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Liu X, Wu J, He S, Ge F, Liu N. Interaction between polycyclic aromatic hydrocarbons and thymine (T)-base induces double-strand DNA distortion in different species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175338. [PMID: 39117206 DOI: 10.1016/j.scitotenv.2024.175338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are potent inhibitors of DNA that can induce genetic damage, abnormal gene expression, and metabolic disorders upon interfacing with biological macromolecules. However, the mechanism of their interactions with DNA remains elusive. Therefore, this study selected three representative PAHs, including phenanthrene (Phen), pyrene (Pyre), and benzo[a]pyrene (B[a]P), and explored their binding mechanisms with the double-strand DNA (dsDNA) from different species, including 1J1V (Escherichia coli), 6J5B (Arabidopsis thaliana), and 6Q1V (Homo sapiens). The results revealed that binding between PAHs and dsDNA occurred in the groove via van der Waals forces and π-π stacking, with the carboxyl oxygen atom of the thymine (T)-base within dsDNA being the key binding site. This result was further confirmed by the spectroscopic experiments, where significant changes in the peak of the T-base were observed after PAHs-dsDNA binding. More interestingly, the total binding energies of Pyre with the three dsDNA were -138.800 kJ/mol (Pyre-1J1V), -105.523 kJ/mol (Pyre-6J5B), and -127.567 kJ/mol (Pyre-6Q1V), respectively, all of which were higher than those of Phen and B[a]P. This suggests that that Pyre has the strongest dsDNA binding ability. Additionally, analysis of the thermodynamic parameters indicated that the interactions between the three PAHs and dsDNA were exothermic reactions. In contrast, the Pyre-dsDNA interaction predominantly involved van der Waals forces and hydrogen bonding due to the enthalpy change (∆H) < 0 and entropy change (∆S) < 0, while the Phen-dsDNA and B[a]P-dsDNA interactions predominantly involved hydrophobic forces due to ∆H > 0 and ∆S > 0. Furthermore, Pyre caused local distortion of dsDNA, which was more pronounced under atomic force microscopy (AFM). In summary, this study has unveiled a new phenomenon of binding between PAHs and dsDNA. This sheds light on the carcinogenic potential and environmental impacts of PAHs pollution.
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Affiliation(s)
- Xinyue Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Jianjian Wu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Shichong He
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Fei Ge
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Na Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
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2
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Feng X, Wang X, Liu J, Fu A, Wang Y, Wei S, Chen H, She R, Wang Y, Cui X, Hou H, Xu Y, Wu Y, Meng Q, Zhang L, Wang S, Zhao J. Accelerated Screening of Alternative DNA Base-Organic Molecule-Base Architectures via Integrated Theory and Experiment. Angew Chem Int Ed Engl 2024; 63:e202408003. [PMID: 38771290 DOI: 10.1002/anie.202408003] [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: 04/27/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
Organic molecule-mediated noncanonical DNA self-assembly expands the standard DNA base-pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base-pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub-stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule-incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA-molecule architectures beyond Watson-Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA-based delivery system and probe design for sensitive detection of certain molecules.
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Affiliation(s)
- Xinyu Feng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xianwen Wang
- School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Jiahe Liu
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Aiting Fu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Ying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Shuheng Wei
- Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Huichao Chen
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Rui She
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yangying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xiao Cui
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hui Hou
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yuanyuan Xu
- Department of Pediatric Critical Care Medicine, Children's Medical Center of Anhui Medical University, Hefei, Anhui, 230051, China
| | - Yujing Wu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Qian Meng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Song Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jiemin Zhao
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
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3
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Ye R, Wang Y, Liu Y, Cai P, Song J. Self-assembled methodologies for the construction of DNA nanostructures and biological applications. Biomater Sci 2024; 12:3712-3724. [PMID: 38912847 DOI: 10.1039/d4bm00584h] [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: 06/25/2024]
Abstract
Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.
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Affiliation(s)
- Rui Ye
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuqi Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Cai
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Dore MD, Rafique MG, Yang TP, Zorman M, Platnich CM, Xu P, Trinh T, Rizzuto FJ, Cosa G, Li J, Guarné A, Sleiman HF. Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly. Nat Commun 2024; 15:4384. [PMID: 38782917 PMCID: PMC11116425 DOI: 10.1038/s41467-024-48722-2] [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: 11/03/2022] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly. Here we show that highly charged, monodisperse DNA-oligomers assemble via seeded growth into length-controlled supramolecular fibers during heating; when the temperature is lowered, these metastable fibers slowly disassemble. Furthermore, the specific molecular structures of oligomers that promote fiber formation contradict the typical theory of block copolymer self-assembly. Efficient curling and packing of the oligomers - or 'curlamers' - determine morphology, rather than hydrophobic to hydrophilic ratio. Addition of a small molecule stabilises the DNA fibers, enabling temporal control of polymer lifetime and underscoring their potential use in nucleic-acid delivery, stimuli-responsive biomaterials, and soft robotics.
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Affiliation(s)
- Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | | | - Tianxiao Peter Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Marlo Zorman
- Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Pengfei Xu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47906, USA
| | - Alba Guarné
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
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Han J, Lv X, Zhang Y, Wang J, Fan D, Dong S. Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits. Anal Chem 2023; 95:16725-16732. [PMID: 37906527 DOI: 10.1021/acs.analchem.3c03793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.
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Affiliation(s)
- Jiawen Han
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Xujuan Lv
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Yuwei Zhang
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Intelligent Wearable Engineering Research Center of Qingdao, Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China
| | - Daoqing Fan
- Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, Shandong, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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Zhang Z, Jin J, Paluzzi VE, Jin Z, Wen Y, Huang CZ, Li CM, Mao C, Zuo H. AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing. J Am Chem Soc 2023; 145:19503-19507. [PMID: 37638713 DOI: 10.1021/jacs.3c06260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jin Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuoer Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuandong Wen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, 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, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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Song N, Chu Y, Li S, Dong Y, Fan X, Tang J, Guo Y, Teng G, Yao C, Yang D. Cascade dynamic assembly/disassembly of DNA nanoframework enabling the controlled delivery of CRISPR-Cas9 system. SCIENCE ADVANCES 2023; 9:eadi3602. [PMID: 37647403 PMCID: PMC10468128 DOI: 10.1126/sciadv.adi3602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
CRISPR-Cas9 has been explored as a therapeutic agent for down-regulating target genes; the controlled delivery of Cas9 ribonucleoprotein (RNP) is essential for therapeutic efficacy and remains a challenge. Here, we report cascade dynamic assembly/disassembly of DNA nanoframework (NF) that enables the controlled delivery of Cas9 RNP. NF was prepared with acrylamide-modified DNA that initiated cascade hybridization chain reaction (HCR). Through an HCR, single-guide RNA was incorporated to NF; simultaneously, the internal space of NF was expanded, facilitating the loading of Cas9 protein. NF was designed with hydrophilic acylamino and hydrophobic isopropyl, allowing dynamic swelling and aggregation. The responsive release of Cas9 RNP was realized by introducing disulfide bond-containing N,N-bis(acryloyl)cystamine that was specifically in response to glutathione of cancer cells, triggering the complete disassembly of NF. In vitro and in vivo investigations demonstrated the high gene editing efficiency in cancer cells, the hypotoxicity in normal cells, and notable antitumor efficacy in a breast cancer mouse model.
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Affiliation(s)
- Nachuan Song
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Yiwen Chu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Xiaoting Fan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Yanfei Guo
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Guangshuai Teng
- Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P.R. China
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8
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Cao W, Shan S, Xing K, Jing X, Peng J, Xiao X, Liu D, Xia J, Lai W. Novel rapid detection of melamine based on the synergistic aggregation of gold nanoparticles. Food Chem 2023; 428:136789. [PMID: 37423110 DOI: 10.1016/j.foodchem.2023.136789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
A simple and rapid colorimetric method for the detection of melamine in milk samples is described. Polythymidine oligonucleotide was adsorbed on to the surface of gold nanoparticles (AuNPs), protecting it from aggregation. In the presence of melamine, polythymidine oligonucleotide combined with melamine formed a double-strand DNA-like structure, allowing AuNPs aggregation. In the presence of positively charged SYBR Green I (SG I), AuNPs were further aggregated. In the presence of melamine and SG I, aggregation of AuNPs was synergistic. Thus, in this principle, melamine can be detected visually. Plasmon resonance peak changes enabled detection of melamine quantitatively using UV-vis spectroscopy. The limit of detection for this colorimetric method was 16 μg L-1 with a good linear range from 19.5 μg L-1 to 1.25 × 103 μg L-1, and detection took only 1 min. The method was successfully applied for detection of melamine in milk samples.
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Affiliation(s)
- Wenkai Cao
- State Key Laboratory of Food Science and Resources, Nanchang University 235, East Nanjing Road, Nanchang 330047, China
| | - Shan Shan
- College of Life Science, National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China
| | - Keyu Xing
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Xudong Jing
- State Key Laboratory of Food Science and Resources, Nanchang University 235, East Nanjing Road, Nanchang 330047, China
| | - Juan Peng
- State Key Laboratory of Food Science and Resources, Nanchang University 235, East Nanjing Road, Nanchang 330047, China
| | - Xiaoyue Xiao
- State Key Laboratory of Food Science and Resources, Nanchang University 235, East Nanjing Road, Nanchang 330047, China
| | - Daofeng Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Province Center for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China.
| | - Jun Xia
- Jiangxi Agricultural Technology Extension Center, Animal Epidemic Control Building, 698 Gaoxin Seventh Road, China.
| | - Weihua Lai
- State Key Laboratory of Food Science and Resources, Nanchang University 235, East Nanjing Road, Nanchang 330047, China.
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Xiong X, Yin K, Bai J, Zhu P, Fan J, Zhang X, Shi Q, Guo Y, Wang Z, Ma D, Han J. Ordered Assembly of DNA on Topological Insulator Bi 2Se 3 and Octadecylamine for a Sensitive Biosensor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4466-4474. [PMID: 36929878 DOI: 10.1021/acs.langmuir.3c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Controlling the assembly of DNA in order on a suitable electrode surface is of great significance for biosensors and disease diagnosis, but it is full of challenges. In this work, we creatively assembled DNA on the surface of octadecylamine (ODA)-modified topological insulator (Tls) Bi2Se3 and developed an electrochemical biosensor to detect biomarker DNA of coronavirus disease 2019 (COVID-19). A high-quality Bi2Se3 sheet was obtained from a single crystal synthesized in our lab. A uniform ODA layer was coated in argon by chemical vapor deposition (CVD). We observed and analyzed the assembly and mechanism of single-strand DNA (ssDNA) and double-strand DNA (dsDNA) on the Bi2Se3 surface through atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The electrochemical signal revealed that the biosensor based on the DNA/ODA/Bi2Se3 electrode has a wide linear detection range from 1.0 × 10-12 to 1.0 × 10-8 M, with the limit of detection as low as 5 × 10-13 M. Bi2Se3 has robust surface states and improves the electrochemical signal-to-noise ratio, while the uniform ODA layer guides high-density ordered DNA, enhancing the sensitivity of the biosensor. Our work demonstrates that the ordered DNA/ODA/Bi2Se3 electrode surface has great application potential in the field of biosensing and disease diagnosis.
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Affiliation(s)
- Xiaolu Xiong
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314000, China
| | - Kangjie Yin
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jiangyue Bai
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Peng Zhu
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jing Fan
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Xu Zhang
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Qingfan Shi
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Yao Guo
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Zhiwei Wang
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Dashuai Ma
- Institute for Structure and Function & Department of Physics, Chongqing University, Chongqing 400044, China
| | - Junfeng Han
- Centre for Quantum Physics, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurement (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314000, China
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10
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Yee DW, Lee MS, An J, Macfarlane RJ. Reversible Diffusionless Phase Transitions in 3D Nanoparticle Superlattices. J Am Chem Soc 2023; 145:6051-6056. [PMID: 36898204 DOI: 10.1021/jacs.3c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Nanocomposite tectons (NCTs), polymer brush-grafted nanoparticles that use supramolecular interactions to drive their assembly, form ordered nanoparticle superlattices (NPSLs) with well-defined unit cell symmetries when thermally annealed. In this work, we demonstrate that appropriate assembly and processing conditions can also enable control over the microstructure of NCT lattices by balancing the enthalpic and entropic factors associated with ligand packing and supramolecular bonding during crystallization. Unary systems of NCTs are assembled via the addition of a small molecule capable of binding to multiple nanoparticle ligands; these NCTs initially form face-centered-cubic (FCC) structures in solvents that are favorable for the particles' polymer brushes. However, the FCC lattices undergo a reversible, diffusionless phase transition to body-centered-cubic (BCC) lattices when transferred to a solvent that induces polymer brush collapse. The BCC superlattices maintain the same crystal habit as the parent FCC phase but exhibit significant transformation twinning similar to that seen in martensitic alloys. This previously unseen diffusionless phase transformation in NPSLs enables unique microstructural features in the resulting assemblies, suggesting that NPSLs could serve as models for the investigation of microstructural evolution in crystalline systems and extend our understanding of NPSLs as atomic material analogues.
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Affiliation(s)
- Daryl W Yee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Margaret S Lee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Joyce An
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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11
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Liu M, Chen H, Huang Y, Liu J, Chen Q, Zuo H, Fang L, Mao C. Enriching adenosine by thymine-rich DNA oligomers. Analyst 2023; 148:1858-1866. [PMID: 36942467 DOI: 10.1039/d3an00297g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Adenosine levels are important in various physiological and pathological activities, but detecting them is difficult because of interference from a complex matrix. This study designed a series of DNA oligomers rich in thymine to enrich adenosine. Their binding affinity (Kd range: 1.25-5.0 mM) to adenosine varied based on the DNA secondary structures, with a clamped hairpin structure showing the highest binding affinity. Compared to other designs, this clamped DNA hairpin underwent the least conformational change during adenosine binding. These DNAs also suppressed the precipitation of supersaturated adenine. Taken together, these results suggest that thymine-rich DNAs could be used to enrich and separate adenosine.
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Affiliation(s)
- Mingchun Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Huaiqing Chen
- Biological Sciences Research Center, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Yuhan Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jian Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Qianfeng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Liang Fang
- Department of Oncology, The Ninth Chongqing People's Hospital, Chongqing 400700, China.
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette 47907, IN, USA.
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12
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Tang J, Liang A, Yao C, Yang D. Assembly of Rolling Circle Amplification-Produced Ultralong Single-Stranded DNA to Construct Biofunctional DNA Materials. Chemistry 2023; 29:e202202673. [PMID: 36263767 DOI: 10.1002/chem.202202673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
The Review by Yang, Yao and colleagues (DOI: 10.1002/chem.202202673) describes recent developments in biofunctional DNA hydrogels and DNA nanocomplexes based on rolling circle amplification (RCA) and introduces assembly strategies and functionalization methods of the ultralong single-strand DNA produced by RCA to construct biofunctional materials.
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Affiliation(s)
- Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Aiqi Liang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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13
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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14
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Cao N, Cai W, Qian L, Nie Z, Mao C, Cui S. Emulating Titin by a Multidomain DNA Structure. ACS Macro Lett 2023; 12:59-64. [PMID: 36573670 DOI: 10.1021/acsmacrolett.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Titin, a giant protein containing multiple tandem domains, is essential in maintaining the superior mechanical performance of muscle. The consecutive and reversible unfolding and refolding of the domains are crucial for titin to serve as a modular spring. Since the discovery of the mechanical features of a single titin molecule, the exploration of biomimetic materials with titin-emulating modular structures has been an active field. However, it remains a challenge to prepare these modular polymers on a large scale due to the complex synthesis process. In this study, we propose modular DNA with multiple hairpins (MH-DNA) as the fundamental block for the bottom-up design of advanced materials. By analyzing the unfolding and refolding dynamics of modular hairpins by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), we find that MH-DNA shows comparable stability to those of polyproteins like titin. The unique low hysteresis of modular hairpin makes it an ideal molecular spring with remarkable mechanical efficiency. On the basis of the well-established DNA synthesis techniques, we anticipate that MH-DNA can be used as a promising building block for advanced materials with a combination of superior structural stability, considerable extensibility, and high mechanical efficiency.
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Affiliation(s)
- Nanpu Cao
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Wanhao Cai
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Lu Qian
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shuxun Cui
- College of Chemistry, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
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15
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Schuster GB, Hud NV, Alenaizan A. Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions. J Phys Chem B 2022; 126:10758-10767. [PMID: 36502412 DOI: 10.1021/acs.jpcb.2c05934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
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16
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Lu B, Vecchioni S, Ohayon YP, Canary JW, Sha R. The wending rhombus: Self-assembling 3D DNA crystals. Biophys J 2022; 121:4759-4765. [PMID: 36004779 PMCID: PMC9808540 DOI: 10.1016/j.bpj.2022.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York
| | - James W Canary
- Department of Chemistry, New York University, New York, New York.
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York.
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17
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Wang J, Wicher B, Maurizot V, Huc I. Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination. Chemistry 2022; 28:e202201345. [PMID: 35965255 PMCID: PMC9826129 DOI: 10.1002/chem.202201345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Indexed: 01/11/2023]
Abstract
Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.
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Affiliation(s)
- Jinhua Wang
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660-780PoznanPoland
| | - Victor Maurizot
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance,Department of PharmacyLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MünchenGermany,Cluster of Excellence e-conversion85748GarchingGermany
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18
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Liu Q, Xia J, Yu Q, Gu P, Yuan Y, Liu K, Huang C, Chen C, Guo X, Qian H. Engineering the Surface Properties of DNA Nanostructures by Tuning the Valency of Assembling Species for Biomedical Applications. Macromol Biosci 2022; 22:e2200248. [PMID: 35983867 DOI: 10.1002/mabi.202200248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Indexed: 12/25/2022]
Abstract
Self-assembled DNA nanostructures hold great potentials in biomedical applications. Nevertheless, the negatively charged DNA backbone and susceptivity to enzyme degradation pose challenges to this regard. Engineering the surface properties of DNA nanostructures by assembling DNA with guest molecules in magnesium-free system is promising to solve these issues. In this study, the polyamines-mediated DNA self-assembly with an emphasis on the valency of polyamines is investigated. Both spermine, spermidine, and putrescine can assemble DNA tetrahedron under appropriate concentrations. The cytotoxicity and cellular uptake efficiencies vary with the polyamine valency. Compared with magnesium-assembled DNA tetrahedron, polyamine-assembled DNA tetrahedron exhibits higher cellular uptake efficiency and serum stability. Circular dichroism spectrum results indicate that polyamines induce DNA conformation slightly shifting from B form to A form. The improved performances of polyamine-assembled DNA tetrahedrons under physiological settings are attributed to the surface properties that altered by guest molecules polyamine. The current study suggests that engineering the surface properties of DNA nanostructures by assembling them with guest cationic species is promising to further their biomedical applications.
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Affiliation(s)
- Qian Liu
- Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Jingruo Xia
- Department of Laboratory Medicine, Affiliated Hospital of North Sichuan Medical University, Nanchong, Sichuan, 637000, China
| | - Qingtao Yu
- Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Pengcheng Gu
- Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yue Yuan
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Ke Liu
- Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Chaowang Huang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Xiaolan Guo
- Department of Laboratory Medicine, Affiliated Hospital of North Sichuan Medical University, Nanchong, Sichuan, 637000, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
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19
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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20
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Aliev TA, Timralieva AA, Kurakina TA, Katsuba KE, Egorycheva YA, Dubovichenko MV, Kutyrev MA, Shilovskikh VV, Orekhov N, Kondratyuk N, Semenov SN, Kolpashchikov DM, Skorb EV. Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade. NANO SELECT 2022. [DOI: 10.1002/nano.202200092] [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] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - Nikita Orekhov
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- Bauman Moscow State Technical University Moscow Russia
| | - Nikolay Kondratyuk
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- National Research University Higher School of Economics Moscow Russia
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot Israel
| | - Dmitry M. Kolpashchikov
- ITMO University Saint Petersburg Russia
- University of Central Florida Chemistry Department Orlando Florida USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando Florida USA
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21
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Alenaizan A. Structural Analysis of the Poly(thymidine)-Melamine Assembly. J Phys Chem B 2022; 126:6948-6954. [PMID: 36027577 DOI: 10.1021/acs.jpcb.2c04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia 31261
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22
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Yan Y, Fang X, Yao N, Gu H, Yang G, Hua Z. Bioinspired Hydrogen Bonds of Nucleobases Enable Programmable Morphological Transformations of Mixed Nanostructures. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yangyang Yan
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xinzi Fang
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Nan Yao
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Haojie Gu
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Guang Yang
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zan Hua
- Biomass Molecular Engineering Center and Department of Materials Science and Engineering, Anhui Agricultural University, Hefei, Anhui 230036, China
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23
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You Y, Liu H, Zhu J, Wang Y, Pu F, Ren J, Qu X. A DNAzyme-augmented bioorthogonal catalysis system for synergistic cancer therapy. Chem Sci 2022; 13:7829-7836. [PMID: 35865897 PMCID: PMC9258401 DOI: 10.1039/d2sc02050e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
As one of the representative bioorthogonal reactions, the copper-catalyzed click reaction provides a promising approach for in situ prodrug activation in cancer treatment. To solve the issue of inherent toxicity of Cu(i), biocompatible heterogeneous copper nanoparticles (CuNPs) were developed for the Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. However, the unsatisfactory catalytic activity and off-target effect still hindered their application in biological systems. Herein, we constructed a DNAzyme-augmented and targeted bioorthogonal catalyst for synergistic cancer therapy. The system could present specificity to cancer cells and promote the generation of Cu(i) via DNAzyme-induced value state conversion of DNA-templated ultrasmall CuNPs upon exposure to endogenous H2O2, thereby leading to high catalytic activity for in situ drug synthesis. Meanwhile, DNAzyme could produce radical species to damage cancer cells. The synergy of in situ drug synthesis and chemodynamic therapy exhibited excellent anti-cancer effects and minimal side effects. The study offers a simple and novel avenue to develop highly efficient and safe bioorthogonal catalysts for biological applications.
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Affiliation(s)
- Yawen You
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Hao Liu
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Jiawei Zhu
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
| | - Fang Pu
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization, Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
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24
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Zhang W, Jiang C, Guo X, Muhammad Faran Ashraf Baig M, Ni C, Xiao SJ. 2D DNA lattices assembled from DX-coupled tiles. J Colloid Interface Sci 2022; 616:499-508. [DOI: 10.1016/j.jcis.2022.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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25
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Devari S, Bhunia D, Bong D. Synthesis of Bifacial Peptide Nucleic Acids with Diketopiperazine Backbones. Synlett 2022; 33:965-968. [PMID: 35874045 PMCID: PMC9306277 DOI: 10.1055/a-1802-6873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report a synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases, as well as native bases. To examine the structure-function scope of DKP bPNAs, we synthesized a set of bPNAs by using diaminopropionic acid, diaminobutyric acid, ornithine, and lysine derivatives to display the base-tripling motifs, which result in one, two, three, or four carbons linking the alpha carbon to the side-chain amine. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal side-chain linkage was four carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per side-chain were prepared through double reductive alkylation of the ε-amine of Fmoc-lysine with acetaldehyde derivatives of adenine, cytidine, uridine, and melamine. With these building blocks in hand, DKP bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine- and melamine-displaying bPNAs to T-rich DNAs of noncanonical structure, though full characterization of this behavior is ongoing. The convenient and potentially scalable method described enables rapid access to DNA-binding scaffolds of low (<1 kD) molecular weight and previously established cell permeability. We expect that this straightforward and efficient approach to nucleic acid binders will enable studies on noncanonical nucleic acid hybridization.
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Affiliation(s)
- Shekaraiah Devari
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, USA
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26
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Abstract
Single-molecule mechanochemical sensing (SMMS) is a novel biosensing technique using mechanical force as a signal transduction mechanism. In the mechanochemical sensing, the chemical binding of an analyte molecule to a sensing template is converted to mechanical signals, such as tensile force, of the template. Since mechanical force can be conveniently monitored by single-molecule tools, such as optical tweezers, magnetic tweezers, or Atomic Force Microscopy, mechanochemical sensing is often carried out at the single molecule level. In traditional format of ensemble sensing, sensitivity can be achieved via chemical or electrical amplifications, which are materials intensive and time-consuming. To address these problems, in 2011, we used the principle of mechanochemical coupling in a single molecular template to detect single nucleotide polymorphism (SNP) in DNA fragments. The single-molecule sensitivity in such SMMS strategy allows to removing complex amplification steps, drastically conserving materials and increasing temporal resolution in the sensing. By placing many probing units throughout a single-molecule sensing template, SMMS can have orders of magnitude better efficiency in the materials usage (i.e., high Atom Economy) with respect to the ensemble biosensing. The SMMS sensing probes also enable topochemical arrangement of different sensing units. By placing these units in a spatiotemporally addressable fashion, single-molecule topochemical sensors have been demonstrated in our lab to detect an expandable set of microRNA targets. Because of the stochastic behavior of single-molecule binding, however, it is challenging for the SMMS to accurately report analyte concentrations in a fixed time window. While multivariate analysis has been shown to rectify background noise due to stochastic nature of single-molecule probes, a template containing an array of sensing units has shown ensemble average behaviors to address the same problem. In this so-called ensemble single-molecule sensing, collective mechanical transitions of many sensing units occur in the SMMS sensing probes, which allows accurate quantification of analytes. For the SMMS to function as a viable sensing approach readily adopted by biosensing communities, the future of the SMMS technique relies on the reduction in the complexity and cost of instrumentation to report mechanical signals. In this account, we first explain the mechanism and main features of the SMMS. We then specify basic elements employed in SMMS. Using DNA as an exemplary SMMS template, we further summarize different types of SMMS which present multiplexing capability and increased throughput. Finally, recent efforts to develop simple and affordable high throughput methods for force generation and measurement are discussed in this Account for potential usage in the mechanochemical sensing.
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Affiliation(s)
- Changpeng Hu
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Rabia Tahir
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
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27
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Hennecker CD, Lachance-Brais C, Sleiman H, Mittermaier A. Using transient equilibria (TREQ) to measure the thermodynamics of slowly assembling supramolecular systems. SCIENCE ADVANCES 2022; 8:eabm8455. [PMID: 35385301 PMCID: PMC8985918 DOI: 10.1126/sciadv.abm8455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Supramolecular chemistry involves the noncovalent assembly of monomers into materials with unique properties and wide-ranging applications. Thermal analysis is a key analytical tool in this field, as it provides quantitative thermodynamic information on both the structural stability and nature of the underlying molecular interactions. However, there exist many supramolecular systems whose kinetics are so slow that the thermodynamic methods currently applied are unreliable or fail completely. We have developed a simple and rapid spectroscopic method for extracting accurate thermodynamic parameters from these systems. It is based on repeatedly raising and lowering the temperature during assembly and identifying the points of transient equilibrium as they are passed on the up- and down-scans. In a proof-of-principle application to the coassembly of polydeoxyadenosine (polyA) containing 15 adenosines and cyanuric acid (CA), we found that roughly 30% of the CA binding sites on the polyA chains were unoccupied, with implications for high-valence systems.
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28
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Fortunati S, Vasini I, Giannetto M, Mattarozzi M, Porchetta A, Bertucci A, Careri M. Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout. Anal Chem 2022; 94:5075-5083. [PMID: 35303407 PMCID: PMC8968946 DOI: 10.1021/acs.analchem.1c05294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Carbon nanotube (CNT)-based
electrodes are cheap, highly performing,
and robust platforms for the fabrication of electrochemical sensors.
Engineering programmable DNA nanotechnologies on the CNT surface can
support the construction of new electrochemical DNA sensors providing
an amperometric output in response to biomolecular recognition. This
is a significant challenge, since it requires gaining control of specific
hybridization processes and functional DNA systems at the interface,
while limiting DNA physisorption on the electrode surface, which contributes
to nonspecific signal. In this study, we provide design rules to program
dynamic DNA structures at the surface of single-walled carbon nanotubes
electrodes, showing that specific DNA interactions can be monitored
through measurement of the current signal provided by redox-tagged
DNA strands. We propose the use of pyrene as a backfilling agent to
reduce nonspecific adsorption of reporter DNA strands and demonstrate
the controlled formation of DNA duplexes on the electrode surface,
which we then apply in the design and conduction of programmable DNA
strand displacement reactions. Expanding on this aspect, we report
the development of novel amperometric hybridization platforms based
on artificial DNA structures templated by the small molecule melamine.
These platforms enable dynamic strand exchange reactions orthogonal
to conventional toehold-mediated strand displacement and may support
new strategies in electrochemical sensing of biomolecular targets,
combining the physicochemical properties of nanostructured carbon-based
materials with programmable nucleic acid hybridization.
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Affiliation(s)
- Simone Fortunati
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Ilaria Vasini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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29
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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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30
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Li F, Song N, Dong Y, Li S, Li L, Liu Y, Li Z, Yang D. A Proton-Activatable DNA-Based Nanosystem Enables Co-Delivery of CRISPR/Cas9 and DNAzyme for Combined Gene Therapy. Angew Chem Int Ed Engl 2022; 61:e202116569. [PMID: 34982495 DOI: 10.1002/anie.202116569] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Indexed: 12/11/2022]
Abstract
CRISPR/Cas9 is emerging as a platform for gene therapeutics, and the treatment efficiency is expected to be enhanced by combination with other therapeutic agents. Herein, we report a proton-activatable DNA-based nanosystem that enables co-delivery of Cas9/sgRNA and DNAzyme for the combined gene therapy of cancer. Ultra-long ssDNA chains, which contained the recognition sequences of sgRNA in Cas9/sgRNA, DNAzyme sequence and HhaI enzyme cleavage site, were synthesized as the scaffold of the nanosystem. The DNAzyme cofactor Mn2+ was used to compress DNA chains to form nanoparticles and acid-degradable polymer-coated HhaI enzymes were assembled on the surface of nanoparticles. In response to protons in lysosome, the polymer coating was decomposed and HhaI enzyme was consequently exposed to recognize and cut off the cleavage sites, thus triggering the release of Cas9/sgRNA and DNAzyme to regulate gene expressions to achieve a high therapeutic efficacy of breast cancer.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Nachuan Song
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Yujie Liu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Zhemian Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
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31
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Li F, Song N, Dong Y, Li S, Li L, Liu Y, Li Z, Yang D. A Proton‐Activatable DNA‐Based Nanosystem Enables Co‐Delivery of CRISPR/Cas9 and DNAzyme for Combined Gene Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Nachuan Song
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Yujie Liu
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Zhemian Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P.R. China
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32
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [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: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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33
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Wang J, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Cui YX, Kong DM. Recent advances in constructing high-order DNA structures. Chem Asian J 2022; 17:e202101315. [PMID: 34989140 DOI: 10.1002/asia.202101315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Indexed: 11/07/2022]
Abstract
Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.
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Affiliation(s)
- Jing Wang
- Nankai University, Department of Chemistry, CHINA
| | | | - Bo Liu
- Nankai University, College of Chemistry, CHINA
| | - Xiao Jing
- Nankai University, College of Chemistry, CHINA
| | - Dan-Ye Chen
- Nankai University, College of Chemistry, CHINA
| | - An-Na Tang
- Nankai University, College of Chemistry, CHINA
| | - Yun-Xi Cui
- Nankai University, College of Chemistry, CHINA
| | - De Ming Kong
- Nankai University, Key Laboratory of Functional Polymer Materials, Weijin road 94, 30071, Tianjin, CHINA
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34
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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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35
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Yang C, Du C, Su R, Wang J, Li Y, Ma X, Li Z, Sun C. A signal-on fluorescent aptasensor by sensitized Tb 3+ luminescence for detection of melamine in milk. Talanta 2022; 236:122842. [PMID: 34635232 DOI: 10.1016/j.talanta.2021.122842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
A fluorescent aptasensor based on sensitized terbium(III) luminescence was constructed to detect melamine in milk. Tb3+ as the fluorescence probe can be sensitized by a guanine-rich single-stranded DNA sequence, so the complementary sequence of the polythymidine aptamer (cDNA) was modified with six consecutive guanine bases (G6). In the absence of melamine, melamine aptamer combined with cDNA to form a double helix structure, and G6 hybridized with the extended cytosine bases in the aptamer, resulting in low fluorescence intensity of Tb3+. In the presence of melamine, cDNA was released due to the specific recognition of melamine to the aptamer, resulting in stronger sensitized fluorescence intensity of Tb3+. Under the optimum conditions, the linear concentration of melamine in the milk ranged from 1.0 μg/mL to 10.0 μg/mL. This aptasensor can be used for the accurate and rapid detection of melamine in milk with a detection limit of 0.02 μg/mL, and has the advantages of high sensitivity, high efficiency, simple operation and low cost.
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Affiliation(s)
- Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Caiyi Du
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ruifang Su
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Zhihong Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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36
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Bindu Ramesan A, Vittala SK, Joseph J. DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 226:112352. [PMID: 34798504 DOI: 10.1016/j.jphotobiol.2021.112352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022]
Abstract
DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.
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Affiliation(s)
- Anjali Bindu Ramesan
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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37
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Pari AA, Yousefi M, Samadi S, Allahgholi Ghasri MR, Torbati MB. Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil. MAIN GROUP CHEMISTRY 2021. [DOI: 10.3233/mgc-210079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An idea of employing an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was examined in this work by analyzing structural features for singular and bimolecular models. Density functional theory (DFT) calculations were performed for optimizing the structures and evaluating molecular and atomic descriptors for analyzing the models systems. Two bimolecular models were obtained assigning by S-FeC and O-FeC models, in which each of S and O atom of 2TU was relaxed towards the Fe region of FeC surface in the mentioned models, respectively. The results indicated that both models were achievable with slightly more favorability for formation of S-FeC model. The obtained molecular orbital properties revealed the dominant role of FeC monolayer for managing future interactions of attached 2TU, which is indeed a major role for employing nanomaterials for targeted drug delivery purposes. In addition to energies and molecular orbital features, atomic quadrupole coupling constants indicated the benefit of employing FeC monolayer for drug delivery of 2TU.
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Affiliation(s)
- Azar Asgari Pari
- Department of Chemistry, Yadegar-e Imam Khomeini (RAH) Shahr-e-Rey Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Yousefi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Susan Samadi
- Department of Chemistry, Yadegar-e Imam Khomeini (RAH) Shahr-e-Rey Branch, Islamic Azad University, Tehran, Iran
| | | | - Maryam Bikhof Torbati
- Department of Biology, Yadegar-e Imam Khomeini (RAH) Shahr-e-Rey Branch, Islamic Azad University, Tehran, Iran
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38
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Wu S, Chen Q. Advances and New Opportunities in the Rheology of Physically and Chemically Reversible Polymers. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01605] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shilong Wu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Quan Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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39
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Rad AJ, Abbasi M, Zohrevand B. Iron Chelation by thiocytosine: Investigating electronic and structural features for describing tautomerism and metal chelation processes. MAIN GROUP CHEMISTRY 2021. [DOI: 10.3233/mgc-210110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This work was performed regarding the importance of iron (Fe) chelation for biological systems. This goal was investigated by assistance of a model of thiocytosine (TC) for participating in Fe-chelation processes. First, formations of tautomeric conformations were investigated to explore existence of possible structures of TC. Next, Fe-chelation processes were examined for all four obtained tautomers of TC. The results indicated that thiol tautomers could be seen at higher stability than thio tautomers, in which one of such thiol tautomers yielded the strongest Fe-chelation process to build FeTC3 model. As a consequence, parallel to the results of original TC tautomers, Fe-chelated models were found to be achievable for meaningful chelation processes or sensing the existence of Fe in media. Examining molecular orbital features could help for sensing purposes. The results of this work were obtained by performing density functional theory (DFT) calculations proposing TC compounds suitable for Fe-chelation purposes.
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Affiliation(s)
- Azadeh Jafari Rad
- Department of Chemistry, Omidiyeh Branch, Islamic Azad University, Omidiyeh, Iran
| | - Maryam Abbasi
- Department of Chemistry, Payame Noor University, Tehran, Iran
| | - Bahareh Zohrevand
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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40
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Malla JA, Ahmad M, Talukdar P. Molecular Self-Assembly as a Tool to Construct Transmembrane Supramolecular Ion Channels. CHEM REC 2021; 22:e202100225. [PMID: 34766703 DOI: 10.1002/tcr.202100225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/16/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022]
Abstract
Self-assembly has become a powerful tool for building various supramolecular architectures with applications in material science, environmental science, and chemical biology. One such area is the development of artificial transmembrane ion channels that mimic naturally occurring channel-forming proteins to unveil various structural and functional aspects of these complex biological systems, hoping to replace the defective protein channels with these synthetically accessible moieties. This account describes our recent approaches to construct supramolecular ion channels using synthetic molecules and their applications in medicinal chemistry.
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Affiliation(s)
- Javid Ahmad Malla
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhaba Road, Pune, Maharashtra, 411008, India
| | - Manzoor Ahmad
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhaba Road, Pune, Maharashtra, 411008, India
| | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhaba Road, Pune, Maharashtra, 411008, India
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41
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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42
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Li J, Li J, Yan Z, Ding XL, Xia XH. Revealing the Hydrogen Bonding Interaction of DNA with Unnatural Bases via Plasmonic Antenna Enhanced Infrared Spectroscopy. J Phys Chem Lett 2021; 12:10255-10261. [PMID: 34652166 DOI: 10.1021/acs.jpclett.1c02901] [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: 06/13/2023]
Abstract
The incorporation of unnatural bases in DNA programming can break through the limits of Watson-Crick and Hoogsteen base pairing to expand the diversity of DNA structures. Thus, understanding the interaction between DNA and unnatural bases is of great importance in DNA nanotechnology. Here, we propose an approach of plasmonic antenna enhanced infrared spectroscopy to study the hydrogen bonding interaction between poly(thymine) DNA (poly T DNA) and melamine. The formation of multiple hydrogen bonds between melamine and thymine of poly T DNA is revealed by the appearance of a new infrared (IR) feature of the NH2 deformation vibration at 1680 cm-1. The binding rate constant (kb) and the dissociation rate constant (kd) of the affinity reaction reach 39.70 M-1·s-1 and 4.49 × 10-5 s-1, respectively. This work offers a valuable IR technique to study DNA nanostructures at the molecular level, providing unique physicochemical views of the interaction mechanism between DNA and unnatural bases in DNA programming.
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Affiliation(s)
- Jin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhendong Yan
- College of Science, Nanjing Forestry University, Nanjing 210037, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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43
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Huang Z, Yao N, Li X, Tian Y, Duan Y. Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications. Anal Chem 2021; 93:14334-14342. [PMID: 34648262 DOI: 10.1021/acs.analchem.1c03636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Signal amplification is critical to achieving sensitive biosensing, but complex strategies often bring problems like system instability, false positive, or narrow target spectrum. Here, a self-extending DNA-mediated isothermal amplification (SEIA) system with simple reaction components is introduced to achieve rapid, robust, and significant signal amplification. In SEIA, based on spontaneous refolding of specific DNA domains and using the previous generation product as a template, a DNA strand can extend continuously in an approximate exponential growth pattern, which was accurately predicted by our formula and well supported by AFM results. Based on a set of proof-of-concept experiments, it was proved that the SEIA system can output different signals and flexibly integrate various functional nucleic acids, which makes it suitable for different scenarios and realizes broad-spectrum target detection. Taking into account the advantages of simplicity, flexibility, and efficiency, the SEIA system as an independent signal amplification module will enrich the toolbox of biosensing design.
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Affiliation(s)
- Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, PR China
| | - Naizhi Yao
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, PR China
| | - Xiaoting Li
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, PR China
| | - Yonghui Tian
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, PR China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, PR China
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44
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Yang H, Wu S, Chen Q. How to Choose a Secondary Interaction to Improve Stretchability of Associative Polymers? Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huanhuan Yang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
- University of Science and Technology of China, 230026 Hefei, China
| | - Shilong Wu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
| | - Quan Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
- University of Science and Technology of China, 230026 Hefei, China
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45
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Liang J, Liang J, Hao A, Xing P. Symmetry breaking-induced double-strand helices in H-bonded coassembly. NANOSCALE 2021; 13:12929-12937. [PMID: 34477776 DOI: 10.1039/d1nr02515e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Double-strand helical structures are important in information storage of biomacromolecules, while the artificial synthesis depends on chirality transfer from the molecular to supramolecular scale, and the synthesis through symmetry breaking has yet been accomplished. In this work, we present the multiple-constituent coassembly of a melamine derivative and an N-terminal aromatic amino acid into double helical nanoarchitectures via symmetry breaking. Multiple intramolecular H-bond formation between constituents played key roles in directing the formation of helical structures. Intertwining of single helices with identical helical parameters afforded double helical structures, benefiting from the uniformity and monodispersity of nanoarchitectures. With introduction of coded chiral amino acid derivatives as chiral sources, the handedness could be readily manipulated with exclusive correlation to the absolute chirality of amino acids. Molecular flexibility of the melamine derivative facilitates the propeller-shaped complex formation to afford helical columnar coassemblies and double helical structures. This work presents a rational control over the emergence and properties of double helical structures in multiple-constituent coassemblies through symmetry breaking, which provides an alternative method towards the synthesis of topological chiral composites and chiroptical materials.
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Affiliation(s)
- Juncong Liang
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China.
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46
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A dissipative pathway for the structural evolution of DNA fibres. Nat Chem 2021; 13:843-849. [PMID: 34373598 DOI: 10.1038/s41557-021-00751-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.
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47
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Zhou Z, Ouyang Y, Wang J, Willner I. Dissipative Gated and Cascaded DNA Networks. J Am Chem Soc 2021; 143:5071-5079. [DOI: 10.1021/jacs.1c00486] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhixin Zhou
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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48
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Wang D, Chen C, Liu Q, Zhao Q, Wu D, Yuan Y, Huang C, Sun X, Huang C, Leong DT, Wang G, Qian H. Functionalizing DNA nanostructures with natural cationic amino acids. Bioact Mater 2021; 6:2946-2955. [PMID: 33732965 PMCID: PMC7930363 DOI: 10.1016/j.bioactmat.2021.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/04/2022] Open
Abstract
Complexing self-assembled DNA nanostructures with various functional guest species is the key to unlocking new and exciting biomedical applications. Cationic guest species not only induce magnesium-free DNA to self-assemble into defined structures but also endow the final complex nanomaterials with new properties. Herein, we propose a novel strategy that employs naturally occurring cationic amino acids to induce DNA self-assembly into defined nanostructures. Natural l-arginine and l-lysine can readily induce the assembly of tile-based DNA nanotubes and DNA origami sheets in a magnesium-free manner. The self-assembly processes are demonstrated to be pH- and concentration-dependent and are achieved at constant temperatures. Moreover, the assembled DNA/amino acid complex nanomaterials are stable at a physiological temperature of 37 °C. Substituting l-arginine with its D form enhances its serum stability. Further preliminary examination of this complex nanomaterial platform for biomedical applications indicates that DNA/amino acids exhibit distinct cellular uptake behaviors compared with their magnesium-assembled counterparts. The nanomaterial mainly clusters around the cell membrane and might be utilized to manipulate molecular events on the membrane. Our study suggests that the properties of DNA nanostructures can be tuned by complexing them with customized guest molecules for a designed application. The strategy proposed herein might be promising to advance the biomedical applications of DNA nanostructures. A “noncanonical DNA self-assembly” strategy is proposed. Cationic amino acids can assemble DNA nanostructures in a magnesium-free system. The complex nanomaterial exhibited high structural and serum stability. DNA nanostructures can be engineered with customized guest molecules for multiple applications.
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Affiliation(s)
- Dong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China.,Department of Respiratory Medicine, Jinling Hospital, Nanjing, Jiangsu, 210002, China
| | - Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Qian Liu
- Laboratory of Pharmacy and Chemistry, And Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Qianwen Zhao
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Di Wu
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Yue Yuan
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chaowang Huang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Xiaorong Sun
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chunji Huang
- Basic Medical College, Third Military Medical University, Chongqing, 400038, China
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Guansong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
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49
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Alenaizan A, Fauché K, Krishnamurthy R, Sherrill CD. Noncovalent Helicene Structure between Nucleic Acids and Cyanuric Acid. Chemistry 2021; 27:4043-4052. [DOI: 10.1002/chem.202004390] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/08/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
- Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta GA 30332-0400 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Kévin Fauché
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - C. David Sherrill
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
- Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta GA 30332-0400 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
- School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0765 USA
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50
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He F, Shen Y, Liu J. SYBR Green I promotes melamine binding to poly-thymine DNA and FRET-based ratiometric sensing. Analyst 2021; 146:1642-1649. [DOI: 10.1039/d1an00102g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using SYBR Green I for DNA melting experiments, polythymine DNA binding to melamine was found to be an intramolecular reaction, allowing the design of a FRET-based biosensor and its sensitivity was enhanced by SYBR Green I.
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Affiliation(s)
- Fan He
- College of Food Science
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University
- Guangzhou 510642
- P. R. China
| | - Yudong Shen
- College of Food Science
- Guangdong Provincial Key Laboratory of Food Quality and Safety
- South China Agricultural University
- Guangzhou 510642
- P. R. China
| | - Juewen Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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