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Zhao B, Kamanzi A, Zhang Y, Chan KYT, Robertson M, Leslie S, Cullis PR. Determination of the interior pH of lipid nanoparticles using a pH-sensitive fluorescent dye-based DNA probe. Biosens Bioelectron 2024; 251:116065. [PMID: 38330772 DOI: 10.1016/j.bios.2024.116065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Lipid nanoparticles (LNPs) containing ionizable cationic lipids are proven delivery systems for therapeutic nucleic acids, such as small interfering RNA (siRNA). It is important to understand the relationship between the interior pH of LNPs and the pH of the external environment to understand LNP formulation and function. Here, we developed a simple and rapid approach for determining the pH of the LNP core using a pH-sensitive fluorescent dye-based DNA probe. LNP siRNA systems containing pH-responsive DNA probes (LNP-siRNA&DNA) were generated by rapid mixing of lipids in ethanol and pH 4 aqueous buffer containing siRNA and DNA probes. We demonstrated that DNA probes were readily encapsulated in LNP systems and were sequestered into an environment at a high concentration as evidenced by an inter-probe FRET signal. It was shown that the pH of LNP encapsulated probes closely follows the pH increase or decrease of the external environment. This indicates that the clinically approved LNP RNA systems with similar lipid compositions (e.g., Onpattro and Comirnaty) are highly permeable to protons and that the pH of the interior environment closely mirrors the external environment. The pH-dependent response of the probe in LNPs was also confirmed under buffer conditions at various pHs. Furthermore, we showed that the pH-sensitive DNA probe can be incorporated into LNP systems at levels that allow the pH response to be monitored at a single LNP level using convex lens-induced confinement (CLiC) confocal microscopy. Direct visualization of the internal pH of single particles with the fluorescent DNA probe was achieved by CLiC for LNP-siRNA&DNA systems formulated under both high and normal ionic strength conditions.
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Affiliation(s)
- Bin Zhao
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Albert Kamanzi
- Michael Smith Laboratories and Department of Physics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Yao Zhang
- Michael Smith Laboratories and Department of Physics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Karen Y T Chan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Madelaine Robertson
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sabrina Leslie
- Michael Smith Laboratories and Department of Physics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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2
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Wang Z, Chen Z, Zhang Z, Wang H, Zhang H. Highly-ordered assembled organic fluorescent materials for high-resolution bio-sensing: a review. Biomater Sci 2024; 12:2019-2032. [PMID: 38469672 DOI: 10.1039/d3bm02070c] [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: 03/13/2024]
Abstract
Organic fluorescent materials (OFMs) play a crucial role in the development of biosensors, enabling the extraction of biochemical information within cells and organisms, extending to the human body. Concurrently, OFM biosensors contribute significantly to the progress of modern medical and biological research. However, the practical applications of OFM biosensors face challenges, including issues related to low resolution, dispersivity, and stability. To overcome these challenges, scientists have introduced interactive elements to enhance the order of OFMs. Highly-ordered assembled OFMs represent a novel material type applied to biosensors. In comparison to conventional fluorescent materials, highly-ordered assembled OFMs typically exhibit robust anti-diffusion properties, high imaging contrast, and excellent stability. This approach has emerged as a promising method for effectively tracking bio-signals, particularly in the non-invasive monitoring of chronic diseases. This review introduces several highly-ordered assembled OFMs used in biosensors and also discusses various interactions that are responsible for their assembly, such as hydrogen bonding, π-π interaction, dipole-dipole interaction, and ion electrostatic interaction. Furthermore, it delves into the various applications of these biosensors while addressing the drawbacks that currently limit their commercial application. This review aims to provide a theoretical foundation for designing high-performance, highly-ordered assembled OFM biosensors suitable for practical applications. Additionally, it sheds light on the evolving trends in OFM biosensors and their application fields, offering valuable insights into the future of this dynamic research area.
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Affiliation(s)
- Zheng Wang
- Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao, 266042, PR China.
| | - Zilong Chen
- Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao, 266042, PR China.
| | - Zhenhao Zhang
- Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao, 266042, PR China.
| | - Hongzhen Wang
- Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao, 266042, PR China.
| | - Haichang Zhang
- Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao, 266042, PR China.
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3
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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4
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Xing H, Zhu Y, Xu D, Wu R, Xing X, Li LS. DNA tetrahedron-mediated triplex molecular switch for extracellular pH monitoring. Anal Chim Acta 2023; 1265:341336. [PMID: 37230576 DOI: 10.1016/j.aca.2023.341336] [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: 01/27/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
This study aimed to construct a novel DNA triplex molecular switch modified with DNA tetrahedron (DTMS-DT) with sensitive response to extracellular pH using a DNA tetrahedron as the anchoring unit and DNA triplex as the response unit. The results showed that the DTMS-DT had desirable pH sensitivity, excellent reversibility, outstanding anti-interference ability, and good biocompatibility. Confocal laser scanning microscopy suggested that the DTMS-DT could not only be stably anchored on the cell membrane but also be employed to dynamically monitor the change in extracellular pH. Compared with the reported probes for extracellular pH monitoring, the designed DNA tetrahedron-mediated triplex molecular switch exhibited higher cell surface stability and brought the pH-responsive unit closer to the cell membrane surface, making the results more reliable. In general, developing the DNA tetrahedron-based DNA triplex molecular switch is helpful for understanding and illustrating the pH dependent cell behaviors and disease diagnostics.
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Affiliation(s)
- Huanhuan Xing
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Yazhen Zhu
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Dangdang Xu
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Ruili Wu
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China
| | - Xiaojing Xing
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, 473061, China.
| | - Lin Song Li
- Key Lab for Special Functional Materials of Ministry of Education, and School of Materials, Henan University, Kaifeng, 475004, China.
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5
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Zhao C, Zhang L, Hu Y, Nie C, Chen TT, Chu X. Simultaneous Imaging and Visualizing the Association of Survivin mRNA and Telomerase in Living Cells by Using a Dual-Color Encoded DNA Nanomachine. Anal Chem 2023; 95:1498-1504. [PMID: 36598384 DOI: 10.1021/acs.analchem.2c04531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Simultaneous imaging and especially visualizing the association of survivin mRNA and telomerase in living cells are of great value for the diagnosis and prognosis of cancer because their co-expression facilitates the development of cancer and identifies patients at high risk of tumor-related death. The challenge is to develop methods that enable visualizing the association of multiplex targets and avoid the distorted signals due to the different delivery efficiency of probes. Herein, we engineered a DNA triangular prism nanomachine (DTPN) for simultaneous multicolor imaging of survivin mRNA and telomerase and visualizing their association in living cells. Two recognizing probes targeted survivin mRNA and telomerase, and the reporter probe was assembled on the DTP in equal amounts, ensuring the same delivery efficiency of the probes to the living cells. The results showed that this DTPN could quantify intracellular survivin mRNA expression and telomerase activity. Moreover, it also enabled us to visualize the effect of the down-regulation of one target on the expression of another target under different drug stimulations. The results implied that our DTPN provided a promising platform for cancer diagnosis, prognosis, drug screening, and related biological research.
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Affiliation(s)
- Chuan Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Lan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yanlei Hu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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6
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Dong Q, Ding Q, Yuan R, Yuan Y. AuNPs/CdS QDs/CeO 2 ternary nanocomposite coupled with scrollable three-dimensional DNA walker mediated cycling amplification for sensitive photoelectrochemical miRNA assay. Anal Chim Acta 2022; 1228:340344. [PMID: 36127010 DOI: 10.1016/j.aca.2022.340344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/15/2022]
Abstract
Herein, a novel ternary nanocomposite (AuNPs/CdS QDs/CeO2) with excellent photoelectrochemical (PEC) performance was synthesized as signal probe to construct a near-zero background biosensor for sensitive miRNA-182-5p detection, by integrating with a scrollable three-dimensional (3D) DNA walker mediated cleavage cycling amplification. Impressively, the formation and rolling of scrollable 3D DNA walker triggered by target could realize dynamic, rapid and specific digestion of hairpin DNA on electrode with the aid of Exonuclease III (Exo III), which thus exposed abundant binding sites for assembling stable DNA labeled AuNPs/CdS QDs/CeO2 nanoprobes. Thanks to the formation of type-II heterojunction (between CeO2 and CdS QDs) and Schottky junction (generated by CeO2 and AuNPs), an ideal photoelectric conversion efficiency accompanied with stunningly improved photocurrent was thus acquired for significantly improving the detection sensitivity. It turned out that the detection limit (LOD) of biosensor was ultralow (31 aM). Significantly, the proposed PEC biosensor would exhibit great potential for the composite as a splendid indicator and provide an avenue for constructing the sensing platform with excellent sensitivity and ultralow background.
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Affiliation(s)
- Qingyuan Dong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Qiao Ding
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yali Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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7
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8
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Rodgers MT, Seidu YS, Israel E. Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1697-1715. [PMID: 35921530 DOI: 10.1021/jasms.2c00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Yakubu S Seidu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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9
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Integrated DNA triangular prism nanomachines for two-stage dynamic recognizing and bio-imaging from surface to the inside of living cells. Biosens Bioelectron 2022; 213:114478. [PMID: 35732084 DOI: 10.1016/j.bios.2022.114478] [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: 03/23/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022]
Abstract
The identification and detection of biomarkers in cancer cells play an essential role in the early detection of diseases, especially the detection of dual-biomarker. However, one of the most important limiting factors is how to realize the identification and labeling of biomarkers dynamically from the plasma membrane to the cytoplasm in living cells. In this study, integrated DNA triangular prism nanomachines (IDTPNs), a two-stage identification and dynamic bio-imaging strategy, recognize biomarkers from the plasma membrane to the cytoplasm have been designed. DNA triangular prism (DTP) was selected to act as a delivery platform with the aptamer Sgc8c and P53 modified on the side as the recognition molecules. Through the specific recognition of aptamers and the superior internalization of DTP, the IDTPNs realize the dynamic responses to PTK7 and p53 from the membrane to the cytoplasm in living cells. It is proved that the IDTPNs can be used for dynamic dual-biomarker recognition and bio-image from the surface to the inside of tumor cells automatically. Therefore, the strategy we developed provides a reliable platform for tumor diagnosis and biomarker research.
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10
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Yang P, Chen H, Zhu Q, Chen Z, Yang Z, Yuan R, Li Y, Liang W. A target-initiated autocatalytic 3D DNA nanomachine for high-efficiency amplified detection of MicroRNA. Talanta 2022; 240:123219. [PMID: 35026639 DOI: 10.1016/j.talanta.2022.123219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/18/2022]
Abstract
Considering the challenges of generating simple and efficient DNA (deoxyribonucleic acid) nanomachines for sensitive bioassays and the great potential of target-induced self-cycling catalytic systems, herein, a novel autocatalytic three-dimensional (3D) DNA nanomachine was constructed based on cross-catalytic hairpin assembly on gold nanoparticles (AuNPs) to generate self-powered efficient cyclic amplification. Typically, the DNA hairpins H1, H2, H3 and H4 were immobilized onto AuNPs first. In the presence of target microRNA-203a, the 3D DNA nanomachines were triggered to activate a series of CHA (catalytic hairpin assembly) reactions. Based on the rational design of the system, the products of the CHA 1 reaction were the trigger of the CHA 2 reaction, which could trigger the CHA 1 reaction in turn, generating an efficient self-powered CHA amplification strategy without adding fuel DNA strands or protein enzymes externally and producing high-efficiency fluorescence signal amplification. More importantly, the proposed autocatalytic 3D DNA nanomachines outperformed conventional 3D DNA nanomachines combined with the single-directional cyclic amplification strategy to maximize the amplification efficiency. This strategy not only achieves high-efficiency analysis of microRNAs (microribonucleic acids) in vitro and intracellularly but also provides a new pathway for highly processive DNA nanomachines, offering a new avenue for bioanalysis and early clinical diagnosis.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Haoran Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Quanjing Zhu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China
| | - Zhaopeng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Zezhou Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, PR China.
| | - Wenbin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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11
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Liu J, Yan L, He S, Hu J. Engineering DNA quadruplexes in DNA nanostructures for biosensor construction. NANO RESEARCH 2021; 15:3504-3513. [PMID: 35401944 PMCID: PMC8983328 DOI: 10.1007/s12274-021-3869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 06/14/2023]
Abstract
DNA quadruplexes are nucleic acid conformations comprised of four strands. They are prevalent in human genomes and increasing efforts are being directed toward their engineering. Taking advantage of the programmability of Watson-Crick base-pairing and conjugation methodology of DNA with other molecules, DNA nanostructures of increasing complexity and diversified geometries have been artificially constructed since 1980s. In this review, we investigate the interweaving of natural DNA quadruplexes and artificial DNA nanostructures in the development of the ever-prosperous field of biosensing, highlighting their specific roles in the construction of biosensor, including recognition probe, signal probe, signal amplifier and support platform. Their implementation in various sensing scenes was surveyed. And finally, general conclusion and future perspective are discussed for further developments.
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Affiliation(s)
- Jingxin Liu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Li Yan
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Shiliang He
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Junqing Hu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
- Shenzhen Bey Laboratory, Shenzhen, 518132 China
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12
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Yang P, Zhou R, Kong C, Fan L, Dong C, Chen J, Hou X, Li F. Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces. ACS NANO 2021; 15:16870-16877. [PMID: 34596378 DOI: 10.1021/acsnano.1c07598] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Chuipeng Kong
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Li Fan
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China, 030006
| | - Chuan Dong
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, Shanxi, China, 030006
| | - Junbo Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Xiandeng Hou
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, China, 610064
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
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13
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Chang Y, Tang X, Huang J, Chai Y, Zhuo Y, Li H, Yuan R. Programming a " Crab Claw"-like DNA Nanomachine as a Super Signal Amplifier for Ultrasensitive Electrochemical Assay of Hg 2. Anal Chem 2021; 93:12075-12080. [PMID: 34427443 DOI: 10.1021/acs.analchem.1c02343] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, with skillfully engaging stable T-Hg2+-T bonding, a "Crab Claw"-like DNA nanomachine with concise and highly efficient assembly and enhanced recognition/conversion efficiency was engineered as a super signal amplifier, which was united with Pd@Cu@Pt multimetallic mesoporous nanomaterials (Pd@Cu@Pt MMNs) for ultrasensitive electrochemical assay of mercury ions (Hg2+). Specifically, the formed "Crab Claw"-like DNA nanomachine could simultaneously trigger four same cascade DNAzyme cleavage reactions with the help of Mg2+ DNAzyme for markedly converting target Hg2+ to enormous DNA segments labeled with ferrocene (Fc), improving the detection sensitivity. Subsequently, the prepared Pd@Cu@Pt MMNs could not only show commendable electrochemical catalysis to Fc but also act as an excellent immobilization matrix for capturing and accumulating abundant Fc around them to further strengthen the electrochemical signal. As a result, the well-designed electrochemical sensor could achieve a low limit of detection of 3.58 fM in the range from 10 fM to 100 nM for Hg2+detection. This strategy offers a simple and rapid avenue to detect heavy metal ions and shows promising application potential for environmental pollutant monitoring.
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Affiliation(s)
- Yuanyuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xiaolu Tang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Junqing Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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14
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He JY, Chen ZH, Deng HL, Yuan R, Xu WJ. Antibody-powered DNA switches to initiate the hybridization chain reaction for the amplified fluorescence immunoassay. Analyst 2021; 146:5067-5073. [PMID: 34297024 DOI: 10.1039/d1an01045j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Designing antibody-powered DNA nanodevice switches is crucial and fascinating to perform a variety of functions in response to specific antibodies as regulatory inputs, achieving highly sensitive detection by integration with simple amplified methods. In this work, we report a unique DNA-based conformational switch, powered by a targeted anti-digoxin mouse monoclonal antibody (anti-Dig) as a model, to rationally initiate the hybridization chain reaction (HCR) for enzyme-free signal amplification. As a proof-of-concept, both a fluorophore Cy3-labeled reporter hairpin (RH) in the 3' terminus and a single-stranded helper DNA (HS) were individually hybridized with a recognition single-stranded DNA (RS) modified with Dig hapten, while the unpaired loop of RH was hybridized with the exposed 3'-toehold of HS, isothermally self-assembling an intermediate metastable DNA structure. The introduction of target anti-Dig drove the concurrent conjugation with two tethered Dig haptens, powering the directional switch of this DNA structure into a stable conformation. In this case, the unlocked 3'-stem of RH was implemented to unfold the 5'-stem of the BHQ-2-labeled quench hairpin (QH), rationally initiating the HCR between them by the overlapping complementary hybridization. As a result, numerous pairs of Cy3 and BHQ-2 in the formed long double helix were located in spatial proximity. In response to this, the significant quenching of the fluorescence intensity of Cy3 by BHQ-2 was dependent on the variable concentration of anti-Dig, achieving a highly sensitive quantification down to the picomolar level based on a simplified protocol integrated with enzyme-free amplification.
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Affiliation(s)
- Jia-Yang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ze-Hui Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Hui-Lin Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Wen-Ju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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15
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Hu X, Huang Y, Yin H, Dai L, Tian Y. DNA‐Based
Architectures for
in situ
Target Biomolecule Analysis in Confined Nano‐space
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaoxue Hu
- Shenzhen Research Institute Nanjing University Shenzhen Guangdong 518000 China
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Yide Huang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Hao Yin
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Ye Tian
- Shenzhen Research Institute Nanjing University Shenzhen Guangdong 518000 China
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
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16
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Yue X, Qiao Y, Gu D, Qi R, Zhao H, Yin Y, Zhao W, Xi R, Meng M. DNA-Based pH Nanosensor with Adjustable FRET Responses to Track Lysosomes and pH Fluctuations. Anal Chem 2021; 93:7250-7257. [PMID: 33944568 DOI: 10.1021/acs.analchem.1c00436] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extensive attention has been recently focused on designing signal adjustable biosensors. However, there are limited approaches available in this field. In this work, to visually track lysosomes with high contrast, we used the i-motif structure as a pH-responsive unit and proposed a novel strategy to regulate the fluorescence resonance energy transfer (FRET) response of the pH sensor. By simply splitting the i-motif into two parts and modulating the split parameters, we can tune the pH transition midpoint (pHt) from 5.71 to 6.81 and the signal-to-noise ratio (S/N) from 1.94 to 18.11. To facilitate the lysosome tracking, we combined the i-motif split design with tetrahedral DNA (Td). The obtained pH nanosensor (pH-Td) displays appropriate pHt (6.12) to trace lysosomes with high S/N (10.3). Benefited from the improved stability, the superior cell uptake and lysosomal location of pH-Td, the visualization of the distribution of lysosomes, the lysosome-mitochondria interaction, and the pH changes of lysosomes in response to different stimuli were successfully achieved in NIH 3T3 cells. We believe that the design concept of controlling the split sequence distance will provide a novel insight into the design of i-motif-based nanosensors and even inspire the construction of smart DNA nanodevices for sensing, disease diagnosis, and controllable drug delivery.
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Affiliation(s)
- Xinmin Yue
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Yanqi Qiao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Dening Gu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Rui Qi
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Hongjie Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Yongmei Yin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Wei Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Rimo Xi
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
| | - Meng Meng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and KLMDASR of Tianjin, Nankai University, Tongyan Road, Haihe Education Park, Tianjin 300350, People's Republic of China
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17
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Chen E, Cai K, Liu X, Wu S, Wu Z, Ma M, Chen B, Zhao Z. Label-Free Ratiometric Upconversion Nanoprobe for Spatiotemporal pH Mapping in Living Cells. Anal Chem 2021; 93:6895-6900. [PMID: 33904297 DOI: 10.1021/acs.analchem.1c00321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sensing and imaging pH inside living cells are of paramount importance for better penetrating cellular functions and disease diagnostics. Herein, we engineered an original pH sensor by a simple one-step self-assembly of poly(ethylene glycol) (PEG)ylated phospholipid (DSPE-PEG) and a phenol red small molecule on the surface of upconversion nanoparticles (UCNPs) to form a phospholipid monolayer for sensing and imaging the change of intracellular pH. The sensor showed excellent reversibility and rapid response to the pH variations. Furthermore, this pH sensing system could measure spatial and temporal pH changes during endocytosis and interrogate the pH fluctuations inside cells under external stimuli. Our experimental results revealed that the pH sensor was able to map spatial and temporal pH fluctuations inside living cells, showing its potential application in diagnostics and pH-related study of cell biology.
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Affiliation(s)
- E Chen
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Ke Cai
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Xin Liu
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Shuai Wu
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Zhan Wu
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province, and Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University Changsha 410081, China
| | - Zilong Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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18
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He S, Liu M, Yin F, Liu J, Ge Z, Li F, Li M, Shi J, Wang L, Mao X, Zuo X, Li Q. Programming folding cooperativity of the dimeric i-motif with DNA frameworks for sensing small pH variations. Chem Commun (Camb) 2021; 57:3247-3250. [PMID: 33646233 DOI: 10.1039/d1cc00266j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The response sensitivity of a molecular sensor is determined by the folding cooperativity of its responsive module. Using an H+-responsive dimeric DNA i-motif as a model, we demonstrate the enhancement of its folding cooperativity through preorganization by a DNA framework, and with it we fabricate robust intracellular pH sensors with high response sensitivity.
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Affiliation(s)
- Shiliang He
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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19
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Hu X, Xu Z, Min Q, Teng C, Tian Y. Endogenous Stimuli-Responsive DNA Nanostructures Toward Cancer Theranostics. FRONTIERS IN NANOTECHNOLOGY 2020. [DOI: 10.3389/fnano.2020.574328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nanostructures specifically responsive to endogenous biomolecules hold great potential in accurate diagnosis and precision therapy of cancers. In the pool of nanostructures with responsiveness to unique triggers, nanomaterials derived from DNA self-assembly have drawn particular attention due to their intrinsic biocompatibility and structural programmability, enabling the selective bioimaging, and site-specific drug delivery in cancer cells and tumor tissues. In this mini review, we summarize the most recent advances in the development of endogenous stimuli-responsive DNA nanostructures featured with precise self-assembly, targeted delivery, and controlled drug release for cancer theranostics. This mini review briefly discusses the diverse dynamic DNA nanostructures aiming at bioimaging and biomedicine, including DNA self-assembling materials, DNA origami structures, DNA hydrogels, etc. We then elaborate the working principles of DNA nanostructures activated by biomarkers (e.g., miRNA, mRNA, and proteins) in tumor cells and microenvironments of tumor tissue (e.g., pH, ATP, and redox gradient). Subsequently, applications of the endogenous stimuli-responsive DNA nanostructures in biological imaging probes for detecting cancer hallmarks as well as intelligent carriers for drug release in vivo are discussed. In the end, we highlight the current challenges of DNA nanotechnology and the further development of this promising research direction.
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20
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Peng X, Yang ZZ, Yang P, Chai YQ, Liang WB, Li ZH, Yuan R. Rapid self-disassembly of DNA diblock copolymer micelles via target induced hydrophilic-hydrophobic regulation for sensitive MiRNA detection. Chem Commun (Camb) 2020; 56:10215-10218. [PMID: 32748935 DOI: 10.1039/d0cc03858j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, a novel DNA nanostructure with a shorter assembly time and larger loading capacity was constructed using amphiphilic DNA-alkane group (Spacer C12)10 conjugates encapsulating plentiful fat-soluble fluorescent dyes into the hydrophobic core to form the DNA micelles, which could be rapidly self-disassembled via target induced hydrophilic-hydrophobic regulation to release fluorescent dyes from micelles to the organic phase, realizing the fast and sensitive detection of microRNA.
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Affiliation(s)
- Xin Peng
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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21
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Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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22
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Zhang F, Liu B, Lopez A, Wang S, Liu J. Opposite salt-dependent stability of i-motif and duplex reflected in a single DNA hairpin nanomachine. NANOTECHNOLOGY 2020; 31:195503. [PMID: 31978920 DOI: 10.1088/1361-6528/ab6fdf] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We herein report a DNA hairpin structure containing a polycytosine loop region, and this hairpin can operate like a nanomachine allowing independently controlled stability of the i-motif loop and duplex stem region. This was made possible by the opposite salt-dependent stability of DNA duplex and hairpin, thus providing a new method for designing molecular devices or switches design. A singly-labeled fluorescent method was used to measure the stability of an i-motif DNA in the presence of various metal ions. Salt in general destabilizes the i-motif but stabilizes duplex DNA, allowing us to engineer an i-motif containing hairpin for modulating the stability of each secondary structure independently.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China. Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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23
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Xie N, Wang H, Quan K, Feng F, Huang J, Wang K. Self-assembled DNA-Based geometric polyhedrons: Construction and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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