1
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Banik M, Ledray AP, Wu Y, Lu Y. Delivering DNA Aptamers Across the Blood-Brain Barrier Reveals Heterogeneous Decreased ATP in Different Brain Regions of Alzheimer's Disease Mouse Models. ACS CENTRAL SCIENCE 2024; 10:1585-1593. [PMID: 39220690 PMCID: PMC11363336 DOI: 10.1021/acscentsci.4c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 09/04/2024]
Abstract
DNA aptamers have been developed as sensors to detect metabolites with high sensitivity, selectivity, and biocompatibility. While they are effective in sensing important targets in the brain, the lack of methods for their efficient delivery across the blood-brain barrier (BBB) has significantly hindered their applications in brain research. To address this issue, we herein report the development of brain cell-derived exosomes as endogenous BBB delivery vehicles to deliver an ATP-responsive aptamer across the BBB of live mice for noninvasive live brain imaging. We found that the system uses endosome recycling to transfer the sensors between the delivered exosomes and native recycling endosomes, resulting in high delivery efficiencies. Using this system, we observed unique signal distributions for ATP across different brain regions, with significant accumulation in the subiculum and cortex in healthy mice. In an Alzheimer's disease transgenic mouse model, ATP levels decreased in the subiculum and cortex, demonstrating this method's capability to determine metabolite location and relative abundance with high spatial resolution in vivo. Since DNA aptamers have been obtained for many other targets, the method developed in this work can be applied to deliver sensors across the BBB to image a wide range of other brain-related metabolites.
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Affiliation(s)
- Mandira Banik
- University
of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
| | - Aaron P. Ledray
- University
of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
| | - Yuting Wu
- University
of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
| | - Yi Lu
- University
of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
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2
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Li Z, Duan S, Liu B. Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization. Chembiochem 2024:e202400416. [PMID: 38979890 DOI: 10.1002/cbic.202400416] [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: 05/07/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/10/2024]
Abstract
Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.
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Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Siyi Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
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3
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Martins ASG, Reis SD, Benson E, Domingues MM, Cortinhas J, Vidal Silva JA, Santos SD, Santos NC, Pêgo AP, Moreno PMD. Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309140. [PMID: 38342712 DOI: 10.1002/smll.202309140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/22/2023] [Indexed: 02/13/2024]
Abstract
The successful translation of therapeutic nucleic acids (NAs) for the treatment of neurological disorders depends on their safe and efficient delivery to neural cells, in particular neurons. DNA nanostructures can be a promising NAs delivery vehicle. Nonetheless, the potential of DNA nanostructures for neuronal cell delivery of therapeutic NAs is unexplored. Here, tetrahedral DNA nanostructures (TDN) as siRNA delivery scaffolds to neuronal cells, exploring the influence of functionalization with two different reported neuronal targeting ligands: C4-3 RNA aptamer and Tet1 peptide are investigated. Nanostructures are characterized in vitro, as well as in silico using molecular dynamic simulations to better understand the overall TDN structural stability. Enhancement of neuronal cell uptake of TDN functionalized with the C4-3 Aptamer (TDN-Apt), not only in neuronal cell lines but also in primary neuronal cell cultures is demonstrated. Additionally, TDN and TDN-Apt nanostructures carrying siRNA are shown to promote silencing in a process aided by chloroquine-induced endosomal disruption. This work presents a thorough workflow for the structural and functional characterization of the proposed TDN as a nano-scaffold for neuronal delivery of therapeutic NAs and for targeting ligands evaluation, contributing to the future development of new neuronal drug delivery systems based on DNA nanostructures.
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Affiliation(s)
- Ana S G Martins
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, s/n, Porto, 4200-465, Portugal
| | - Sara D Reis
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Erik Benson
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Tomtebodavägen 23, Solna, 171 65, Sweden
| | - Marco M Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - João Cortinhas
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Joana A Vidal Silva
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Sofia D Santos
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - Ana P Pêgo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto, 4050-313, Portugal
| | - Pedro M D Moreno
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
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4
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Chau C, Mohanan G, Macaulay I, Actis P, Wälti C. Automated Purification of DNA Origami with SPRI Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308776. [PMID: 38054620 DOI: 10.1002/smll.202308776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Indexed: 12/07/2023]
Abstract
DNA origami synthesis is a well-established technique with wide-ranging applications. In most cases, the synthesized origami must be purified to remove excess materials such as DNA oligos and other functional molecules. While several purification techniques are routinely used, all have limitations, and cannot be integrated with robotic systems. Here the use of solid-phase reversible immobilization (SPRI) beads as a scalable, high-throughput, and automatable method to purify DNA origami is demonstrated. Not only can this method remove unreacted oligos and biomolecules with yields comparable to existing methods while maintaining the high structural integrity of the origami, but it can also be integrated into an automated workflow to purify simultaneously large numbers and quantities of samples. It is envisioned that the SPRI beads purification method will improve the scalability of DNA nanostructures synthesis both for research and commercial applications.
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Affiliation(s)
- Chalmers Chau
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Paolo Actis
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Christoph Wälti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
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5
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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.
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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
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6
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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7
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Yu M, Lim D, Kim J, Song Y. Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303197. [PMID: 37755129 PMCID: PMC10646262 DOI: 10.1002/advs.202303197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/11/2023] [Indexed: 09/28/2023]
Abstract
DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF) system. DNA fragments of discrete sizes (100-500 bps) are synthesized for droplet assembly, and programmed sequence information exchange occurred. The encoded DNA sequences are processed in series and parallel to synthesize the determined DNA pools, enabling random access using polymerase chain reaction amplification. The sequencing results of the assembled DNA data pools can be orderly aligned for decoding and have high fidelity through address primer scanning. Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27-0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.
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Affiliation(s)
- Minsang Yu
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
| | - Doyeon Lim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Jungwoo Kim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Youngjun Song
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
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8
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Hanke M, Dornbusch D, Tomm E, Grundmeier G, Fahmy K, Keller A. Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants. NANOSCALE 2023; 15:16590-16600. [PMID: 37747200 DOI: 10.1039/d3nr02045b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Daniel Dornbusch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Emilia Tomm
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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9
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Baptist AV, Heuer-Jungemann A. Lyophilization Reduces Aggregation of Three-Dimensional DNA Origami at High Concentrations. ACS OMEGA 2023; 8:18225-18233. [PMID: 37251192 PMCID: PMC10210204 DOI: 10.1021/acsomega.3c01680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Although for many purposes, low concentrations of DNA origami are sufficient, certain applications such as cryo electron microscopy, measurements involving small-angle X-ray scattering, or in vivo applications require high DNA origami concentrations of >200 nM. This is achievable by ultrafiltration or polyethylene glycol precipitation but often at the expense of increasing structural aggregation due to prolonged centrifugation and final redispersion in low buffer volumes. Here, we show that lyophilization and subsequent redispersion in low buffer volumes can achieve high concentrations of DNA origami while drastically reducing aggregation due to initially very low DNA origami concentrations in low salt buffers. We demonstrate this for four structurally different types of three-dimensional DNA origami. All of these structures exhibit different aggregation behaviors at high concentrations (tip-to-tip stacking, side-to-side binding, or structural interlocking), which can be drastically reduced by dispersion in larger volumes of a low salt buffer and subsequent lyophilization. Finally, we show that this procedure can also be applied to silicified DNA origami to achieve high concentrations with low aggregation. We thus find that lyophilization is not only a tool for long-term storage of biomolecules but also an excellent way for up-concentrating while maintaining well-dispersed solutions of DNA origami.
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Affiliation(s)
- Anna V. Baptist
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Bavaria, Germany
- Center
for NanoScience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Bavaria, Germany
- Center
for NanoScience, Ludwig-Maximilians University, 80539 Munich, Germany
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10
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Sun N, Zhang C, Wang J, Yue X, Kim HY, Zhang RY, Liu H, Widjaja J, Tang H, Zhang TX, Ye J, Qian A, Liu C, Wu A, Wang K, Johanis M, Yang P, Liu H, Meng M, Liang L, Pei R, Chai-Ho W, Zhu Y, Tseng HR. Hierarchical integration of DNA nanostructures and NanoGold onto a microchip facilitates covalent chemistry-mediated purification of circulating tumor cells in head and neck squamous cell carcinoma. NANO TODAY 2023; 49:101786. [PMID: 38037608 PMCID: PMC10688595 DOI: 10.1016/j.nantod.2023.101786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
It is well-established that the combined use of nanostructured substrates and immunoaffinity agents can enhance the cell-capture performance of the substrates, thus offering a practical solution to effectively capture circulating tumor cells (CTCs) in peripheral blood. Developing along this strategy, this study first demonstrated a top-down approach for the fabrication of tetrahedral DNA nanostructure (TDN)-NanoGold substrates through the hierarchical integration of three functional constituents at various length-scales: a macroscale glass slide, sub-microscale self-organized NanoGold, and nanoscale self-assembled TDN. The TDN-NanoGold substrates were then assembled with microfluidic chaotic mixers to give TDN-NanoGold Click Chips. In conjunction with the use of copper (Cu)-catalyzed azide-alkyne cycloaddition (CuAAC)-mediated CTC capture and restriction enzyme-triggered CTC release, TDN-NanoGold Click Chips allow for effective enumeration and purification of CTCs with intact cell morphologies and preserved molecular integrity. To evaluate the clinical utility of TDN-NanoGold Click Chips, we used these devices to isolate and purify CTCs from patients with human papillomavirus (HPV)-positive (+) head and neck squamous cell carcinoma (HNSCC). The purified HPV(+) HNSCC CTCs were then subjected to RT-ddPCR testing, allowing for detection of E6/E7 oncogenes, the characteristic molecular signatures of HPV(+) HNSCC. We found that the resulting HPV(+) HNSCC CTC counts and E6/E7 transcript copy numbers are correlated with the treatment responses in the patients, suggesting the potential clinical utility of TDN-NanoGold Click Chips for non-invasive diagnostic applications of HPV(+) HNSCC.
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Affiliation(s)
- Na Sun
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ceng Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Xinmin Yue
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Hyo Yong Kim
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan Y. Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hongtao Liu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong 250014, China
| | - Josephine Widjaja
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hubert Tang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tiffany X. Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jinglei Ye
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Audrey Qian
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chensong Liu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alex Wu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Katharina Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Johanis
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peng Yang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Honggang Liu
- Department of Pathology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Meng Meng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Li Liang
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou 510515, Guangdong Province, China
| | - Renjun Pei
- Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Suzhou 215123, China
| | - Wanxing Chai-Ho
- Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
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11
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Mao C, Wang S, Li J, Feng Z, Zhang T, Wang R, Fan C, Jiang X. Metal-Organic Frameworks in Microfluidics Enable Fast Encapsulation/Extraction of DNA for Automated and Integrated Data Storage. ACS NANO 2023; 17:2840-2850. [PMID: 36728704 DOI: 10.1021/acsnano.2c11241] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
DNA as an exceptional data storage medium offers high information density. However, DNA storage requires specialized equipment and tightly controlled environments for storage. Fast encapsulation within minutes for enhanced DNA stability to do away with specialized equipment and fast DNA extraction remain a challenge. Here, we report a DNA microlibrary that can be encapsulated by metal-organic frameworks (MOFs) within 10 min and extracted (5 min) in a single microfluidic chip for automated and integrated DNA-based data storage. The DNA microlibrary@MOFs enhances the stability of data-encoded DNA against harsh environments. The encoded information can be read out perfectly after accelerated aging, equivalent to being readable after 10 years of storage at 25 °C, 50% relative humidity, and 10 000 lx sunlight radiation. Moreover, the library enables fast retrieval of target data via flow cytometry and can be reproduced after each access.
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Affiliation(s)
- Cuiping Mao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Shuchen Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Jiankai Li
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Zhuowei Feng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Tong Zhang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, No 800, DongChuan Road, Minhang District, Shanghai 200240, People's Republic of China
| | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
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12
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Mathur D, Galvan AR, Green CM, Liu K, Medintz IL. Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art. NANOSCALE 2023; 15:2516-2528. [PMID: 36722508 PMCID: PMC10407680 DOI: 10.1039/d2nr05868e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Angelica Rose Galvan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Kevin Liu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
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13
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Freeze-drying: A Flourishing Strategy to Fabricate Stable Pharmaceutical and Biological Products. Int J Pharm 2022; 628:122233. [DOI: 10.1016/j.ijpharm.2022.122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022]
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14
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Hanke M, Hansen N, Tomm E, Grundmeier G, Keller A. Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate. Int J Mol Sci 2022; 23:ijms23158547. [PMID: 35955680 PMCID: PMC9368935 DOI: 10.3390/ijms23158547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.
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15
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Hanke M, Dornbusch D, Hadlich C, Rossberg A, Hansen N, Grundmeier G, Tsushima S, Keller A, Fahmy K. Anion-specific structure and stability of guanidinium-bound DNA origami. Comput Struct Biotechnol J 2022; 20:2611-2623. [PMID: 35685373 PMCID: PMC9163702 DOI: 10.1016/j.csbj.2022.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
While the folding of DNA into rationally designed DNA origami nanostructures has been studied extensively with the aim of increasing structural diversity and introducing functionality, the fundamental physical and chemical properties of these nanostructures remain largely elusive. Here, we investigate the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. Using guanidinium (Gdm) as a DNA-stabilizing but potentially also denaturing cation, we explore the dependence of DNA origami stability on the identity of the accompanying anions. The statistical analyses of atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveals that sulfate and chloride exert stabilizing and destabilizing effects, respectively, already below the global melting temperature of the DNA origami triangles. We identify structural transitions during thermal denaturation and show that heat capacity changes ΔCp determine the temperature sensitivity of structural damage. The different hydration shells of the anions and their potential to form Gdm+ ion pairs in concentrated salt solutions modulate ΔCp by altered wetting properties of hydrophobic DNA surface regions as shown by molecular dynamics simulations. The underlying structural changes on the molecular scale become amplified by the large number of structurally coupled DNA segments and thereby find nanoscopic correlations in AFM images.
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16
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Langlois NI, Clark HA. Characterization of DNA nanostructure stability by size exclusion chromatography. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1006-1014. [PMID: 35171148 PMCID: PMC9491180 DOI: 10.1039/d1ay02146j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA-based nanostructures (DNs) are advantageous for the design of functional materials for biology and medicine due to the nanoscale control provided by their predictable self-assembly. However, the use of DNs in vivo has been limited due to structural instability in biofluids. As the stability of a particular DN sets the scope of its potential biological applications, efficient methods to characterize stability are required. Here, we apply size exclusion chromatography (SEC) to study the stability of a tetrahedron DNA nanostructure (TDN) and demonstrate the analytical capabilities of our method in characterizing degradation by enzymes and a diluted human serum matrix. We show that SEC analysis can reliably assay TDN degradation by a nuclease through direct injection and peak integration. Furthermore, data analysis using a ratio chromatogram technique enables TDN peak deconvolution from the matrix of serum proteins. Using our method, we found that TDNs exhibit half-lives of 23.9 hours and 10.1 hours in 20% and 50% diluted human serum, respectively, which is consistent with reported stability studies in 10% fetal bovine serum. We anticipate that this method can be broadly applicable to characterize a variety of DNs and serve as an efficient technique toward analysis of the stability of new DN designs in complex biological matrixes.
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Affiliation(s)
- Nicole I Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
| | - Heather A Clark
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
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17
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Fan Q, He Z, Xiong J, Chao J. Smart Drug Delivery Systems Based on DNA Nanotechnology. Chempluschem 2022; 87:e202100548. [PMID: 35233992 DOI: 10.1002/cplu.202100548] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/13/2022] [Indexed: 11/12/2022]
Abstract
The development of DNA nanotechnology has attracted tremendous attention in biotechnological and biomedical fields involving biosensing, bioimaging and disease therapy. In particular, precise control over size and shape, easy modification, excellent programmability and inherent homology make the sophisticated DNA nanostructures vital for constructing intelligent drug carriers. Recent advances in the design of multifunctional DNA-based drug delivery systems (DDSs) have demonstrated the effectiveness and advantages of DNA nanostructures, showing the unique benefits and great potential in enhancing the delivery of pharmaceutical compounds and reducing systemic toxicity. This Review aims to overview the latest researches on DNA nanotechnology-enabled nanomedicine and give a perspective on their future opportunities.
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Affiliation(s)
- Qin Fan
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Zhimei He
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Jinxin Xiong
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
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18
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Wang S, Zhou Z, Ma N, Yang S, Li K, Teng C, Ke Y, Tian Y. DNA Origami-Enabled Biosensors. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6899. [PMID: 33287133 PMCID: PMC7731452 DOI: 10.3390/s20236899] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/29/2022]
Abstract
Biosensors are small but smart devices responding to the external stimulus, widely used in many fields including clinical diagnosis, healthcare and environment monitoring, etc. Moreover, there is still a pressing need to fabricate sensitive, stable, reliable sensors at present. DNA origami technology is able to not only construct arbitrary shapes in two/three dimension but also control the arrangement of molecules with different functionalities precisely. The functionalization of DNA origami nanostructure endows the sensing system potential of filling in weak spots in traditional DNA-based biosensor. Herein, we mainly review the construction and sensing mechanisms of sensing platforms based on DNA origami nanostructure according to different signal output strategies. It will offer guidance for the application of DNA origami structures functionalized by other materials. We also point out some promising directions for improving performance of biosensors.
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Affiliation(s)
- Shuang Wang
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
| | - Zhaoyu Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
| | - Sichang Yang
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
| | - Kai Li
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
| | - Chao Teng
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA;
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China; (Z.Z.); (N.M.); (S.Y.); (Y.T.)
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
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19
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Wu X, Wu T, Liu J, Ding B. Gene Therapy Based on Nucleic Acid Nanostructure. Adv Healthc Mater 2020; 9:e2001046. [PMID: 32864890 DOI: 10.1002/adhm.202001046] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/26/2020] [Indexed: 12/25/2022]
Abstract
During the past decades, nucleic acids have been employed for the construction of versatile nanostructures with well-defined shapes and sizes. Owing to the remarkable programmability, addressability, and biocompatibility, nucleic acid nanostructures are extensively applied in biomedical researches, such as bioimaging, biosensing, and drug delivery. In particular, nucleic acid nanostructures can act as promising candidates for the delivery of gene-related nucleic acid drugs based on the inherent homology. In this review, the recent progress in the design of multifunctional nucleic acid nanocarriers for gene therapy through antisense, RNA interference, gene editing, and gene expression is summarized. Furthermore, the challenges and future opportunities of nucleic acid nanotechnology in biomedical applications will be discussed.
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Affiliation(s)
- Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Materials Science and Engineering Henan Institute of Advanced Technology Zhengzhou University Zhengzhou 450001 China
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20
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Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
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Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
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21
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Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
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22
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Chen K, Zhu J, Bošković F, Keyser UF. Nanopore-Based DNA Hard Drives for Rewritable and Secure Data Storage. NANO LETTERS 2020; 20:3754-3760. [PMID: 32223267 DOI: 10.1021/acs.nanolett.0c00755] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanopores are powerful single-molecule tools for label-free sensing of nanoscale molecules including DNA that can be used for building designed nanostructures and performing computations. Here, DNA hard drives (DNA-HDs) are introduced based on DNA nanotechnology and nanopore sensing as a rewritable molecular memory system, allowing for storing, operating, and reading data in the changeable three-dimensional structure of DNA. Writing and erasing data are significantly improved compared to previous molecular storage systems by employing controllable attachment and removal of molecules on a long double-stranded DNA. Data reading is achieved by detecting the single molecules at the millisecond time scale using nanopores. The DNA-HD also ensures secure data storage where the data can only be read after providing the correct physical molecular keys. Our approach allows for easy-writing and easy-reading, rewritable, and secure data storage toward a promising miniature scale integration for molecular data storage and computation.
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Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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23
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Xin Y, Kielar C, Zhu S, Sikeler C, Xu X, Möser C, Grundmeier G, Liedl T, Heuer-Jungemann A, Smith DM, Keller A. Cryopreservation of DNA Origami Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905959. [PMID: 32130783 DOI: 10.1002/smll.201905959] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+ -containing buffer at moderate temperatures. Here, means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing cycles are investigated. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze-thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. Whereas no freeze damage could be detected in 3D DNA origami nanostructures subjected to 32 freeze-thaw cycles, 1000 freeze-thaw cycles result in significant fragmentation. The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10-3 and 200 × 10-3 m and without any negative effects on DNA origami shape. This work thus provides a basis for the long-term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Christoph Sikeler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103, Leipzig, Germany
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476, Potsdam, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Amelie Heuer-Jungemann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103, Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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24
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Fu X, Peng F, Lee J, Yang Q, Zhang F, Xiong M, Kong G, Meng HM, Ke G, Zhang XB. Aptamer-Functionalized DNA Nanostructures for Biological Applications. Top Curr Chem (Cham) 2020; 378:21. [PMID: 32030541 DOI: 10.1007/s41061-020-0283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.
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Affiliation(s)
- Xiaoyi Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Mengyi Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gezhi Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Kielar C, Xin Y, Xu X, Zhu S, Gorin N, Grundmeier G, Möser C, Smith DM, Keller A. Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability. Molecules 2019; 24:E2577. [PMID: 31315177 PMCID: PMC6680526 DOI: 10.3390/molecules24142577] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023] Open
Abstract
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Nelli Gorin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476 Potsdam, Germany
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103 Leipzig, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
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