1
|
Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
Collapse
Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| |
Collapse
|
2
|
Liang H, Jiang L, Li H, Zhang J, Zhuo Y, Yuan R, Yang X. DNA-Guided One-Dimensional Plasmonic Nanostructures for the SERS Bioassay. ACS Sens 2023; 8:1192-1199. [PMID: 36915228 DOI: 10.1021/acssensors.2c02574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Plasmonic nanostructures have a desirable surface-enhanced Raman scattering (SERS) response related to particle spacing. However, precisely controlling the distance of plasmonic nanostructures is still a challenge. DNA has the merit of specific recognition, and flexible modification of functional groups, which can be used to flexibly adjust the gaps between plasmonic nanostructures for improving the stability of SERS. In this paper, DNA-guided gold nanoparticles formed one-dimensional ordered structures and they were self-assembled at the water-oil interface by a bottom-up approach. Notably, an output switching strategy successfully transfers a small amount of target into a large amount of reporter DNA; thereby, Raman probes are captured on the sensing interface and achieve the SERS assay of microRNA 155 (miRNA-155). This study is an exciting strategy for obtaining ordered plasmonic structures and providing surveillance, which is important for the clinical diagnosis of early-stage cancer.
Collapse
Affiliation(s)
- Huan Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Lingling Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hongying Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiale Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xia Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education; College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
3
|
Büchl A, Kopperger E, Vogt M, Langecker M, Simmel FC, List J. Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking. Biophys J 2022; 121:4849-4859. [PMID: 36071662 PMCID: PMC9808541 DOI: 10.1016/j.bpj.2022.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature's enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.
Collapse
Affiliation(s)
- Adrian Büchl
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Enzo Kopperger
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Matthias Vogt
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Martin Langecker
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University of Munich, Garching, Germany.
| | - Jonathan List
- Physics Department E14, Technical University of Munich, Garching, Germany.
| |
Collapse
|
4
|
Hübner K, Raab M, Bohlen J, Bauer J, Tinnefeld P. Salt-induced conformational switching of a flat rectangular DNA origami structure. NANOSCALE 2022; 14:7898-7905. [PMID: 35587049 DOI: 10.1039/d1nr07793g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A rectangular DNA origami structure is one of the most studied and often used motif for applications in DNA nanotechnology. Here, we present two assays to study structural changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA origami structure induced by bivalent cations such as magnesium or calcium. First, we applied one-color and two-color superresolution DNA-PAINT with protruding strands along the long edges of the DNA origami rectangle. At increasing salt concentration, a single line instead of two lines is observed as a first indicator of rolling-up. Two-color measurements also revealed different conformations with parallel and angled edges. Second, we placed a gold nanoparticle and a dye molecule at different positions on the DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle reports on dynamic transitions as well as it provides evidence that the rolling-up occurs preferentially along the diagonal of the DNA origami rectangle. The results will be helpful to test DNA structural models and the assays presented will be useful to study further structural transitions in DNA nanotechnology.
Collapse
Affiliation(s)
- Kristina Hübner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Mario Raab
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| |
Collapse
|
5
|
Pal N. Single-Molecule FRET: A Tool to Characterize DNA Nanostructures. Front Mol Biosci 2022; 9:835617. [PMID: 35330798 PMCID: PMC8940195 DOI: 10.3389/fmolb.2022.835617] [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: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
DNA nanostructures often involve temporally evolving spatial features. Tracking these temporal behaviors in real time requires sophisticated experimental methods with sufficiently high spatial and temporal resolution. Among the several strategies developed for this purpose, single-molecule FRET (smFRET) offers avenues to observe the structural rearrangement or locomotion of DNA nanostructures in real time and quantitatively measure the kinetics as well at the single nanostructure level. In this mini review, we discuss a few applications of smFRET-based techniques to study DNA nanostructures. These examples exemplify how smFRET signals not only have played an important role in the characterization of the nanostructures but also often have helped to improve the design and overall performance of the nanostructures and the devices designed from those structures. Overall, this review consolidates the potential of smFRET in providing crucial quantitative information on structure–function relations in DNA nanostructures.
Collapse
|
6
|
Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [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: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
Collapse
Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
7
|
Liu F, Liu X, Shi Q, Maffeo C, Kojima M, Dong L, Aksimentiev A, Huang Q, Fukuda T, Arai T. A tetrahedral DNA nanorobot with conformational change in response to molecular trigger. NANOSCALE 2021; 13:15552-15559. [PMID: 34596187 DOI: 10.1039/d1nr02757c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dynamic DNA origami nanostructures that respond to external stimuli are promising platforms for cargo delivery and nanoscale sensing. However, the low stability of such nanostructures under physiological conditions presents a major obstacle for their use in biomedical applications. This article describes a stable tetrahedral DNA nanorobot (TDN) programmed to undergo a controlled conformational change in response to epithelial cell adhesion molecule (EpCAM), a molecular biomarker specifically expressed on the circulating tumor cells. Multiresolution molecular dynamics simulations verified the overall stability of the folded TDN design and characterized local distortions in the folded structure. Atomic force microscopy and gel electrophoresis results showed that tetragonal structures are more stable than unfolded DNA origami sheets. Live cell experiments demonstrated the low cytotoxicity and target specificity of TDN. In summary, the proposed TDN can not only effectively resist nuclease catalysis but also has the potential to monitor EpCAM-positive cells precisely.
Collapse
Affiliation(s)
- Fengyu Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Xiaoming Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Qing Shi
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana Champaign, Urbana IL 61802, USA
| | - Masaru Kojima
- Department of Materials Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Lixin Dong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana Champaign, Urbana IL 61802, USA
| | - Qiang Huang
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Toshio Fukuda
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Tatsuo Arai
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China.
| |
Collapse
|
8
|
Mollarasouli F, Badilli U, Bakirhan NK, Ozkan SA, Ozkan Y. Advanced DNA nanomachines: Strategies and bioapplications. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|