1
|
Liu W, Liao N, Lei Y, Liang W, Yang X, Yuan R, Yang C, Zhuo Y. Detachable DNA Assembly Module to Dissect Tumor Cells Heterogeneity via RNA Pinpoint Screening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401253. [PMID: 39422178 DOI: 10.1002/advs.202401253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 09/21/2024] [Indexed: 10/19/2024]
Abstract
Differential RNA expression is becoming increasingly valuable in evaluating tumor heterogeneity for a better understanding of malignant tumors and guiding personalized therapy. However, traditional techniques for analyzing cellular RNA are mainly focused on determining the absolute level of RNA, which may lead to inaccuracies in understanding tumor heterogeneity, primarily due to i) the subtle differences in certain RNA types that have similar total concentrations and ii) the existence of variations in RNA expression across different samples. Herein, a detachable DNA assembly module is proposed that is capable not only of quantifying the expression level of target RNA but also of innovatively evaluating its proportion within its RNA family population through a sequential assembly and disassembly route. Using the let-7 family as an experimental model, a significant difference is discovered in let-7a proportion between normal mammary epithelial cells and breast cancer cells, a characteristic that is often missed in bulk analysis of traditional techniques. By combining concentration and proportion information, the detachable DNA assembly module demonstrates markedly higher efficiency in discerning among various types of cells compared to traditional techniques. This innovative assembly module is expected to offer a new perspective to highlight tumor heterogeneity and guide personalized therapy.
Collapse
Affiliation(s)
- Wei Liu
- Key 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
| | - Ni Liao
- College of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, P. R. China
| | - Yanmei Lei
- Key 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
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. 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, P. R. China
| | - Xia Yang
- Key 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
| | - 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, P. R. China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. 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, P. R. China
| |
Collapse
|
2
|
Li X, Ge W, Guo S, Bai J, Hong W. Characterization and Application of Supramolecular Junctions. Angew Chem Int Ed Engl 2023; 62:e202216819. [PMID: 36585932 DOI: 10.1002/anie.202216819] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
The convergence of supramolecular chemistry and single-molecule electronics offers a new perspective on supramolecular electronics, and provides a new avenue toward understanding and application of intermolecular charge transport at the molecular level. In this review, we will provide an overview of the advances in the characterization technique for the investigation of intermolecular charge transport, and summarize the experimental investigation of several non-covalent interactions, including π-π stacking interactions, hydrogen bonding, host-guest interactions and σ-σ interactions at the single-molecule level. We will also provide a perspective on supramolecular electronics and discuss the potential applications and future challenges.
Collapse
Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenhui Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Shuhan Guo
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| |
Collapse
|
3
|
Li P, Jia C, Guo X. Molecule-Based Transistors: From Macroscale to Single Molecule. CHEM REC 2020; 21:1284-1299. [PMID: 33140918 DOI: 10.1002/tcr.202000114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022]
Abstract
Molecule-based field-effect transistors (FETs) are of great significance as they have a wide range of application prospects, such as logic operations, information storage and sensor monitoring. This account mainly introduces and reviews our recent work in molecular FETs. Specifically, through molecular and device design, we have systematically investigated the construction and performance of FETs from macroscale to nanoscale and even single molecule. In particular, we have proposed the broad concept of molecular FETs, whose functions can be achieved through various external controls, such as light stimulation, and other physical, chemical or biological interactions. In the end, we tend to focus the discussion on the development challenges of single-molecule FETs, and propose prospects for further breakthroughs in this field.
Collapse
Affiliation(s)
- Peihui Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
| |
Collapse
|
4
|
Li Y, Yang C, Guo X. Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science. Acc Chem Res 2020; 53:159-169. [PMID: 31545589 DOI: 10.1021/acs.accounts.9b00347] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ultimate limit of analytical chemistry is single-molecule detection, which allows one to visualize the dynamic processes of chemical/biological interactions with single-molecule or single-event sensitivity and hence enables the study of stochastic fluctuations under equilibrium conditions and the observation of time trajectories and reaction pathways of individual species in nonequilibrated systems. In addition, such studies may also allow the direct observation of novel microscopic quantum effects and fundamental discoveries of underlying molecular mechanisms in organic reactions and biological processes that are not accessible in ensemble experiments, thus providing unique opportunities to solve the key problems of physical, chemical, and life sciences. Consequently, the field of single-molecule detection has received considerable attention and has witnessed tremendous advances in different directions in combination with other disciplines. This Account describes our ongoing work on the development of groundbreaking methods (termed "single-molecule electrical approaches") of translating the detailed processes of chemical reactions or biological functions into detectable electrical signals at the single-event level on the platform of single-molecule electronic devices, with a particular focus on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) and silicon-nanowire-based single-molecule electrical nanocircuits. These nanocircuit-based architectures are complementary to conventional optical or mechanical techniques but exhibit obvious advantages such as the absence of problems associated with bleaching and fluorescent labeling. Dash-line lithography (DLL) is an efficient lithographic method of cutting graphene and forming carboxylic-acid-functionalized nanogapped graphene point contact arrays developed to address the formidable challenges of molecular device fabrication difficulty and poor stability. Molecules of interest terminated by amines on both ends can be covalently sandwiched between graphene point contacts to create high-throughput robust GMG-SMJs containing only one molecule as the conductive element. In conjunction with the ease of device fabrication and device stability, this feature distinguishes GMG-SMJs as a new testbed platform for single-molecule analysis characterized by high temporal resolution and superior signal-to-noise ratios. By exploiting the DLL method, we have fabricated molecular devices that are sensitive to external stimuli and are capable of transducing chemical/biochemical events into electrical signals at the single-molecule level, with notable examples including host-guest interaction, hydrogen bond dynamics, DNA intercalation, photoinduced conformational transition, carbocation formation, nucleophilic addition, and stereoelectronic effect. In addition to GMG-SMJs and considering compatibility with the silicon-based industry, we have also developed a reliable method of point-functionalizing silicon-nanowire-based nanotransistors to afford single-molecule electrical nanocircuits. This approach proved to be a robust platform for single-molecule electrical analysis capable of probing fast dynamic processes such as single-protein detection, DNA hybridization/polymorphism, and motor rotation dynamics. The above systematic investigations emphasize the importance and unique advantages of universal single-molecule electrical approaches for realizing direct, label-free, real-time electrical measurements of reaction dynamics with single-event sensitivity. These approaches promise a fascinating mainstream platform to explore the dynamics of stochastic processes in chemical/biological systems as well as gain information in fields ranging from reaction chemistry for elucidating the intrinsic mechanisms to genomics or proteomics for accurate molecular and even point-of-care clinical diagnoses.
Collapse
Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chen Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| |
Collapse
|
5
|
Li Y, Zhao L, Yao Y, Guo X. Single-Molecule Nanotechnologies: An Evolution in Biological Dynamics Detection. ACS APPLIED BIO MATERIALS 2019; 3:68-85. [DOI: 10.1021/acsabm.9b00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Lihua Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yuan Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| |
Collapse
|
6
|
Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| |
Collapse
|
7
|
Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017; 56:5045-5049. [DOI: 10.1002/anie.201701420] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| |
Collapse
|