Key Laboratory of Environmental and Biological Analysis
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