1
|
Jin Y, Yu W, Chen L, Yuan R, Liu J, Fu Y, Chai Y. Dual-sensitized heterojunction Ag 2S/ZnS/NiS composites with entire visible-light region absorption for ultrasensitive photoelectrochemical detection of tobramycin. Biosens Bioelectron 2024; 260:116459. [PMID: 38838575 DOI: 10.1016/j.bios.2024.116459] [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: 03/19/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
In this study, an ultrasensitive photoelectrochemical (PEC) aptasensor based on dual-sensitized heterojunction Ag2S/ZnS/NiS composites as a signal probe was proposed for the detection of tobramycin (TOB) by combining a cascaded quadratic signal amplification strategy. Specifically, compared to the limited visible light-harvesting capability of single sensitized composites, Ag2S/ZnS/NiS composites with p-n and n-n heterojunction could greatly improve the light energy utilization to tremendously strengthen the optical absorption in the entire visible-light region. Moreover, dual-sensitized heterojunction could effectively hinder the rapid recombination of photoelectrons and holes (carriers) to obtain a good photocurrent for improving the sensitivity of the aptasensor. Furthermore, a cascaded quadratic signal amplification strategy was applied to convert trace target TOB into plentiful gold nanoclusters (Au NCs) labelled double-stranded DNA for the construction of PEC aptasensor, with a broad linear detection range from 0.01 to 100 ng mL-1 and a low detection limit of 3.38 pg mL-1. Importantly, this study provided a versatile and sensitive PEC biosensing platform for TOB analysis, and demonstrated its successful application for TOB detection in milk samples. This protocol provides a novel dual-sensitized heterojunction composites to develop a highly efficient and harmfulless PEC aptasensor, which is expected to be used in food safety, environmental monitoring and other areas.
Collapse
Affiliation(s)
- Yushuang Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wanqing Yu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Li Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, 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, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Jiali Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Yingzi Fu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, 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, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| |
Collapse
|
2
|
Chen H, Wang S, Cao Y, Lei H. Molecular Force Sensors for Biological Application. Int J Mol Sci 2024; 25:6198. [PMID: 38892386 PMCID: PMC11173168 DOI: 10.3390/ijms25116198] [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: 04/29/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.
Collapse
Affiliation(s)
- Huiyan Chen
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Shouhan Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Hai Lei
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
3
|
Amouzadeh Tabrizi M, Bhattacharyya P, Zheng R, You M. Electrochemical DNA-based sensors for measuring cell-generated forces. Biosens Bioelectron 2024; 253:116185. [PMID: 38457863 PMCID: PMC10947853 DOI: 10.1016/j.bios.2024.116185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Mechanical forces play an important role in cellular communication and signaling. We developed in this study novel electrochemical DNA-based force sensors for measuring cell-generated adhesion forces. Two types of DNA probes, i.e., tension gauge tether and DNA hairpin, were constructed on the surface of a smartphone-based electrochemical device to detect piconewton-scale cellular forces at tunable levels. Upon experiencing cellular tension, the unfolding of DNA probes induces the separation of redox reporters from the surface of the electrode, which results in detectable electrochemical signals. Using integrin-mediated cell adhesion as an example, our results indicated that these electrochemical sensors can be used for highly sensitive, robust, simple, and portable measurements of cell-generated forces.
Collapse
Affiliation(s)
- Mahmoud Amouzadeh Tabrizi
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA, 01003, USA.
| | - Priyanka Bhattacharyya
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA, 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA, 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA, 01003, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA, 01003, USA.
| |
Collapse
|
4
|
Huang Y, Chen T, Chen X, Chen X, Zhang J, Liu S, Lu M, Chen C, Ding X, Yang C, Huang R, Song Y. Decoding Biomechanical Cues Based on DNA Sensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310330. [PMID: 38185740 DOI: 10.1002/smll.202310330] [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: 11/11/2023] [Revised: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.
Collapse
Affiliation(s)
- Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ting Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiaodie Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ximing Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sinong Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Menghao Lu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chong Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiangyu Ding
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ruiyun Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| |
Collapse
|
5
|
Han Z, Hayes OG, Partridge BE, Huang C, Mirkin CA. Reversible strain-promoted DNA polymerization. SCIENCE ADVANCES 2024; 10:eado8020. [PMID: 38657068 PMCID: PMC11042731 DOI: 10.1126/sciadv.ado8020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Molecular strain can be introduced to influence the outcome of chemical reactions. Once a thermodynamic product is formed, however, reversing the course of a strain-promoted reaction is challenging. Here, a reversible, strain-promoted polymerization in cyclic DNA is reported. The use of nonhybridizing, single-stranded spacers as short as a single nucleotide in length can promote DNA cyclization. Molecular strain is generated by duplexing the spacers, leading to ring opening and subsequent polymerization. Then, removal of the strain-generating duplexers triggers depolymerization and cyclic dimer recovery via enthalpy-driven cyclization and entropy-mediated ring contraction. This reversibility is retained even when a protein is conjugated to the DNA strands, and the architecture of the protein assemblies can be modulated between bivalent and polyvalent states. This work underscores the utility of using DNA not only as a programmable ligand for assembly but also as a route to access restorable bonds, thus providing a molecular basis for DNA-based materials with shape-memory, self-healing, and stimuli-responsive properties.
Collapse
Affiliation(s)
- Zhenyu Han
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Oliver G. Hayes
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Benjamin E. Partridge
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chi Huang
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | | |
Collapse
|
6
|
Tabrizi MA, Ali AA, Singuru MMR, Mi L, Bhattacharyya P, You M. A portable electrochemical DNA sensor for sensitive and tunable detection of piconewton-scale cellular forces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586508. [PMID: 38585754 PMCID: PMC10996547 DOI: 10.1101/2024.03.24.586508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cell-generated forces are a key player in cell biology, especially during cellular shape formation, migration, cancer development, and immune response. A new type of label-free smartphone-based electrochemical DNA sensor is developed here for cellular force measurement. When cells apply tension forces to the DNA sensors, the rapid rupture of DNA duplexes allows multiple redox reporters to reach the electrode and generate highly sensitive electrochemical signals. The sensitivity of these portable sensors can be further enhanced by incorporating a CRISPR-Cas12a system. Meanwhile, the threshold force values of these DNA-based sensors can be rationally tuned based on the force application geometries and also DNA intercalating agents. Overall, these highly sensitive, portable, cost-efficient, and easy-to-use electrochemical sensors can be powerful tools for detecting different cell-generated molecular forces.
Collapse
Affiliation(s)
- Mahmoud Amouzadeh Tabrizi
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| | - Ahsan Ausaf Ali
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| | - Murali Mohana Rao Singuru
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| | - Lan Mi
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| | - Priyanka Bhattacharyya
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003, USA
| |
Collapse
|
7
|
Jiang M, Xu S, Liu Y, Wang ZG. A designed DNA/amino acid amphiphile-based supramolecular oxidase-mimetic catalyst for colorimetric DNA detection. Chem Commun (Camb) 2023; 59:14540-14543. [PMID: 37987146 DOI: 10.1039/d3cc04047j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
DNA is self-assembled with Fmoc-amino acids and Cu2+ to construct a supramolecular catechol oxidase-mimetic catalyst, which exhibits remarkable activity in catalyzing colorimetric reactions. This catalytic system is used for the detection of DNA hybridization with a high selectivity and a low detection limit.
Collapse
Affiliation(s)
- Minquan Jiang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
8
|
Wang Y, Wu D, Cao X, Guo Y. The Amplified DNA Logic Gates Based on Aptamer-Receptor Recognition for Cell Detection and Bioimaging. BIOSENSORS 2023; 13:968. [PMID: 37998143 PMCID: PMC10669702 DOI: 10.3390/bios13110968] [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: 08/23/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
A powerful and accurate method for identifying and isolating cells would be of great importance due to its sensitivity, gentleness and effectiveness. Here, we designed a receptor-based DNA logic device that allows Boolean logic analysis of multiple cells. For ease of expression, the molecules on the cell surface that can bind to the aptamer are referred to as "receptors". This DNA logic device sends signals based on cell surface sgc8c and sgc4f receptor expression by performing NOT, NOR, AND and OR logic operations, and amplifies and evaluates the signals using HCR. Meanwhile, the release of ICG from the endopore of HMSNs is controlled by affecting structural changes in the DNA logic device. This approach can accurately identify and treat multiple cells on demand based on the presence or absence of cell-specific receptors, facilitating the development of personalized medicine.
Collapse
Affiliation(s)
- Yajing Wang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China; (Y.W.); (D.W.); (X.C.)
| | - Di Wu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China; (Y.W.); (D.W.); (X.C.)
| | - Xiuping Cao
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China; (Y.W.); (D.W.); (X.C.)
| | - Yingshu Guo
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| |
Collapse
|
9
|
Duan Y, Szlam F, Hu Y, Chen W, Li R, Ke Y, Sniecinski R, Salaita K. Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand. Nat Biomed Eng 2023; 7:1404-1418. [PMID: 37957275 DOI: 10.1038/s41551-023-01114-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Molecular forces generated by cell receptors are infrequent and transient, and hence difficult to detect. Here we report an assay that leverages the CRISPR-associated protein 12a (Cas12a) to amplify the detection of cellular traction forces generated by as few as 50 adherent cells. The assay involves the immobilization of a DNA duplex modified with a ligand specific for a cell receptor. Traction forces of tens of piconewtons trigger the dehybridization of the duplex, exposing a cryptic Cas12-activating strand that sets off the indiscriminate Cas12-mediated cleavage of a fluorogenic reporter strand. We used the assay to perform hundreds of force measurements using human platelets from a single blood draw to extract individualized dose-response curves and half-maximal inhibitory concentrations for a panel of antiplatelet drugs. For seven patients who had undergone cardiopulmonary bypass, platelet dysfunction strongly correlated with the need for platelet transfusion to limit bleeding. The Cas12a-mediated detection of cellular traction forces may be used to assess cell state, and to screen for genes, cell-adhesion ligands, drugs or metabolites that modulate cell mechanics.
Collapse
Affiliation(s)
- Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Fania Szlam
- Department of Anesthesiology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Wenchun Chen
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Departments of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Departments of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Roman Sniecinski
- Department of Anesthesiology, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
| |
Collapse
|
10
|
Ma R, Rashid SA, Velusamy A, Deal BR, Chen W, Petrich B, Li R, Salaita K. Molecular mechanocytometry using tension-activated cell tagging. Nat Methods 2023; 20:1666-1671. [PMID: 37798479 DOI: 10.1038/s41592-023-02030-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/22/2023] [Indexed: 10/07/2023]
Abstract
Flow cytometry is used routinely to measure single-cell gene expression by staining cells with fluorescent antibodies and nucleic acids. Here, we present tension-activated cell tagging (TaCT) to label cells fluorescently based on the magnitude of molecular force transmitted through cell adhesion receptors. As a proof-of-concept, we analyzed fibroblasts and mouse platelets after TaCT using conventional flow cytometry.
Collapse
Affiliation(s)
- Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | | | - Brendan R Deal
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Wenchun Chen
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Brian Petrich
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Renhao Li
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
11
|
Yu W, Mo F, Guo J, Yang Y, Jin Y, Fu Y. Ultrasensitive MicroRNA Photoelectric Assay Based on a Mimosa-like CdS-NiS/Au Schottky Junction. Anal Chem 2023; 95:12097-12103. [PMID: 37531089 DOI: 10.1021/acs.analchem.3c02153] [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: 08/03/2023]
Abstract
Seeking and constructing superior photoactive materials have the potential to improve the performance of photoelectrochemical (PEC) biosensors. In this work, we proposed a novel mimosa-like ternary inorganic composite with a significantly enhanced light-harvesting ability and photogenerated carrier separation rate. This ternary photoactive material was obtained via electrodeposition of gold nanoparticles (Au) on the surface of transition metal sulfide composite of CdS and NiS (CdS-NiS/Au). The experimental results showed that the high initial photocurrent was acquired on CdS-NiS/Au (68-fold higher than that of individual CdS) with the synergistic effect of p-n heterojunction, Schottky junction, and the eminent optical properties of gold nanoparticles. Meanwhile, using silver nanoclusters prepared by link DNA protection as an effective quencher, integrating the duplex-specific nuclease-assisted rolling circle amplification strategy, a "Signal ON" PEC biosensor was fabricated for the detection of microRNA 21 (miRNA 21). With the release of the quencher, the recovered photocurrent is able to achieve determination of miRNA 21 within the range from 10 aM to 1 pM with a detection limit down to 4.6 aM (3σ). Importantly, this work not only provides a superb idea for designing ternary inorganic heteromaterials with exceptional photoactive ability but also allows the detection of other biomarkers by selecting appropriate recognition units.
Collapse
Affiliation(s)
- Wanqing Yu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Fangjing Mo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Jiang Guo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yuqin Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yushuang Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yingzi Fu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| |
Collapse
|
12
|
Li S, Xiang J, Yang F, Yuan R, Xiang Y. Aptamer/proximity hybridization-based label-free and highly sensitive colorimetric detection of methotrexate via polymerization/nicking recycling amplifications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 295:122633. [PMID: 36965245 DOI: 10.1016/j.saa.2023.122633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/22/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Methotrexate (MTX) is one of the commonly used therapeutic drugs for treating various tumors and autoimmune diseases. However, high dose usage of MTX may cause severe side effects and the monitoring of MTX is therefore critical. By coupling a new MTX aptamer-based proximity hybridization with polymerization/nicking reaction (PNR) recycling amplifications, we develop here a sensitive and label-free colorimetric approach for MTX detection in diluted human serums. The MTX molecules can bind and switch the conformation of aptamers in the DNA duplex probes to initiate subsequent proximity hybridization-induced PNR recycling processes for the yield of a great deal of G-quadruplexes with the assistance of two single-stranded assistant DNA sequences. Hemin subsequently combines with these G-quadruplexes to produce lots of G-quadruplex/hemin horseradish peroxidase (HRP) mimicking DNAzymes, which then catalyze intensified color transition of the substrate solution to exhibit highly magnified UV-Vis absorption for label-free and ultrasensitive detection of MTX at concentration as low as 5.66 nM in the range of 10 nM to 1 μM. High selectivity of the developed method also enables it to monitor low levels of MTX in diluted serum samples, which offers such a method enormous potentials for convenient and highly sensitive detection of other small molecule drugs for various clinical applications.
Collapse
Affiliation(s)
- Shunmei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jie Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Fang Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| |
Collapse
|
13
|
Chai Q, Chen J, Zeng S, Zhu T, Chen J, Qi C, Mao G, Liu Y. Closed Cyclic DNA Machine for Sensitive Logic Operation and APE1 Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207736. [PMID: 36916696 DOI: 10.1002/smll.202207736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/16/2023] [Indexed: 06/08/2023]
Abstract
DNA self-assembly has been developed as a kind of robust signal amplification strategy, but most of reported assembly pathways are programmed to amplify signal in one direction. Herein, based on mutual-activated cascade cycle of hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA), a closed cycle circuit (CCC) based DNA machine is developed for sensitive logic operation and molecular recognition. Benefiting from the synergistically accelerated signal amplification, the closed cyclic DNA machine enabled the logic computing with strong and significant output signals even at weak input signals. The typical logic operations such as OR, YES, AND, INHIBIT, NOR, and NAND gate, are conveniently and clearly executed with this DNA machine through rational design of the input and computing elements. Moreover, by integrating the target recognition module with the CCC module, the proposed DNA machine is further employed in the homogeneous detection of apurinic/apyrimidinic endonuclease 1 (APE1). The precise recognition and exponential signal amplification facilitated the highly selective and sensitive detection of APE1 with limit of detection (LOD) of 7.8 × 10-5 U mL-1 . Besides, the normal cells and tumor cells are distinguished unambiguously by this method according to the detected concentration difference of cellular APE1, which indicates the robustness and practicability of this method.
Collapse
Affiliation(s)
- Qingli Chai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jinyang Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Shasha Zeng
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Ting Zhu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jintao Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Chunjiao Qi
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Guobin Mao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Yucheng Liu
- Core Facility of Wuhan University, Wuhan, Hubei, 430072, China
| |
Collapse
|
14
|
Pawlak MR, Smiley AT, Ramirez MP, Kelly MD, Shamsan GA, Anderson SM, Smeester BA, Largaespada DA, Odde DJ, Gordon WR. RAD-TGTs: high-throughput measurement of cellular mechanotype via rupture and delivery of DNA tension probes. Nat Commun 2023; 14:2468. [PMID: 37117218 PMCID: PMC10147940 DOI: 10.1038/s41467-023-38157-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
Mechanical forces drive critical cellular processes that are reflected in mechanical phenotypes, or mechanotypes, of cells and their microenvironment. We present here "Rupture And Deliver" Tension Gauge Tethers (RAD-TGTs) in which flow cytometry is used to record the mechanical history of thousands of cells exerting forces on their surroundings via their propensity to rupture immobilized DNA duplex tension probes. We demonstrate that RAD-TGTs recapitulate prior DNA tension probe studies while also yielding a gain of fluorescence in the force-generating cell that is detectable by flow cytometry. Furthermore, the rupture propensity is altered following disruption of the cytoskeleton using drugs or CRISPR-knockout of mechanosensing proteins. Importantly, RAD-TGTs can differentiate distinct mechanotypes among mixed populations of cells. We also establish oligo rupture and delivery can be measured via DNA sequencing. RAD-TGTs provide a facile and powerful assay to enable high-throughput mechanotype profiling, which could find various applications, for example, in combination with CRISPR screens and -omics analysis.
Collapse
Affiliation(s)
- Matthew R Pawlak
- Departments of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adam T Smiley
- Departments of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Maria Paz Ramirez
- Departments of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Marcus D Kelly
- Departments of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ghaidan A Shamsan
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Sarah M Anderson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | | | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Wendy R Gordon
- Departments of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
15
|
Peng X, Mei X, Yang J, Liu J, Li Y. Ultrasensitive Hybridization Chain Reaction-Assisted Multisite Exonuclease III Amplification Strategy Combined with a Direct Quantitative Fluorescence Lateral Flow Technique for Multiple Bacterial 16S rRNA Detection. Anal Chem 2023; 95:5807-5814. [PMID: 36946074 DOI: 10.1021/acs.analchem.3c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Accurate and in-time detection of bacteria conduces to preventing their rapid spread around the environment, while a nucleic acid test (NAT) is a powerful tool for early diagnosis of pathogens. Herein, we propose a hybridization chain reaction (HCR)-mediated multisite exonuclease III (Exo-III) amplification strategy (HCR/Exo-III amplifier) to achieve the one-pot and ultrasensitive isothermal amplification of bacterial 16S rRNA and a portable fluorescence detection device (PFD) to directly read signals in a lateral flow assay (LFA). In detail, the target-initiated HCR products present multiple binding sites for triggering the Exo-III amplifier that produces numerous target amplicons. Following that, the target amplicons travel up on the strip and bridge between the DNA-CdTe/CdS probes and the capture DNA to form a positive fluorescence line. After that, the strip is inserted into the PFD to accomplish the fluorescence signal reading. The constructed HCR/Exo-III amplifier-based PFD-LFA implemented the simultaneous and specific detection of three bacteria with a detection limit of a few tenths of fM for synthetic 16S rRNA fragments and dozens of CFU/mL for Staphylococcus aureus, Listeria monocytogenes, and Salmonella typhimurium in pure cultures. The sensing platform features isothermal amplification, convenient operation, and good economy, displaying great potential for on-site testing toward multiple nucleic acid analytes.
Collapse
Affiliation(s)
- Xin Peng
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Xuecui Mei
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiao Yang
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiang Liu
- School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yingchun Li
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| |
Collapse
|
16
|
Sun Z, Wu Y, Gao F, Li H, Wang C, Du L, Dong L, Jiang Y. In situ detection of exosomal RNAs for cancer diagnosis. Acta Biomater 2023; 155:80-98. [PMID: 36343908 DOI: 10.1016/j.actbio.2022.10.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Exosomes are considered as biomarkers reflecting the physiological state of the human body. Studies have revealed that the expression levels of specific exosomal RNAs are closely associated with certain cancers. Thus, detection of exosomal RNA offers a new avenue for liquid biopsy of cancers. Many exosomal RNA detection methods based on various principles have been developed, and most of the methods detect the extracted RNAs after lysing exosomes. Besides complex and time-consuming extraction steps, a major drawback of this approach is the degradation of the extracted RNAs in the absence of plasma membrane and cytosol. In addition, there is considerable loss of RNAs during their extraction. In situ detection of exosomal RNAs can avoid these drawbacks, thus allowing higher diagnostic reliability. In this paper, in situ detection of exosomal RNAs was systematically reviewed from the perspectives of detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, and involved functional materials. Furthermore, the limitations and possible improvements of the current in situ detection methods for exosomal RNAs towards the clinical diagnostic application are discussed. This review aims to provide a valuable reference for the development of in situ exosomal RNA detection strategies for non-invasive diagnosis of cancers. STATEMENT OF SIGNIFICANCE: Certain RNAs have been identified as valuable biomarkers for some cancers, and sensitive detection of cancer-related RNAs is expected to achieve better diagnostic efficacy. Currently, the detection of exosomal RNAs is receiving increasing attention due to their high stability and significant concentration differences between patients and healthy individuals. In situ detection of exosomal RNAs has greater diagnostic reliability due to the avoidance of RNA degradation and loss. However, this mode is still limited by some factors such as detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, etc. This review focuses on the progress of in situ detection of exosomal RNAs and aims to promote the development of this field.
Collapse
Affiliation(s)
- Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Yanqiu Wu
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Fucheng Gao
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Hui Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China.
| | - Lun Dong
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan 250012, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China.
| |
Collapse
|
17
|
Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
18
|
Dutta D, Baishya T, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Bhattacharyya MK. Supramolecular Assemblies involving Energetically Significant Unconventional π(CN)-π and Anion-π(nitrile) Contacts in Zn(II) Coordination Compounds: Antiproliferative Evaluation and Theoretical Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
19
|
Zhang J, Huang Y, Sun M, Song T, Wan S, Yang C, Song Y. Mechanosensing view of SARS-CoV-2 infection by a DNA nano-assembly. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101048. [PMID: 36157982 PMCID: PMC9490855 DOI: 10.1016/j.xcrp.2022.101048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/18/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
The mechanical force between a virus and its host cell plays a critical role in viral infection. However, characterization of the virus-cell mechanical force at the whole-virus level remains a challenge. Herein, we develop a platform in which the virus is anchored with multivalence-controlled aptamers to achieve transfer of the virus-cell mechanical force to a DNA tension gauge tether (Virus-TGT). When the TGT is ruptured, the complex of binding module-virus-cell is detached from the substrate, accompanied by decreased host cell-substrate adhesion, thus revealing the mechanical force between whole-virus and cell. Using Virus-TGT, direct evidence about the biomechanical force between SARS-CoV-2 and the host cell is obtained. The relative mechanical force gap (<10 pN) at the cellular level between the wild-type virus to cell and a variant virus to cell is measured, suggesting a possible positive correlation between virus-cell mechanical force and infectivity. Overall, this strategy provides a new perspective to probe the SARS-CoV-2 mechanical force.
Collapse
Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Miao Sun
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Ting Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuang Wan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| |
Collapse
|
20
|
Maroju PA, Ganesan R, Ray Dutta J. Boronic acid chemistry for fluorescence-based quantitative DNA sensing. Chem Commun (Camb) 2022; 58:7936-7939. [PMID: 35748662 DOI: 10.1039/d2cc02584a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Contrary to the long-standing opinion of boronic acids being typically reactive with 1,2- and 1,3-diols and hence not suitable for quantitative sensing of DNA containing only a mono-ol unit, this proof-of-concept study has successfully shown the feasibility to quantitatively detect DNA in the concentration range of 5 to 50 nM plausibly through boronic acid-mediated bridging of two DNA double helices via the 3' hydroxy groups, which opens up new avenues in the realm of oligonucleotide biochemistry.
Collapse
Affiliation(s)
- Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
| | - Ramakrishnan Ganesan
- Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
| | - Jayati Ray Dutta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
| |
Collapse
|
21
|
Li S, Cheng Y, Qin M, Zhou G, Li P, Yang L. Intelligent and robust DNA robots capable of swarming into leakless nonlinear amplification in response to a trigger. NANOSCALE HORIZONS 2022; 7:634-643. [PMID: 35527720 DOI: 10.1039/d2nh00018k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nonlinear DNA signal amplification with an enzyme-free isothermal self-assembly process is uniquely useful in nanotechnology and nanomedicine. However, progress in this direction is hampered by the lack of effective design models of leak-resistant DNA building blocks. Here, we propose two conceptual models of intelligent and robust DNA robots to perform a leakless nonlinear signal amplification in response to a trigger. Two conceptual models are based on super-hairpin nanostructures, which are designed by innovating novel principles in methodology and codifying them into embedded programs. The dynamical and thermodynamical analyses reveal the critical elements and leak-resistant mechanisms of the designed models, and the leak-resistant behaviors of the intelligent DNA robots and morphologies of swarming into nonlinear amplification are separately verified. The applications of the designed models are also illustrated in specific signal amplification and targeted payload enrichment via integration with an aptamer, a fluorescent molecule and surface-enhanced Raman spectroscopy. This work has the potential to serve as design guidelines of intelligent and robust DNA robots and leakless nonlinear DNA amplification, and also as the design blueprint of cargo delivery robots with the performance of swarming into nonlinear amplification in response to a target automatically, facilitating their future applications in biosensing, bioimaging and biomedicine.
Collapse
Affiliation(s)
- Shaofei Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- School of Life Science, Anhui University, Hefei 230601, Anhui, China
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Yizhuang Cheng
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Miao Qin
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Guoliang Zhou
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Pan Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
| | - Liangbao Yang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| |
Collapse
|
22
|
Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202115489. [PMID: 35076991 DOI: 10.1002/anie.202115489] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 12/15/2022]
Abstract
Lowly expressed analyte in complex cytoplasmic milieu necessitates the development of non-enzymatic autocatalytic DNA circuits with high amplification and anti-interference performance. Herein, we engineered a versatile and robust stimuli-responsive autocatalytic hybridization assembly (AHA) circuit for high-performance in vivo bioanalysis. Under a moderately confined condition, the initiator motivated the autonomous and cooperative cross-activation of cascade hybridization reaction and catalytic DNA assembly for generating an exponentially amplified readout without the parasite steric hindrance and random diffusion side effects. The AHA circuit was systematically investigated by a series of experimental studies and theoretical simulations. The successively guaranteed target recognition and synergistically accelerated signal-amplification enabled the sensitive and selective detection of analyte, and realized the robust miRNA imaging in living cells and mice. This autocatalytic DNA circuit could substantially expand the toolbox for accurate diagnosis and programmable therapeutics.
Collapse
Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China.,College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| |
Collapse
|
23
|
Abstract
Cellular processes and functions can be regulated by mechanical forces. Nanodevices that can measure and manipulate these forces are critical tools in chemical and cellular biology. Synthetic DNA oligonucleotides have been used to develop a wide range of powerful nanodevices due to their programmable nature and precise and predictable self-assembly. In recent years, various types of DNA-based mechanical nanodevices have been engineered for studying molecular-level forces. With the help of these nanodevices, our understanding of cellular responses to physical forces has been significantly advanced. In this article, we have reviewed some recent developments in DNA-based mechanical sensors and regulators for application in the characterization of cellular biomechanics and the manipulation of cellular morphology, motion and other functions. The design principles discussed in this article can be further used to inspire other types of powerful DNA-based mechanical nanodevices.
Collapse
Affiliation(s)
- Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| |
Collapse
|
24
|
Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified
In Vivo
MicroRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- College of Biological and Pharmaceutical Sciences China Three Gorges University 443002 Yichang P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| |
Collapse
|