1
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Namani S, Kavetsky K, Lin CY, Maharjan S, Gamper HB, Li NS, Piccirilli JA, Hou YM, Drndic M. Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores. ACS NANO 2024. [PMID: 38906834 DOI: 10.1021/acsnano.4c04625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
This study investigates transfer ribonucleic acid (tRNA) conformational dynamics in the context of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) using solid-state silicon nitride (SiN) nanopore technology. SiN nanopores in thin membranes with specific dimensions exhibit high signal resolution, enabling real-time and single-molecule electronic detection of tRNA conformational changes. We focus on human mitochondrial tRNALeu(UAA) (mt-Leu(UAA)) that decodes Leu codons UUA/UUG (UUR) during protein synthesis on the mt-ribosome. The single A14G substitution in mt-Leu(UAA) is the major cause of MELAS disease. Measurements of current blockades and dwell times reveal distinct conformational dynamics of the wild-type (WT) and the A14G variant of mt-Leu(UAA) in response to the conserved post-transcriptional m1G9 methylation. While the m1G9-modified WT transcript adopts a more stable structure relative to the unmodified transcript, the m1G9-modified MELAS transcript adopts a less stable structure relative to the unmodified transcript. Notably, these differential features were observed at 0.4 M KCl, but not at 3 M KCl, highlighting the importance of experimental settings that are closer to physiological conditions. This work demonstrates the feasibility of the nanopore platform to discern tRNA molecules that differ by a single-nucleotide substitution or by a single methylation event, providing an important step forward to explore changes in the conformational dynamics of other RNA molecules in human diseases.
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Affiliation(s)
- Srilahari Namani
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyril Kavetsky
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Marija Drndic
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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2
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Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix. ACS NANO 2024; 18:15013-15024. [PMID: 38822455 PMCID: PMC11171748 DOI: 10.1021/acsnano.4c01466] [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: 01/30/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
Electrophoretic transport plays a pivotal role in advancing sensing technologies. So far, systematic studies have focused on the translocation of canonical B-form or A-form nucleic acids, while direct RNA analysis is emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of noncanonical RNA:DNA hybrids in electrophoretic transport to the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that RD duplexes present a noncanonical helix, with distinct transport properties from B-form DD molecules. We find that RD and DD molecules, with the same contour length, move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, atomistic molecular dynamics simulations, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and molecular dynamics simulations, we find the effective force per unit length applied by the electric field to a fragment of RD or DD duplex in nanopores with various geometries or shapes to be approximately the same. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and the molecular understanding of electrophoretic transport.
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Affiliation(s)
- Filip Bošković
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Christopher Maffeo
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
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3
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Tian R, Ma W, Wang L, Xie W, Wang Y, Yin Y, Weng T, He S, Fang S, Liang L, Wang L, Wang D, Bai J. The combination of DNA nanostructures and materials for highly sensitive electrochemical detection. Bioelectrochemistry 2024; 157:108651. [PMID: 38281367 DOI: 10.1016/j.bioelechem.2024.108651] [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: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.
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Affiliation(s)
- Rong Tian
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Wenhao Ma
- Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Lue Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Wanyi Xie
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yunjiao Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yajie Yin
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Ting Weng
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shixuan He
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shaoxi Fang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liyuan Liang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Deqiang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
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4
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Ahmed SA, Liu Y, Xiong T, Zhao Y, Xie B, Pan C, Ma W, Yu P. Iontronic Sensing Based on Confined Ion Transport. Anal Chem 2024; 96:8056-8077. [PMID: 38663001 DOI: 10.1021/acs.analchem.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Saud Asif Ahmed
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yueru Zhao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Boyang Xie
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Cong Pan
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
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5
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Platnich CM, Earle MK, Keyser UF. Chemical Annealing Restructures RNA for Nanopore Detection. J Am Chem Soc 2024; 146:12919-12924. [PMID: 38691627 PMCID: PMC11099964 DOI: 10.1021/jacs.4c03753] [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: 03/18/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/03/2024]
Abstract
RNA is a key biochemical marker, yet its chemical instability and complex secondary structure hamper its integration into DNA nanotechnology-based sensing platforms. Relying on the denaturation of the native RNA structure using urea, we show that restructured DNA/RNA hybrids can readily be prepared at room temperature. Using solid-state nanopore sensing, we demonstrate that the structures of our DNA/RNA hybrids conform to the design at the single-molecule level. Employing this chemical annealing procedure, we mitigate RNA self-cleavage, enabling the direct detection of restructured RNA molecules for biosensing applications.
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Affiliation(s)
- Casey M. Platnich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Max K. Earle
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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6
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Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.12.557357. [PMID: 37745457 PMCID: PMC10515835 DOI: 10.1101/2023.09.12.557357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Electrophoretic transport plays a pivotal role in advancing sensing technologies. So far, systematic studies have focused on translocation of canonical B-form or A-form nucleic acids, while direct RNA analysis is emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of non-canonical RNA:DNA hybrids in electrophoretic transport with the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that RD duplexes present a non-canonical helix with distinct transport properties from B-form DD molecules. We find RD and DD molecules with the same contour length move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, atomistic molecular dynamics simulations, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and molecular dynamics simulations, we find the effective force per unit length applied by the electric field to a fragment of RD or DD duplex in nanopores with various geometries or shapes to be approximately the same within experimental errors. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and molecular understanding of electrophoretic transport.
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7
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Chen S, He W, Li J, Xu D, Zhao R, Zhu L, Wu H, Xu F. Pulley Effect in the Capture of DNA Translocation through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5799-5808. [PMID: 38501264 DOI: 10.1021/acs.langmuir.3c03596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Nanopores are powerful single-molecule sensors for analyzing biomolecules such as DNA and proteins. Understanding the dynamics of DNA capture and translocation through nanopores is essential for optimizing their performance. In this study, we examine the effects of applied voltage and pore diameter on current blockage, translocation time, collision, and capture location by translocating λ-DNA through 5.7 and 16 nm solid-state nanopores. Ionic current changes are used to infer DNA conformations during translocation. We find that translocation time increases with pore diameter, which can be attributed to the decrease of the stall force. Linear and exponential decreases of collision frequency with voltage are observed in the 16 and 5.7 nm pores, respectively, indicating a free energy barrier in the small pore. Moreover, the results reveal a voltage-dependent bias in the capture location toward the DNA ends, which is explained by a "pulley effect" deforming the DNA as it approaches the pore. This study provides insights into the physics governing DNA capture and translocation, which can be useful for promoting single-file translocation to enhance nanopore sensing.
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Affiliation(s)
- Shulan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, China
| | - Wen He
- Analysis and Testing Center, Nanchang Hangkong University, Nanchang 330063, China
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Derong Xu
- Jiangxi Institute of Translational Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Rui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Libo Zhu
- School of Medical Imageology, Wannan Medical College, Wuhu 241002, China
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Fei Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- National Regional Center for Respiratory Medicine, China-Japan Friendship Jiangxi Hospital, Nanchang 330006, China
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8
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [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: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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9
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Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. Nat Commun 2024; 15:1699. [PMID: 38402271 PMCID: PMC10894232 DOI: 10.1038/s41467-024-45968-8] [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: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
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Affiliation(s)
| | - Jovan Pešović
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Marko Panić
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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10
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Acharjee MC, Ledden B, Thomas B, He X, Messina T, Giurleo J, Talaga D, Li J. Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor. SENSORS (BASEL, SWITZERLAND) 2023; 24:81. [PMID: 38202943 PMCID: PMC10781269 DOI: 10.3390/s24010081] [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: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study estimates the amyloid fibrils' length and diameter, the quantity of the βLGa aggregates, and their distribution. The nanopore results align with the DLS and AFM data and offer additional insight at the level of individual protein molecular assemblies. As a further demonstration of the nanopore technique, βLGa self-association and aggregation at pH 4.6 as a function of temperature were measured at high (2 M KCl) and low (0.1 M KCl) ionic strength. This research highlights the advantages and limitations of using solid-state nanopore methods for analyzing protein aggregation.
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Affiliation(s)
- Mitu C. Acharjee
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brad Ledden
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brian Thomas
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Xianglan He
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
| | - Troy Messina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Physics, Berea College, Berea, KY 40404, USA
| | - Jason Giurleo
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Talaga
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Chemistry, Sokol Institute, Montclair State University, Montclair, NJ 07043, USA
| | - Jiali Li
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
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11
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Zheng F, Alawami M, Zhu J, Platnich CM, Sha J, Keyser UF, Chen K. DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore. NANO LETTERS 2023; 23:11145-11151. [PMID: 38033205 PMCID: PMC10722531 DOI: 10.1021/acs.nanolett.3c03605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.
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Affiliation(s)
- Fei Zheng
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Mohammed Alawami
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian 116024, China
| | - Casey M Platnich
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Nanoscience and Nanotechnology, University of Chinese Academy of Sciences, Beijing 101408, China
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12
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [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: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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13
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Li Y, Sandler SE, Keyser UF, Zhu J. DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals. NANO LETTERS 2023; 23:7054-7061. [PMID: 37487050 PMCID: PMC10416563 DOI: 10.1021/acs.nanolett.3c01823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Nanopores have developed into powerful single-molecule sensors capable of identifying and characterizing small polymers, such as DNA, by electrophoretically driving them through a nanoscale pore and monitoring temporary blockades in the ionic pore current. However, the relationship between nanopore signals and the physical properties of DNA remains only partly understood. Herein, we introduce a programmable DNA carrier platform to capture carefully designed DNA nanostructures. Controlled translocation experiments through our glass nanopores allowed us to disentangle this relationship. We vary DNA topology by changing the length, strand duplications, sequence, unpaired nucleotides, and rigidity of the analyte DNA and find that the ionic current drop is mainly determined by the volume and flexibility of the DNA nanostructure in the nanopore. Finally, we use our understanding of the role of DNA topology to discriminate circular single-stranded DNA molecules from linear ones with the same number of nucleotides using the nanopore signal.
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Affiliation(s)
- Yunxuan Li
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Sarah E. Sandler
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
- School
of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
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14
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Zhu J, Tivony R, Bošković F, Pereira-Dias J, Sandler SE, Baker S, Keyser UF. Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches. J Am Chem Soc 2023. [PMID: 37220424 DOI: 10.1021/jacs.3c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
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15
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Chau C, Marcuccio F, Soulias D, Edwards MA, Tuplin A, Radford SE, Hewitt E, Actis P. Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore. ACS NANO 2022; 16:20075-20085. [PMID: 36279181 PMCID: PMC9798860 DOI: 10.1021/acsnano.2c08312] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.
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Affiliation(s)
- Chalmers Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry & Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Andrew Tuplin
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
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16
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Doricchi A, Platnich CM, Gimpel A, Horn F, Earle M, Lanzavecchia G, Cortajarena AL, Liz-Marzán LM, Liu N, Heckel R, Grass RN, Krahne R, Keyser UF, Garoli D. Emerging Approaches to DNA Data Storage: Challenges and Prospects. ACS NANO 2022; 16:17552-17571. [PMID: 36256971 PMCID: PMC9706676 DOI: 10.1021/acsnano.2c06748] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103 GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.
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Affiliation(s)
- Andrea Doricchi
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
di Genova, via Dodecaneso
31, 16146 Genova, Italy
| | - Casey M. Platnich
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Andreas Gimpel
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Friederikee Horn
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Max Earle
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - German Lanzavecchia
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Aitziber L. Cortajarena
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11.
Planta 0, 28029 Madrid, Spain
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, 70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, 70569 Stuttgart, Germany
| | - Reinhard Heckel
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Robert N. Grass
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
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