1
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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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2
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Zhang R, Chen R, Ma Y, Liang J, Ren S, Gao Z. Application of DNA Nanotweezers in biosensing: Nanoarchitectonics and advanced challenges. Biosens Bioelectron 2023; 237:115445. [PMID: 37421799 DOI: 10.1016/j.bios.2023.115445] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/20/2023] [Accepted: 05/31/2023] [Indexed: 07/10/2023]
Abstract
Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict complementary base-pairing assembly mode, which stimulates the use of DNA to build a variety of nanomachines, including DNA tweezers, motors, walkers, and robots. DNA nanomachines have become prevalent for signal amplification and transformation in the field of biosensing, providing a new method for constructing highly sensitive sensing analysis strategies. DNA tweezers have exhibited unique advantages in biosensing applications owing to their simple structures and fast responses. The two-state conformation of DNA tweezers, the open and closed states, enable them to open and close autonomously after stimulation, thus facilitating the quick detection of corresponding signal changes of different targets. This review discusses the recent progress in the application of DNA nanotweezers in the field of biosensing, and the trends in their development for application in the field of biosensing are summarized.
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Affiliation(s)
- Rui Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yujing Ma
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jun Liang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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3
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Ko S, Kim JY, Park JY, Jung YJ, Choi MJ, Jin KS, Kim Y, Lim YB, Jeong WJ. Modulating the folding and binding of peptides using a stimuli-responsive molecular tweezer. Chem Sci 2023; 14:9600-9607. [PMID: 37712040 PMCID: PMC10498507 DOI: 10.1039/d3sc03758d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 09/16/2023] Open
Abstract
This study presents the development of a β-hairpin (tryptophan zipper, Trpzip)-based molecular tweezer (MT) that can control the folding and binding of α-helical peptides. When an α-helix isolated from the p53 protein was conjugated with Trpzip in an optimized macrocyclic structure, the folded β-hairpin stabilized the helix conformation through the side chain-to-side chain stapling strategy, which notably enhanced target (hDM2) affinity of the peptide. On the other hand, the helicity and binding affinity were significantly reduced when the hairpin was unfolded by a redox stimulus. This stimulus-responsive property was translated into the effective capture and release of model multivalent biomaterials, hDM2-gold nanoparticle conjugates. Since numerous protein interactions are mediated by α-helical peptides, these results suggest that the β-hairpin-based MT holds great potential to be utilized in various biomedical applications, such as protein interaction inhibition and cancer biomarker (e.g., circulating tumor cells and exosomes) detection.
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Affiliation(s)
- Sooho Ko
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Joo-Young Kim
- Department of Biological Sciences and Bioengineering, Inha University Incheon 22212 Republic of Korea
| | - Jung Yeon Park
- KU-KIST Graduate School of Converging Science and Technology, Department of Integrative Energy Engineering, Korea University Seoul 02841 Republic of Korea
| | - You-Jin Jung
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Min-Jae Choi
- Department of Chemical & Biochemical Engineering, Dongguk University Seoul 06420 Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology Pohang 790-784 Republic of Korea
| | - Yongju Kim
- KU-KIST Graduate School of Converging Science and Technology, Department of Integrative Energy Engineering, Korea University Seoul 02841 Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University Seoul 03722 Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University Incheon 22212 Republic of Korea
- Department of Biological Engineering, Inha University Incheon 22212 Republic of Korea
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4
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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5
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A DNA tweezers fluorescence aptasensor based on split aptamer -assisted magnetic nanoparticles for the detection of enrofloxacin in food. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Luteran EM, Paukstelis PJ. The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands. Acta Crystallogr D Struct Biol 2022; 78:299-309. [PMID: 35234144 PMCID: PMC8900823 DOI: 10.1107/s2059798322000304] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
DNA can adopt noncanonical structures that have important biological functions while also providing structural diversity for applications in nanotechnology. Here, the crystal structures of two oligonucleotides composed of d(CGA) triplet repeats in the parallel-stranded duplex form are described. The structure determination of four unique d(CGA)-based parallel-stranded duplexes across two crystal structures has allowed the structural parameters of d(CGA) triplets in the parallel-stranded duplex form to be characterized and established. These results show that d(CGA) units are highly uniform, but that each strand in the duplex is structurally unique and has a distinct role in accommodating structural asymmetries induced by the C-CH+ base pair.
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Affiliation(s)
- Emily M. Luteran
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Paul J. Paukstelis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA,Correspondence e-mail:
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7
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Liu S, Xiang K, Wang C, Zhang Y, Fan GC, Wang W, Han H. DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects. ACS Sens 2022; 7:3-20. [PMID: 34989231 DOI: 10.1021/acssensors.1c01647] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.
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Affiliation(s)
- Shanshan Liu
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Kaikai Xiang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Chunyan Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Yutian Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Gao-Chao Fan
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, Shandong, People’s Republic of China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, People’s Republic of China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
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8
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Saliba D, Trinh T, Lachance-Brais C, Prinzen AL, Rizzuto FJ, de Rochambeau D, Sleiman HF. Asymmetric patterning drives the folding of a tripodal DNA nanotweezer. Chem Sci 2021; 13:74-80. [PMID: 35059153 PMCID: PMC8694393 DOI: 10.1039/d1sc04793k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | | | - Alexander L Prinzen
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Felix J Rizzuto
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Donatien de Rochambeau
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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9
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Hu Y, Wang Z, Chen Z, Pan L. Switching the activity of Taq polymerase using clamp-like triplex aptamer structure. Nucleic Acids Res 2020; 48:8591-8600. [PMID: 32644133 PMCID: PMC7470972 DOI: 10.1093/nar/gkaa581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/31/2020] [Accepted: 06/27/2020] [Indexed: 01/22/2023] Open
Abstract
In nature, allostery is the principal approach for regulating cellular processes and pathways. Inspired by nature, structure-switching aptamer-based nanodevices are widely used in artificial biotechnologies. However, the canonical aptamer structures in the nanodevices usually adopt a duplex form, which limits the flexibility and controllability. Here, a new regulating strategy based on a clamp-like triplex aptamer structure (CLTAS) was proposed for switching DNA polymerase activity via conformational changes. It was demonstrated that the polymerase activity could be regulated by either adjusting structure parameters or dynamic reactions including strand displacement or enzymatic digestion. Compared with the duplex aptamer structure, the CLTAS possesses programmability, excellent affinity and high discrimination efficiency. The CLTAS was successfully applied to distinguish single-base mismatches. The strategy expands the application scope of triplex structures and shows potential in biosensing and programmable nanomachines.
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Affiliation(s)
- Yingxin Hu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei 050043, China
| | - Zhiyu Wang
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Linqiang Pan
- To whom correspondence should be addressed. Tel: +86 27 87556070; Fax: +86 27 87543130;
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10
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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12
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Li J, Wang W, Zhang H, Lu Z, Wu W, Shu M, Han H. Programmable DNA Tweezer-Actuated SERS Probe for the Sensitive Detection of AFB1. Anal Chem 2020; 92:4900-4907. [DOI: 10.1021/acs.analchem.9b04822] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jinjie Li
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Wenjing Wang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Hao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Zhicheng Lu
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Wenxin Wu
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Mingbo Shu
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
| | - Heyou Han
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, Hubei 430070, People’s Republic of China
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13
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Jahanban-Esfahlan A, Seidi K, Jaymand M, Schmidt TL, Majdi H, Javaheri T, Jahanban-Esfahlan R, Zare P. Dynamic DNA nanostructures in biomedicine: Beauty, utility and limits. J Control Release 2019; 315:166-185. [PMID: 31669209 DOI: 10.1016/j.jconrel.2019.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/16/2023]
Abstract
DNA composite materials are at the forefront, especially for biomedical science, as they can increase the efficacy and safety of current therapies and drug delivery systems. The specificity and predictability of the Watson-Crick base pairing make DNA an excellent building material for the production of programmable and multifunctional objects. In addition, the principle of nucleic acid hybridization can be applied to realize mobile nanostructures, such as those reflected in DNA walkers that sort and collect cargo on DNA tracks, DNA robots performing tasks within living cells and/or DNA tweezers as ultra-sensitive biosensors. In this review, we present the diversity of dynamic DNA nanostructures functionalized with different biomolecules/functional units, imaging smart biomaterials capable of sensing, interacting, delivery and performing complex tasks within living cells/organisms.
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Affiliation(s)
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Thorsten L Schmidt
- Physics Department, 103 Smith Hall, Kent State University, Kent, OH, 44240, USA
| | - Hasan Majdi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria.
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland.
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland.
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14
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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15
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Wang B, Song L, Jin B, Deng N, Wu X, He J, Deng Z, Li Y. Base‐Sequence‐Independent Efficient Redox Switching of Self‐Assembled DNA Nanocages. Chembiochem 2019; 20:2743-2746. [DOI: 10.1002/cbic.201900253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Bang Wang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Lei Song
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Ning Deng
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Xiaojing Wu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Jianbo He
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
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16
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Iacovelli F, Cabungcal Hernandez K, Desideri A, Falconi M. Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation. J Chem Inf Model 2019; 59:2746-2752. [PMID: 31074618 DOI: 10.1021/acs.jcim.9b00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The topology of a pH-dependent triple helix DNA nanoswitch family has been characterized through simulative analysis to evaluate the efficiency of the switching mechanism varying the length of the loop connecting the two strands forming the double helix portion. In detail, the system is formed by a double helix made by two six base complementary sequences, connected by one loop having an increasing number of thymidines, namely 5, 7, or 9. The triplex-forming sequence made by six bases, connected to the double helix through a constant 25 base loop, interacts at pH 5.0 through Hoogsteen hydrogen bonds with one strand of the double helical region. We demonstrate, through molecular dynamics simulation, that the thymidine loop length exerts a fine regulatory role for the stability of the triple helix structure and is critical in modulating the switching mechanism triggered by the pH increase.
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Affiliation(s)
- Federico Iacovelli
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Kevin Cabungcal Hernandez
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Alessandro Desideri
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Mattia Falconi
- Department of Biology, Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB) , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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17
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Yang W, Shen Y, Zhang D, Li C, Yuan R, Xu W. Programmed Dual-Functional DNA Tweezer for Simultaneous and Recognizable Fluorescence Detection of microRNA and Protein. Anal Chem 2019; 91:7782-7789. [DOI: 10.1021/acs.analchem.9b01266] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wenting Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yu Shen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Danyang Zhang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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18
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Yu Y, Jin B, Li Y, Deng Z. Stimuli-Responsive DNA Self-Assembly: From Principles to Applications. Chemistry 2019; 25:9785-9798. [PMID: 30931536 DOI: 10.1002/chem.201900491] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 01/01/2023]
Abstract
Stimuli-responsive DNA self-assembly shares the advantages of both designed stimuli-responsiveness and the molecular programmability of DNA structures, offering great opportunities for basic and applied research in dynamic DNA nanotechnology. In this minireview, we summarize the most recent progress in this rapidly developing field. The trigger mechanisms of the responsive DNA systems are first divided into six categories, which are then explained with illustrative examples following this classification. Subsequently, proof-of-concept applications in terms of biosensing, in vivo pH-mapping, drug delivery, and therapy are discussed. Finally, we provide some remarks on the challenges and opportunities of this highly promising research direction in DNA nanotechnology.
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Affiliation(s)
- Yang Yu
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
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19
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Amodio A, Del Grosso E, Troina A, Placidi E, Ricci F. Remote Electronic Control of DNA-Based Reactions and Nanostructure Assembly. NANO LETTERS 2018; 18:2918-2923. [PMID: 29608313 DOI: 10.1021/acs.nanolett.8b00179] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The use of synthetic DNA to design and build molecular machines and well-defined structures at the nanoscale has greatly impacted the field of nanotechnology. Here we expand the current toolkit in this field by demonstrating an efficient, quantitative, and versatile approach that allows us to remotely control DNA-based reactions and DNA nanostructure self-assembly using electronic inputs. To do so we have deposited onto the surface of disposable chips different DNA input strands that upon the application of a cathodic potential can be desorbed in a remote and controlled way and trigger DNA-based reactions and DNA nanostructure self-assembly. We demonstrate that this effect is specific and versatile and allows the orthogonal control of multiple reactions and multiple structures in the same solution. Moreover, the strategy is highly tunable and can be finely modulated by varying the cathodic potential, the period of applied potential, and the density of the DNA strand on the chip surface. Our approach thus represents a versatile way to remotely control DNA-based circuits and nanostructure assembly and can allow new possible applications of DNA-based nanotools.
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Affiliation(s)
- Alessia Amodio
- Department of Chemical Science and Technologies , University of Rome , Tor Vergata, Via della Ricerca Scientifica , 00133 , Rome , Italy
| | - Erica Del Grosso
- Department of Chemical Science and Technologies , University of Rome , Tor Vergata, Via della Ricerca Scientifica , 00133 , Rome , Italy
| | - Alessandra Troina
- Department of Chemical Science and Technologies , University of Rome , Tor Vergata, Via della Ricerca Scientifica , 00133 , Rome , Italy
| | - Ernesto Placidi
- Istituto di Struttura della Materia (ISM-CNR) , via Fosso del Cavaliere 100 , 00133 Rome , Italy
| | - Francesco Ricci
- Department of Chemical Science and Technologies , University of Rome , Tor Vergata, Via della Ricerca Scientifica , 00133 , Rome , Italy
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20
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Li Y, Song L, Wang B, He J, Li Y, Deng Z, Mao C. Universal pH‐Responsive and Metal‐Ion‐Free Self‐Assembly of DNA Nanostructures. Angew Chem Int Ed Engl 2018; 57:6892-6895. [DOI: 10.1002/anie.201804054] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Yongfei Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Lei Song
- CAS Key Laboratory of Soft Matter Chemistry Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Bang Wang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Jianbo He
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
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21
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Li Y, Song L, Wang B, He J, Li Y, Deng Z, Mao C. Universal pH‐Responsive and Metal‐Ion‐Free Self‐Assembly of DNA Nanostructures. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongfei Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Lei Song
- CAS Key Laboratory of Soft Matter Chemistry Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Bang Wang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Jianbo He
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering School of Chemistry and Chemical Engineering Hefei University of Technology Hefei Anhui 230009 China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
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22
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Angell C, Kai M, Xie S, Dong X, Chen Y. Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications. Adv Healthc Mater 2018; 7:e1701189. [PMID: 29350489 DOI: 10.1002/adhm.201701189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Indexed: 12/28/2022]
Abstract
Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.
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Affiliation(s)
- Chava Angell
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Mingxuan Kai
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Sibai Xie
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Xiangyi Dong
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Yi Chen
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
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23
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Chandrasekaran AR, Rusling DA. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res 2018; 46:1021-1037. [PMID: 29228337 PMCID: PMC5814803 DOI: 10.1093/nar/gkx1230] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/30/2017] [Indexed: 11/14/2022] Open
Abstract
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
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Affiliation(s)
| | - David A Rusling
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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24
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Idili A, Ricci F. Design and Characterization of pH-Triggered DNA Nanoswitches and Nanodevices Based on DNA Triplex Structures. Methods Mol Biol 2018; 1811:79-100. [PMID: 29926447 DOI: 10.1007/978-1-4939-8582-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Triplex DNA is becoming a very useful domain to design pH-triggered DNA nanoswitches and nanodevices. The high versatility and programmability of triplex DNA interactions allows the integration of pH-controllable modules into DNA-based reactions and self-assembly processes. Here, we describe the procedure to characterize DNA-based triplex nanoswitches and more in general pH-triggered structure-switching mechanisms. Procedures to characterize pH-triggered DNA nanodevices will be useful for many applications in the field of biosensing, drug delivery systems and smart nanomaterials.
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Affiliation(s)
- Andrea Idili
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy.
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25
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Li Q, Tian C, Li X, Mao C. Can strand displacement take place in DNA triplexes? Org Biomol Chem 2018; 16:372-375. [PMID: 29265153 DOI: 10.1039/c7ob02871g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Toehold-mediated strand displacement can take place in the context of DNA triplexes, slowly.
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Affiliation(s)
- Qian Li
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Cheng Tian
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Xiang Li
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
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26
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Chen W, Fang X, Ye X, Li H, Cao H, Kong J. DNA nanomachine-assisted magnetic bead based target recycling and isothermal amplification for sensitive fluorescence determination of interferon-γ. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2511-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Iacovelli F, Idili A, Benincasa A, Mariottini D, Ottaviani A, Falconi M, Ricci F, Desideri A. Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch. J Am Chem Soc 2017; 139:5321-5329. [PMID: 28365993 DOI: 10.1021/jacs.6b11470] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices.
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Affiliation(s)
- Federico Iacovelli
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Andrea Idili
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Benincasa
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Davide Mariottini
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Mattia Falconi
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Francesco Ricci
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
| | - Alessandro Desideri
- Department of Biology and ‡Department of Chemistry, University of Rome, Tor Vergata , 00173 Rome, Italy
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28
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Yang X, Tang Y, Traynor SM, Li F. Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold. J Am Chem Soc 2016; 138:14076-14082. [DOI: 10.1021/jacs.6b08794] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiaolong Yang
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Yanan Tang
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Sarah M. Traynor
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Feng Li
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
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29
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Li D, Cheng W, Li Y, Xu Y, Li X, Yin Y, Ju H, Ding S. Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs. Anal Chem 2016; 88:7500-6. [PMID: 27367785 DOI: 10.1021/acs.analchem.5b04844] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system. The binary target inputs can be used for successful building of AND logic gate, which is validated by polyacrylamide gel electrophoresis, surface plasmon resonance and the biosensing signal. The developed biosensing system shows a linear response of the output chemiluminescence signal to input binary miRNAs with a detection limit of 30 fM. It can be used for miRNAs analysis in complex sample matrix. This system provides a simple and reusable platform for logic gate operation and enzyme-free, highly sensitive, and specific multianalysis of miRNAs.
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Affiliation(s)
- Dandan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - YongJie Xu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yibing Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University , Nanjing 210023, People's Republic of China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
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30
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Yao D, Li H, Guo Y, Zhou X, Xiao S, Liang H. A pH-responsive DNA nanomachine-controlled catalytic assembly of gold nanoparticles. Chem Commun (Camb) 2016; 52:7556-9. [PMID: 27225943 DOI: 10.1039/c6cc03089k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The toehold-mediated DNA-strand-displacement reaction has unique programmable properties for driving the catalytic assembly of gold nanoparticles (AuNPs). Herein, we introduced a pH-responsive triplex structure into the DNA-strand-displacement-based catalytic assembly system of DNA-AuNPs to add an additional controlling factor, namely the pH. In this catalytic system, the aggregation rate of AuNPs could be regulated by both internal factors (concentrations of substrate, target, etc.) and an external control (pH gradient). This strategy can be used to construct pH-induced DNA logic gates and sophisticated DNA networks as well as to image instantaneous pH changes in living cells.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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31
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Abstract
Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.
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Affiliation(s)
- Na Wu
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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32
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Hwang MT, Landon PB, Lee J, Mo A, Meckes B, Glinsky G, Lal R. DNA nano-carrier for repeatable capture and release of biomolecules. NANOSCALE 2015; 7:17397-17403. [PMID: 26439640 DOI: 10.1039/c5nr05124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA can be manipulated to design nano-machines through specific sequence recognition. We report a switchable DNA carrier for repeatable capture and release of a single stranded DNA. The activity of the carrier was regulated by the interactions among a double-stranded actuator, single stranded target, fuel, and anti-fuel DNA strands. Inosine was used to maintain a stable triple-stranded complex when the actuator's conformation was switched between open (capture) and closed (release) configurations. Time lapse fluorescence measurements show repeatable capture and release of target strands. TEM images also show visible capture of target DNA strands when gold nanoparticles were attached to the DNA carrier and the target DNA strand. The carrier activity was controlled by length of toeholds, number of mismatches, and inosine substitutions. Significantly, unlike in previously published work that reported the devices functioned only when there is a perfect match between the interacting DNA strands, the present device works only when there are mismatches in the fuel strand and the best performance is achieved for 1-3 mismatches. The device was used to successfully capture and release gold nanoparticles when linked to the target single-stranded DNA. In general, this type of devices can be used for transport and delivery of theranostic molecules.
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Affiliation(s)
- Michael T Hwang
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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33
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Porchetta A, Idili A, Vallée-Bélisle A, Ricci F. General Strategy to Introduce pH-Induced Allostery in DNA-Based Receptors to Achieve Controlled Release of Ligands. NANO LETTERS 2015; 15:4467-71. [PMID: 26053894 PMCID: PMC4498449 DOI: 10.1021/acs.nanolett.5b00852] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/29/2015] [Indexed: 05/23/2023]
Abstract
Inspired by naturally occurring pH-regulated receptors, here we propose a rational approach to introduce pH-induced allostery into a wide range of DNA-based receptors. To demonstrate this we re-engineered two model DNA-based probes, a molecular beacon and a cocaine-binding aptamer, by introducing in their sequence a pH-dependent domain. We demonstrate here that we can finely tune the affinity of these model receptors and control the load/release of their specific target molecule by a simple pH change.
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Affiliation(s)
- Alessandro Porchetta
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Alexis Vallée-Bélisle
- Laboratory
of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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Wang H, Li Y, Liu M, Gong M, Deng Z. Overcoming the Coupling Dilemma in DNA-Programmable Nanoparticle Assemblies by "Ag+ Soldering". SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:2247-2251. [PMID: 25641776 DOI: 10.1002/smll.201403108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Strong coupling between nanoparticles is critical for facilitating charge and energy transfers. Despite the great success of DNA-programmable nanoparticle assemblies, the very weak interparticle coupling represents a key barrier to various applications. Here, an extremely simple, fast, and highly efficient process combining DNA-programming and molecular/ionic bonding is developed to address this challenge, which exhibits a seamless fusion with DNA nanotechnology.
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Affiliation(s)
- Huiqiao Wang
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Yulin Li
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Miao Liu
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Ming Gong
- Engineering and Materials Science Experiment Center, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, P.R. China
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35
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Gong X, Zhou W, Li D, Chai Y, Xiang Y, Yuan R. RNA-regulated molecular tweezers for sensitive fluorescent detection of microRNA from cancer cells. Biosens Bioelectron 2015; 71:98-102. [PMID: 25889350 DOI: 10.1016/j.bios.2015.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/23/2015] [Accepted: 04/05/2015] [Indexed: 01/03/2023]
Abstract
We describe here the construction of the DNA self-assembled molecular tweezers and the application of the tweezers for the monitoring of microRNA (miR-141) from human prostate cancer cells. The self-assembly formation of the DNA tweezers and the regulation of the tweezers upon alternative addition of the fuel miR-141 and the anti-fuel strands are characterized by native polyacrylamide gel electrophoresis. The addition of miR-141 to the DNA tweezers turns "off" the tweezers, while subsequent introduction of the anti-fuel strands switches the tweezers back to the "on" state, which verifies the regulatory ability of the tweezers. The miR-141-regulated DNA tweezers are concentration dependent and can be employed for sensitive detection of miR-141 down to 0.6 pM. The DNA tweezers also show high selectivity toward the fuel strand and can be used to monitor miR-141 expression in cancer cells, which provides new opportunities for the application of the dynamic DNA devices in clinical diagnostics.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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Amodio A, Zhao B, Porchetta A, Idili A, Castronovo M, Fan C, Ricci F. Rational design of pH-controlled DNA strand displacement. J Am Chem Soc 2014; 136:16469-72. [PMID: 25369216 DOI: 10.1021/ja508213d] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Achieving strategies to finely regulate with biological inputs the formation and functionality of DNA-based nanoarchitectures and nanomachines is essential toward a full realization of the potential of DNA nanotechnology. Here we demonstrate an unprecedented, rational approach to achieve control, through a simple change of the solution's pH, over an important class of DNA association-based reactions. To do so we took advantage of the pH dependence of parallel Hoogsteen interactions and rationally designed two triplex-based DNA strand displacement strategies that can be triggered and finely regulated at either basic or acidic pHs. Because pH change represents an important input both in healthy and pathological biological pathways, our findings can have implication for the development of DNA nanostructures whose assembly and functionality can be triggered in the presence of specific biological targets.
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Affiliation(s)
- Alessia Amodio
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata , Via della Ricerca Scientifica, 00133, Rome, Italy
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Abstract
We have designed programmable DNA-based nanoswitches whose closing/opening can be triggered over specific different pH windows. These nanoswitches form an intramolecular triplex DNA structure through pH-sensitive parallel Hoogsteen interactions. We demonstrate that by simply changing the relative content of TAT/CGC triplets in the switches, we can rationally tune their pH dependence over more than 5 pH units. The ability to design DNA-based switches with tunable pH dependence provides the opportunity to engineer pH nanosensors with unprecedented wide sensitivity to pH changes. For example, by mixing in the same solution three switches with different pH sensitivity, we developed a pH nanosensor that can precisely monitor pH variations over 5.5 units of pH. With their fast response time (<200 ms) and high reversibility, these pH-triggered nanoswitches appear particularly suitable for applications ranging from the real-time monitoring of pH changes in vivo to the development of pH sensitive smart nanomaterials.
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Affiliation(s)
- Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata , 00133, Rome, Italy
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38
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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39
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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40
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Li XM, Song J, Cheng T, Fu PY. A duplex–triplex nucleic acid nanomachine that probes pH changes inside living cells during apoptosis. Anal Bioanal Chem 2013; 405:5993-9. [DOI: 10.1007/s00216-013-7037-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/25/2013] [Accepted: 04/30/2013] [Indexed: 01/29/2023]
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41
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Pampanin DM, Larssen E, Provan F, Sivertsvik M, Ruoff P, Sydnes MO. Detection of small bioactive peptides from Atlantic herring (Clupea harengus L.). Peptides 2012; 34:423-6. [PMID: 22342594 DOI: 10.1016/j.peptides.2012.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/03/2012] [Accepted: 02/03/2012] [Indexed: 11/17/2022]
Abstract
Recent research has shown that fish residual materials contain a range of components with interesting biological activity. Therefore, there is a great potential in the marine bioprocess industry to utilize these by-products as starting material for generating more valuable products. The aim of the present study was to search for bioactive peptides (in particular small natural bioactive peptides with molecular weight lower than 10 kDa) in Atlantic herring (Clupea harengus L.) by-products such as skin and more general residual materials. By such means a range of peptides with claimed interesting biological activities was found. Herein the activity of the detected bioactive peptides and strategies for isolating peptide fragments containing the bioactive motif is discussed. Identification of bioactive peptides in crude peptide/protein sources (skin and residual materials) was performed directly using a combination of mass spectrometry (Orbitrap), bioinformatics and database search. This method was a good angle of approach in order to map the potential in new species and species that have been very little studied.
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Affiliation(s)
- Daniela M Pampanin
- Biomiljø, International Research Institute of Stavanger, Mekjarvik 12, NO-4070 Randaberg, Norway
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Landon PB, Ramachandran S, Gillman A, Gidron T, Yoon D, Lal R. DNA zipper-based tweezers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:534-540. [PMID: 21875130 DOI: 10.1021/la201267e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Here we report the design and development of DNA zippers and tweezers. Essentially a zipper system consists of a normal strand (N), a weak strand (W), and an opening strand (O). N strand is made up of normal DNA bases, while W is engineered to have inosine substituting for guanine. By altering the number and order of inosine, W is engineered to provide less than natural bonding affinities to N in forming the [N:W] helix. When O is introduced (a natural complement of N), it competitively displaces W from [N:W] and forms [N:O]. This principle is incorporated in the development of a molecular device that can perform the functions of tweezers (sense, hold, and release). Tweezers were constructed by holding N and W together using a hinge at one end. Thus, when the tweezers open, N and W remain in the same vicinity. This allows the tweezers to cycle among open and close positions by their opening and closing strands. Control over their opening and closing kinetics is demonstrated. In contrast to the previously reported DNA tweezers, the zipper mechanism makes it possible to operate them with opening strands that do not contain single-stranded DNA overhangs. Our approach yields a robust, compact, and regenerative tweezer system that could potentially be integrated into complex nanomachines.
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Affiliation(s)
- Preston B Landon
- Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Abstract
The base sequence encoded in nucleic acids yields significant structural and functional properties into the biopolymer. The resulting nucleic acid nanostructures provide the basis for the rapidly developing area of DNA nanotechnology. Advances in this field will be exemplified by discussing the following topics: (i) Hemin/G-quadruplex DNA nanostructures exhibit unique electrocatalytic, chemiluminescence and photophysical properties. Their integration with electrode surfaces or semiconductor quantum dots enables the development of new electrochemical or optical bioanalytical platforms for sensing DNA. (ii) The encoding of structural information into DNA enables the activation of autonomous replication processes that enable the ultrasensitive detection of DNA. (iii) By the appropriate design of DNA nanostructures, functional DNA machines, acting as "tweezers", "walkers" and "stepper" systems, can be tailored. (iv) The self-assembly of nucleic acid nanostructures (nanowires, strips, nanotubes) allows the programmed positioning of proteins on the DNA templates and the activation of enzyme cascades.
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Bai X, Wu J, Han X, Deng Z. Probing DNA's interstrand orientation with gold nanoparticles. Anal Chem 2011; 83:5067-72. [PMID: 21623639 DOI: 10.1021/ac200987e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interstrand orientation of a DNA duplex plays a pivotal role in its biological and chemical functions. Therefore, developing an efficient way to determine (control and monitor) the parallel or antiparallel conformation of a DNA duplex is of great significance, which, however, remains a big challenge under some circumstances. In this work, we demonstrate that gold nanoparticles tagged on DNA are especially useful in trapping and detecting a special interstrand orientation of a DNA double helix, based on inherent electrostatic and steric repulsions between nanoparticles which will affect their self-assembly into a large structure. More importantly, some of the conformations revealed by the gold nanoparticle assay may even not be thermodynamically preferred and thus will be hard to detect using currently available methods. This simple, straightforward, and efficient methodology capable of dictating and probing a special DNA duplex structure provides a useful tool for conformational analyses and functional explorations of biomolecules as well as biophysical and nanobiomedical research.
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46
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Zhang Z, Olsen EM, Kryger M, Voigt NV, Tørring T, Gültekin E, Nielsen M, Zadegan RM, Andersen ES, Nielsen MM, Kjems J, Birkedal V, Gothelf KV. A DNA Tile Actuator with Eleven Discrete States. Angew Chem Int Ed Engl 2011; 50:3983-7. [DOI: 10.1002/anie.201007642] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Indexed: 11/12/2022]
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47
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Zhang Z, Olsen EM, Kryger M, Voigt NV, Tørring T, Gültekin E, Nielsen M, Zadegan RM, Andersen ES, Nielsen MM, Kjems J, Birkedal V, Gothelf KV. A DNA Tile Actuator with Eleven Discrete States. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol 2010; 21:376-91. [PMID: 20727732 DOI: 10.1016/j.copbio.2010.06.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 06/15/2010] [Accepted: 06/15/2010] [Indexed: 12/11/2022]
Abstract
The information encoded in the base sequence of DNA provides instructions for the structural and functional properties of this biopolymer. Structural information includes the formation of duplexes, supramolecular crossover tiles, G-quadruplexes, i-motifs, base-metal-ion complexes, and more. Functional information encoded in the DNA is reflected by specific binding (aptamers) or catalytic properties (DNAzymes). Recent advances in tailoring supramolecular DNA structures for DNA-based machinery and for amplified biosensing are reviewed. Different DNA machines that perform 'tweezer', 'walker' or 'metronome' functions are discussed, and the control of macroscopic surface properties or the motility of micro-objects by molecular DNA devices is introduced. Furthermore, the design of DNA machines for the ultrasensitive detection of DNA, low-molecular-weight substrates, and macromolecules is discussed. Supramolecular aptamer and DNAzyme structures are used as molecular tools for amplified sensing.
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49
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Elbaz J, Wang ZG, Orbach R, Willner I. pH-stimulated concurrent mechanical activation of two DNA "tweezers". A "SET-RESET" logic gate system. NANO LETTERS 2009; 9:4510-4514. [PMID: 19835388 DOI: 10.1021/nl902859m] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A DNA tweezer consisting of C-rich arms is kept in the "closed" form by hybridization of the arms with a nucleic acid cross-linker. At acidic pH (pH = 5.2), the arms are stabilized through the formation of the i-motif, C-quadruplex structures, releasing the cross-linking nucleic acid and transforming the tweezer to its "opened" state. At neutral pH (pH = 7.2), the C-quadruplex structures are dissociated, resulting in the capturing of the cross-linking nucleic acid and the closure of the tweezer. By the reversible treatment of the tweezer at pH = 5.2 and at pH = 7.2, the tweezer system is cycled between the open and closed states, respectively, followed by a FRET process between a fluorophore-quencher pair that labels the tweezer. Also the concurrent activation of two DNA tweezers by pH stimuli is described. The pH-induced opening of one tweezer (tweezer A) by the formation of C-quadruplex (pH = 5.2) and the release of the cross-linking nucleic acid result in the closure of a second tweezer (tweezer B) by the hybridization of the released strand with the arms of tweezer B. The dissociation of the C-quadruplex structures (pH = 7.2) results in the favored translocation of the cross-linking nucleic acid from tweezer B to A. By the cycling of the pH of the system between pH = 5.2 and pH = 7.2, the concurrent opening and closure of the two tweezers are accomplished. The two tweezers system performs a SET-RESET logic gate operation, where the pH stimuli act as inputs.
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Affiliation(s)
- Johann Elbaz
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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50
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Elbaz J, Moshe M, Willner I. Coherent activation of DNA tweezers: a "SET-RESET" logic system. Angew Chem Int Ed Engl 2009; 48:3834-7. [PMID: 19378312 DOI: 10.1002/anie.200805819] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Open sesame: Aptamer-substrate complexes activate the coherent operation of two tweezers that act as a "SET-RESET" logic system. Each tweezer cycles between a fluorescent open state and a closed quenched state (Q = quencher, F = fluorophore) when triggered by adenosine monophosphate (AMP) and adenosine deaminase (AD).
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Affiliation(s)
- Johann Elbaz
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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