1
|
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.
Collapse
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
| |
Collapse
|
2
|
Wang H, Tang H, Qiu X, Li Y. Solid-State Glass Nanopipettes: Functionalization and Applications. Chemistry 2024; 30:e202400281. [PMID: 38507278 DOI: 10.1002/chem.202400281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.
Collapse
Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| |
Collapse
|
3
|
Wang X, Guo Q, Guo J, Wang C. Magnetic composite microspheres with a controlled mesoporous shell for highly efficient DNA extraction and fragment screening. J Mater Chem B 2024; 12:4899-4908. [PMID: 38682549 DOI: 10.1039/d4tb00104d] [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: 05/01/2024]
Abstract
Rapid extraction and screening of high-purity DNA fragments is an indispensable technology in advanced molecular biology. In this article, mesoporous magnetic composite microspheres (MSP@mTiO2) with tunable pore sizes were successfully fabricated for high-purity DNA extraction and fragment screening. Owing to the strong complexation ability of Ti ions with DNA phosphate groups and the high specific surface area of mesoporous microspheres, the MSP@mTiO2 microspheres possess excellent adsorption performance, where the saturated loading capacity of MSP@mTiO2 with a specific surface area of 122 m2 g-1 is as high as 575 μg mg-1 for a salmon sperm specimen. ITC experiments demonstrated that DNA adsorption on MSP@mTiO2 microspheres is mainly driven by entropy, which gives us more potential ways to regulate the balance of adsorption and desorption. Meanwhile, the mesoporous MSP@mTiO2 microspheres exhibit a much higher extraction efficiency compared with non-porous MSP@TiO2 for whole genome DNA from Arabidopsis thaliana plants. Interestingly, DNA fragments with different lengths could be screened by simply regulating the pore size of MSP@mTiO2 or the concentration of Na3PO4 in the eluent. A small pore size and low phosphate concentration are advantageous for the extraction of short-stranded DNA fragments, and DNA fragments (≤1000 bp) can be efficiently extracted when the mesopore size of MSP@mTiO2 is lower than 7.6 nm. The extraction results from the mesoporous composite microspheres provide new promising insights into the purification and screening of DNA from complex biological samples.
Collapse
Affiliation(s)
- Xiuli Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Qilin Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
| |
Collapse
|
4
|
Ge Y, Li W, Tian J, Yu H, Wang Z, Wang M, Dong Z. Single-Stranded Nucleic Acid Transmembrane Molecular Carriers Based on Positively Charged Helical Foldamers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400678. [PMID: 38757406 DOI: 10.1002/advs.202400678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Transmembrane delivery of biologically active nucleic acids is an important process in cells and has inspired one to develop advanced drug delivery techniques. In this contribution, molecular-level single-stranded nucleic acid transmembrane carriers are reported based on 3.2 nm long Huc's foldamers (AOrnQ3Q3)8 and (mQ3Q2)8 with linearly and helically aligned positive charges, respectively. These two foldamers not only show very strong DNA affinity via electrostatic interactions but also discriminatively bind single-stranded DNA (ss-DNA) and double-stranded DNA (ds-DNA), corroborating the importance of precise charge arrangement in the electrostatic interactions. More importantly, these two foldamers are capable of efficiently transporting ss-DNA across the lipid membranes, and the ss-DNA transport activity of (AOrnQ3Q3)8 with linearly aligned charges is higher than that of (mQ3Q2)8 with helically aligned charges. Thus a type of novel single-stranded nucleic acid transmembrane molecular carriers based on positively charged helical foldamers are introduced. Further, effective and enhanced expression in EGFP-mRNA transfection experiments strongly demonstrates the potential of positively charged foldamers for RNA transmembrane transport and therapy.
Collapse
Affiliation(s)
- Yunpeng Ge
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- Center for Supramolecular Chemical Biology, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Wencan Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- Center for Supramolecular Chemical Biology, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Jun Tian
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- Center for Supramolecular Chemical Biology, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Hao Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Zhenzhu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- Center for Supramolecular Chemical Biology, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Zeyuan Dong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- Center for Supramolecular Chemical Biology, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| |
Collapse
|
5
|
Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos LE, Mariappan M, Lusk CP, Xiong Y, Lim RYH, Lin C. Channel width modulates the permeability of DNA origami based nuclear pore mimics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593438. [PMID: 38766144 PMCID: PMC11100828 DOI: 10.1101/2024.05.09.593438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importing substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.
Collapse
Affiliation(s)
- Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Chunxiang Wu
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Eason Cao
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | - Wei Zheng
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Amy Zhang
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Xia Li
- Department of Cell Biology, Yale School of Medicine, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biophysics and Biochemistry, Yale University, USA
| | | | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Yong Xiong
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biomedical Engineering, Yale University, USA
| |
Collapse
|
6
|
Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
Collapse
Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
| |
Collapse
|
7
|
Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
Collapse
Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| |
Collapse
|
8
|
Zhang X, Malle MG, Thomsen RP, Sørensen RS, Sørensen EW, Hatzakis NS, Kjems J. Deconvoluting the Effect of Cell-Penetrating Peptides for Enhanced and Controlled Insertion of Large-Scale DNA Nanopores. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18422-18433. [PMID: 38573069 DOI: 10.1021/acsami.3c18636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA nanopores have emerged as powerful tools for molecular sensing, but the efficient insertion of large DNA nanopores into lipid membranes remains challenging. In this study, we investigate the potential of cell-penetrating peptides (CPPs), specifically SynB1 and GALA, to enhance the insertion efficiency of large DNA nanopores. We constructed SynB1- or GALA-functionalized DNA nanopores with an 11 nm inner diameter and visualized and quantified their membrane insertion using a TIRF microscopy-based single-liposome assay. The results demonstrated that incorporating an increasing number of SynB1 or GALA peptides into the DNA nanopore significantly enhanced the membrane perforation. Kinetic analysis revealed that the DNA nanopore scaffold played a role in prearranging the CPPs, which facilitated membrane interaction and pore formation. Notably, the use of pH-responsive GALA peptides allowed highly efficient and pH-controlled insertion of large DNA pores. Furthermore, single-channel recording elucidated that the insertion process of single GALA-modified nanopores into planar lipid bilayers was dynamic, likely forming transient large toroidal pores. Overall, our study highlights the potential of CPPs as insertion enhancers for DNA nanopores, which opens avenues for improved molecule sensing and the controlled release of cargo molecules.
Collapse
Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
- Novonordisk Center for Protein Research, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
Collapse
Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| |
Collapse
|
11
|
Chamorro A, Rossetti M, Bagheri N, Porchetta A. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:71-106. [PMID: 38273204 DOI: 10.1007/10_2023_235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.
Collapse
Affiliation(s)
| | - Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | | |
Collapse
|
12
|
Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
Collapse
Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
13
|
Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
Collapse
Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [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: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
Collapse
Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| |
Collapse
|
16
|
Cervantes-Salguero K, Gutiérrez Fosado YA, Megone W, Gautrot JE, Palma M. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization. Molecules 2023; 28:molecules28093686. [PMID: 37175096 PMCID: PMC10180480 DOI: 10.3390/molecules28093686] [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: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembles a Feynman diagram. F-units were designed to self-assemble in two dimensions and to display a high DNA density of hydrophobic moieties. oxDNA simulations confirmed the planarity of the F-unit. DNA nanosheets with a thickness of a single DNA duplex layer and with large coverage (at least 30 μm × 30 μm) were assembled from the liquid phase at the solid/liquid interface, as unambiguously evidenced by atomic force microscopy imaging. Interestingly, single-layer nanodiscs formed in solution at low DNA concentrations. DNA nanosheet superstructures were further assembled at liquid/liquid interfaces, as demonstrated by the fluorescence of a double-stranded DNA intercalator. Moreover, the interfacial mechanical properties of the nanosheet superstructures were measured as a response to temperature changes, demonstrating the control of interfacial shear mechanics based on DNA nanostructure engineering. The rational design of the F-unit, along with the presented results, provide an avenue toward the controlled assembly of reconfigurable/responsive nanosheets and membranes at liquid/liquid interfaces, to be potentially used in the characterization of biomechanical processes and materials transport.
Collapse
Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - William Megone
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Julien E Gautrot
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| |
Collapse
|
17
|
Kodr D, Kužmová E, Pohl R, Kraus T, Hocek M. Lipid-linked nucleoside triphosphates for enzymatic synthesis of hydrophobic oligonucleotides with enhanced membrane anchoring efficiency. Chem Sci 2023; 14:4059-4069. [PMID: 37063801 PMCID: PMC10094435 DOI: 10.1039/d2sc06718h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/19/2023] [Indexed: 03/22/2023] Open
Abstract
We designed and synthesized a series of 2'-deoxyribonucleoside triphosphates (dNTPs) bearing various lipid moieties. Fatty acid- and cholesterol-modified dNTPs proved to be substrates for KOD XL DNA polymerase in primer extension reactions. They were also mutually compatible for simultaneous multiple incorporations into the DNA strand. The methodology of enzymatic synthesis opened a pathway to diverse structurally unique lipid-ON probes containing one or more lipid units. We studied interactions of such probes with the plasma membranes of live cells. Employing a rational design, we found a series of lipid-ONs with enhanced membrane anchoring efficiency. The in-membrane stability of multiply modified ONs was superior to that of commonly studied ON analogues, in which a single cholesterol molecule is typically tethered to the thread end. Notably, some of the probes were detected at the cell surface even after 24 h upon removal of the probe solution. Such an effect was general to several studied cell lines.
Collapse
Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague Hlavova 8 Prague-2 12843 Czech Republic
| |
Collapse
|
18
|
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
Collapse
Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| |
Collapse
|
19
|
Yu W, Wei C, Zhang K, Zhang J, Ge Z, Liang X, Guiver MD, Ge X, Wu L, Xu T. Host-Guest Recognition Boosts Biomimetic Mono/Multivalent Cation Separation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5861-5871. [PMID: 36988386 DOI: 10.1021/acs.est.2c09733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Biomimetic ion permselective membranes with ultrahigh ion permeability and selectivity represent a research frontier in ion separation, yet the successful fabrication of such membranes remains a formidable challenge. Here, we demonstrate a 4-sulfocalix[4]arene (4-SCA)-modified graphene oxide (GO) membrane that shows extraordinary performance in separating mono-from multivalent cations, as well as having reversible pH-responsiveness. The resulting 4-SCA-modified GO (SCA-GO) membrane preferentially transports potassium ions (K+) over radionuclide cations (Co2+, UO22+, La3+, Eu3+, and Th4+). The ion selectivities are an order of magnitude higher than that of the unmodified GO membrane. Theoretical calculations and experimental investigations demonstrate that the much-improved ion selectivity arises from the specific recognition between 4-SCA and radionuclide cations. The transport of multivalent radionuclides is impeded by a binding-obstructing mechanism from the host-guest interactions. Interestingly, the host-guest interactions are responsive to the protonation/deprotonation transformation of the 4-SCA. Therefore, the SCA-GO membrane mimics pH-regulated ion selective behavior found in biological ion channels. Our strategy of designing a biomimetic permselective GO membrane may allow efficient nuclear wastewater treatment and, more importantly, deepen our understanding of biomimetic ion transport mechanisms.
Collapse
Affiliation(s)
- Weisheng Yu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Chengpeng Wei
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Kaiyu Zhang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Jianjun Zhang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Zijuan Ge
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Xian Liang
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Michael D Guiver
- State Key Laboratory of Engines, School of Mechanical Engineering, Tianjin University, Tianjin 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xiaolin Ge
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Liang Wu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| | - Tongwen Xu
- Anhui Engineering Laboratory of Functional Membrane Materials and Technology, Collaborative Innovation Centre of Chemistry for Energy Materials, School of Chemistry and Material Science, University of Science and Technology of China, Hefei 230026, China
| |
Collapse
|
20
|
Xing Y, Dorey A, Howorka S. Multi-Stimuli-Responsive and Mechano-Actuated Biomimetic Membrane Nanopores Self-Assembled from DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300589. [PMID: 37029712 DOI: 10.1002/adma.202300589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Indexed: 06/04/2023]
Abstract
In bioinspired design, biological templates are mimicked in structure and function by highly controllable synthetic means. Of interest are static barrel-like nanopores that enable molecular transport across membranes for use in biosensing, sequencing, and biotechnology. However, biological ion channels offer additional functions such as dynamic changes of the entire pore shape between open and closed states, and triggering of dynamic processes with biochemical and physical stimuli. To better capture this complexity, this report presents multi-stimuli and mechano-responsive biomimetic nanopores which are created with DNA nanotechnology. The nanopores switch between open and closed states, whereby specific binding of DNA and protein molecules as stimuli locks the pores in the open state. Furthermore, the physical stimulus of high transmembrane voltage switches the pores into a closed state. In addition, the pore diameters are larger and more tunable than those of natural templates. These multi-stimuli-responsive and mechanically actuated nanopores mimic several aspects of complex biological channels yet offer easier control over pore size, shape and stimulus response. The designer pores are expected to be applied in biosensing and synthetic biology.
Collapse
Affiliation(s)
- Yongzheng Xing
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| |
Collapse
|
21
|
Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
Collapse
Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Lauren A Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Kelsey J Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA.
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA.
- The BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
| |
Collapse
|
22
|
Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
Collapse
Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| |
Collapse
|
23
|
Iwabuchi S, Nomura SIM, Sato Y. Surfactant-Assisted Purification of Hydrophobic DNA Nanostructures. Chembiochem 2023; 24:e202200568. [PMID: 36470849 DOI: 10.1002/cbic.202200568] [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: 09/28/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Purification of functional DNA nanostructures is an essential step in achieving intended functions because misfolded structures and the remaining free DNA strands in a solution can interact and affect their behavior. However, due to hydrophobicity-mediated aggregation, it is difficult to purify DNA nanostructures modified with hydrophobic molecules by conventional methods. Herein, we report the purification of cholesterol-modified DNA nanostructures by using a novel surfactant-assisted gel extraction. The addition of sodium cholate (SC) to the sample solution before structure folding prevented aggregation; this was confirmed by gel electrophoresis. We also found that adding sodium dodecyl sulfate (SDS) to the sample inhibited structural folding. The cholesterol-modified DNA nanostructures prepared with SC were successfully purified by gel extraction, and their ability to bind to the lipid membrane surfaces was maintained. This method will facilitate the purification of DNA nanostructures modified with hydrophobic molecules and expand their applicability in the construction of artificial cell-like systems.
Collapse
Affiliation(s)
- Shoji Iwabuchi
- Department of Robotics, Tohoku University, 6-6-01 Aramaki Aoba-ku, Sendai, 980-0845, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics, Tohoku University, 6-6-01 Aramaki Aoba-ku, Sendai, 980-0845, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 kawazu, lizuka, 820-8502, Japan
| |
Collapse
|
24
|
Shen Q, Xiong Q, Zhou K, Feng Q, Liu L, Tian T, Wu C, Xiong Y, Melia TJ, Lusk CP, Lin C. Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity. J Am Chem Soc 2023; 145:1292-1300. [PMID: 36577119 PMCID: PMC9852090 DOI: 10.1021/jacs.2c11226] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DNA-origami technique has enabled the engineering of transmembrane nanopores with programmable size and functionality, showing promise in building biosensors and synthetic cells. However, it remains challenging to build large (>10 nm), functionalizable nanopores that spontaneously perforate lipid membranes. Here, we take advantage of pneumolysin (PLY), a bacterial toxin that potently forms wide ring-like channels on cell membranes, to construct hybrid DNA-protein nanopores. This PLY-DNA-origami complex, in which a DNA-origami ring corrals up to 48 copies of PLY, targets the cholesterol-rich membranes of liposomes and red blood cells, readily forming uniformly sized pores with an average inner diameter of ∼22 nm. Such hybrid nanopores facilitate the exchange of macromolecules between perforated liposomes and their environment, with the exchange rate negatively correlating with the macromolecule size (diameters of gyration: 8-22 nm). Additionally, the DNA ring can be decorated with intrinsically disordered nucleoporins to further restrict the diffusion of traversing molecules, highlighting the programmability of the hybrid nanopores. PLY-DNA pores provide an enabling biophysical tool for studying the cross-membrane translocation of ultralarge molecules and open new opportunities for analytical chemistry, synthetic biology, and nanomedicine.
Collapse
Affiliation(s)
- Qi Shen
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Kaifeng Zhou
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Longfei Liu
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Taoran Tian
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department of Biomedical Engineering, Yale University, 17 Hillhouse Ave, New Haven, Connecticut 06511, United States
| |
Collapse
|
25
|
Offenbartl‐Stiegert D, Rottensteiner A, Dorey A, Howorka S. A Light-Triggered Synthetic Nanopore for Controlling Molecular Transport Across Biological Membranes. Angew Chem Int Ed Engl 2022; 61:e202210886. [PMID: 36318092 PMCID: PMC10098474 DOI: 10.1002/anie.202210886] [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: 07/25/2022] [Indexed: 11/06/2022]
Abstract
Controlling biological molecular processes with light is of interest in biological research and biomedicine, as light allows precise and selective activation in a non-invasive and non-toxic manner. A molecular process benefitting from light control is the transport of cargo across biological membranes, which is conventionally achieved by membrane-puncturing barrel-shaped nanopores. Yet, there is also considerable gain in constructing more complex gated pores. Here, we pioneer a synthetic light-gated nanostructure which regulates transport across membranes via a controllable lid. The light-triggered nanopore is self-assembled from six pore-forming DNA strands and a lid strand carrying light-switchable azobenzene molecules. Exposure to light opens the pore to allow small-molecule transport across membranes. Our light-triggered pore advances biomimetic chemistry and DNA nanotechnology and may be used in biotechnology, biosensing, targeted drug release, or synthetic cells.
Collapse
Affiliation(s)
- Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Alexia Rottensteiner
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Adam Dorey
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| |
Collapse
|
26
|
Bogawat Y, Krishnan S, Simmel FC, Santiago I. Tunable 2D diffusion of DNA nanostructures on lipid membranes. Biophys J 2022; 121:4810-4818. [PMID: 36243925 PMCID: PMC9811667 DOI: 10.1016/j.bpj.2022.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology facilitates the synthesis of biomimetic models for studying biological systems. This work uses lipid bilayers as platforms for two-dimensional single-particle tracking of the dynamics of DNA nanostructures. Three different DNA origami structures adhere to the membrane through hybridization with cholesterol-modified strands. Their two-dimensional diffusion coefficient is modulated by changing the concentration of monovalent and divalent salts and the number of anchors. In addition, the diffusion coefficient is tuned by targeting cholesterol-modified anchor strands with strand-displacement reactions. We demonstrate a responsive system with changing diffusivity by selectively displacing membrane-bound anchor strands. We also show the programmed release of origami structures from the lipid membranes.
Collapse
Affiliation(s)
- Yash Bogawat
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Swati Krishnan
- Physics Department E14, Technical University of Munich, Garching, Germany; Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University of Munich, Garching, Germany.
| | - Ibon Santiago
- Physics Department E14, Technical University of Munich, Garching, Germany; CIC nanoGUNE BRTA, Donostia-San Sebastián, Spain.
| |
Collapse
|
27
|
Adamczyk AK, Huijben TAPM, Sison M, Di Luca A, Chiarelli G, Vanni S, Brasselet S, Mortensen KI, Stefani FD, Pilo-Pais M, Acuna GP. DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation. ACS NANO 2022; 16:16924-16931. [PMID: 36065997 DOI: 10.1021/acsnano.2c06936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.
Collapse
Affiliation(s)
- Aleksandra K Adamczyk
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Teun A P M Huijben
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Miguel Sison
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Germán Chiarelli
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Kim I Mortensen
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQDCiudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHACiudad Autónoma de Buenos Aires, Argentina
| | - Mauricio Pilo-Pais
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| |
Collapse
|
28
|
Qiao D, Chen Y, Tan H, Zhou R, Feng J. De novo design of transmembrane nanopores. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Ren Q, Hu Y. DNA membrane nanopores with highly tunable shapes and sizes. Chem 2022. [DOI: 10.1016/j.chempr.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|