1
|
Zou W, Lu J, Zhang L, Sun D. Tetrahedral framework nucleic acids for improving wound healing. J Nanobiotechnology 2024; 22:113. [PMID: 38491372 PMCID: PMC10943864 DOI: 10.1186/s12951-024-02365-z] [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: 11/08/2023] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
Wounds are one of the most common health issues, and the cost of wound care and healing has continued to increase over the past decade. In recent years, there has been growing interest in developing innovative strategies to enhance the efficacy of wound healing. Tetrahedral framework nucleic acids (tFNAs) have emerged as a promising tool for wound healing applications due to their unique structural and functional properties. Therefore, it is of great significance to summarize the applications of tFNAs for wound healing. This review article provides a comprehensive overview of the potential of tFNAs as a novel therapeutic approach for wound healing. In this review, we discuss the possible mechanisms of tFNAs in wound healing and highlight the role of tFNAs in modulating key processes involved in wound healing, such as cell proliferation and migration, angiogenesis, and tissue regeneration. The targeted delivery and controlled release capabilities of tFNAs offer advantages in terms of localized and sustained delivery of therapeutic agents to the wound site. In addition, the latest research progress on tFNAs in wound healing is systematically introduced. We also discuss the biocompatibility and biosafety of tFNAs, along with their potential applications and future directions for research. Finally, the current challenges and prospects of tFNAs are briefly discussed to promote wider applications.
Collapse
Affiliation(s)
- Wanqing Zou
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China
| | - Jing Lu
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, Guangdong, China.
| | - Luyong Zhang
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
| | - Duanping Sun
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China.
| |
Collapse
|
2
|
Algharagholy L, García-Suárez VM, Abaas SS. Selective Sensing of DNA Nucleobases with Angular Discrimination. ACS OMEGA 2024; 9:3240-3249. [PMID: 38284083 PMCID: PMC10809688 DOI: 10.1021/acsomega.3c04945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024]
Abstract
The fast and precise selective sensing of DNA nucleobases is a long-pursued method that can lead to huge advances in the field of genomics and have an impact on aspects such as the prevention of diseases, health enhancement, and, in general, all types of medical treatments. We present here a new type of nanoscale sensor based on carbon nanotubes with a specific geometry that can discriminate the type of nucleobase and also its angle of orientation. The proper differentiation of nucleobases is essential to clearly sequence DNA chains, while angular discrimination is key to improving the sensing selectivity. We perform first-principle and quantum transport simulations to calculate the transmission, conductance, and current of the nanotube-based nanoscale sensor in the presence of the four nucleotides (A, C, G, and T), each of them rotated 0, 90, 180, or 270°. Our results show that this system is able to effectively discriminate between the four nucleotides and their angle of orientation. We explain these findings in terms of the interaction between the phosphate group of the nucleotide and the nanotube wall. The phosphate specifically distorts the electronic structure of the nanotube depending on the distance and the orientation and leads to nontrivial changes in the transmission. This work provides a method for finer and more precise sequential DNA chains.
Collapse
Affiliation(s)
- Laith
A. Algharagholy
- Department
of Physics, College of Science, University
of Sumer, Al-Rifai, 64005 Thi-Qar, Iraq
| | | | - Sawsan S. Abaas
- Nasiriyah
Directorate of Education, Ministry of Education, Nasiriyah, 64001 Thi-Qar, Iraq
| |
Collapse
|
3
|
Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nat Commun 2023; 14:8328. [PMID: 38097568 PMCID: PMC10721878 DOI: 10.1038/s41467-023-43168-4] [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: 12/31/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.
Collapse
Affiliation(s)
- Agnese I Curatolo
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Ofer Kimchi
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Carl P Goodrich
- Institute of Science and Technology Austria, A-3400, Klosterneuburg, Austria
| | - Ryan K Krueger
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
4
|
Ji H, Zhu Q. Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery. J Control Release 2023; 361:803-818. [PMID: 37597810 DOI: 10.1016/j.jconrel.2023.08.036] [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: 04/16/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.
Collapse
Affiliation(s)
- Haofei Ji
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| |
Collapse
|
5
|
Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2023:1-21. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
Collapse
Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| |
Collapse
|
6
|
Yang J, Jahnke K, Xin L, Jing X, Zhan P, Peil A, Griffo A, Škugor M, Yang D, Fan S, Göpfrich K, Yan H, Wang P, Liu N. Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks. NANO LETTERS 2023. [PMID: 37440701 DOI: 10.1021/acs.nanolett.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions with precise control at the nanometer level, suggesting a viable tool to artificially engineer membrane morphology. In this work, we demonstrate a DNA origami cross (DOC) structure that can be anchored onto giant unilamellar vesicles (GUVs) and subsequently polymerized into micrometer-scale reconfigurable one-dimensional (1D) chains or two-dimensional (2D) lattices. Such DNA origami-based networks can be switched between left-handed (LH) and right-handed (RH) conformations by DNA fuels and exhibit potent efficacy in remodeling the membrane curvatures of GUVs. This work sheds light on designing hierarchically assembled dynamic DNA systems for the programmable modulation of synthetic cells for useful applications.
Collapse
Affiliation(s)
- Juanjuan Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Ling Xin
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Xinxin Jing
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Marko Škugor
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Sisi Fan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheime Feld 329, 69120 Heidelberg, Germany
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| |
Collapse
|
7
|
Ye J, Zheng J, Lu X, Wu F, Liu N, Dong Y, Shi Q, Xu L, Liu D. Single-Molecular Poly(propylene oxide) (PPO) Nucleus-Guided Assembly for Hydrophobicity-Dependent Molecular Transport in the Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4537-4543. [PMID: 36926892 DOI: 10.1021/acs.langmuir.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
By combining DNA nanotechnology and solid-phase nanopore technology, the aggregation behavior of polymer guided by a single-molecular poly(propylene) (PPO) nucleus in a 3D DNA network has been studied. At low temperature, the PPO chain is evenly dispersed in the rigid 3D DNA network; at higher temperature, the PPO chain self-collapses to a single-molecular nucleus; and upon addition of amphiphilic block copolymers below the critical micelle concentration (CMC), the chains tend to aggregate on the isolated hydrophobic nucleus through intermolecular hydrophobic interactions. The process has been characterized by a rheological test and an electrochemical test. This study not only provides a preliminary understanding of the nucleation and growth process of block copolymers but also offers a theoretical basis for the study of protein self-folding and aggregation in the future. On this basis, utilizing this nucleation and growth event, a novel smart nanopore has been developed for hydrophobicity-dependent molecular transport.
Collapse
Affiliation(s)
- Jianhan Ye
- Department of Chemistry, Renmin University of China, Beijing 100872, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Juanjuan Zheng
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Xin Lu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Nannan Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qian Shi
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Lijin Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
8
|
Saliba D, Luo X, Rizzuto FJ, Sleiman HF. Programming rigidity into size-defined wireframe DNA nanotubes. NANOSCALE 2023; 15:5403-5413. [PMID: 36826342 DOI: 10.1039/d2nr06185f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
Collapse
Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| |
Collapse
|
9
|
Phan TTM, Phan TM, Schmit JD. Beneficial and detrimental effects of non-specific binding during DNA hybridization. Biophys J 2023; 122:835-848. [PMID: 36721368 PMCID: PMC10027450 DOI: 10.1016/j.bpj.2023.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/09/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
DNA strands have to sample numerous states to find the alignment that maximizes Watson-Crick-Franklin base pairing. This process depends strongly on sequence, which affects the stability of the native duplex as well as the prevalence of non-native inter- and intramolecular helices. We present a theory that describes DNA hybridization as a three-stage process: diffusion, registry search, and zipping. We find that non-specific binding affects each of these stages in different ways. Mis-registered intermolecular binding in the registry search stage helps DNA strands sample different alignments and accelerates the hybridization rate. Non-native intramolecular structure affects all three stages by rendering portions of the molecule inert to intermolecular association, limiting mis-registered alignments to be sampled, and impeding the zipping process. Once in-register base pairs are formed, the stability of the native structure is important to hold the molecules together long enough for non-native contacts to break.
Collapse
Affiliation(s)
- Tam T M Phan
- Department of Physics, Kansas State University, Manhattan, Kansas
| | - Tien M Phan
- Department of Physics, Kansas State University, Manhattan, Kansas
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas.
| |
Collapse
|
10
|
Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
Collapse
Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| |
Collapse
|
11
|
Okamura H, Trinh GH, Dong Z, Fan W, Nagatsugi F. Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties. Molecules 2023; 28:molecules28041766. [PMID: 36838761 PMCID: PMC9965804 DOI: 10.3390/molecules28041766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Synthetic unnatural base pairs have been proven to be attractive tools for the development of DNA-based biotechnology. Our group has very recently reported on alkynylated purine-pyridazine pairs, which exhibit selective and stable base-pairing via hydrogen bond formation between pseudo-nucleobases in the major groove of duplex DNA. In this study, we attempted to develop an on-column synthesis methodology of oligodeoxynucleotides (ODNs) containing alkynylated purine derivatives to systematically explore the relationship between the structure and the corresponding base-pairing ability. Through Sonogashira coupling of the ethynyl pseudo-nucleobases and CPG-bound ODNs containing 6-iodopurine, we have demonstrated the synthesis of the ODNs containing three NPu derivatives (NPu1, NPu2, NPu3) as well as three OPu derivatives (OPu1, OPu2, OPu3). The base-pairing properties of each alkynylated purine derivative revealed that the structures of pseudo-nucleobases influence the base pair stability and selectivity. Notably, we found that OPu1 bearing 2-pyrimidinone exhibits higher stability to the complementary NPz than the original OPu, thereby demonstrating the potential of the on-column strategy for convenient screening of the alkynylated purine derivatives with superior pairing ability.
Collapse
Affiliation(s)
- Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Correspondence: (H.O.); (F.N.)
| | - Giang Hoang Trinh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Zhuoxin Dong
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Wenjue Fan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Correspondence: (H.O.); (F.N.)
| |
Collapse
|
12
|
Morzy D, Tekin C, Caroprese V, Rubio-Sánchez R, Di Michele L, Bastings MMC. Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes. NANOSCALE 2023; 15:2849-2859. [PMID: 36688792 PMCID: PMC9909679 DOI: 10.1039/d2nr05368c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electrostatics surely play a pivotal role in interactions between them. Here we discuss how each component of a DNA/ion/lipid system determines its electrostatic attachment. We examine membrane binding of a library of DNA molecules varying from nanoengineered DNA origami through plasmids to short DNA domains, demonstrating the interplay between the molecular structure of the nucleic acid and the phase of lipid bilayers. Furthermore, the magnitude of DNA/lipid interactions is tuned by varying the concentration of magnesium ions in the physiologically relevant range. Notably, we observe that the structural and mechanical properties of DNA are critical in determining its attachment to lipid bilayers and demonstrate that binding is correlated positively with the size, and negatively with the flexibility of the nucleic acid. The findings are utilized in a proof-of-concept comparison of membrane interactions of two DNA origami designs - potential nanotherapeutic platforms - showing how the results can have a direct impact on the choice of DNA geometry for biotechnological applications.
Collapse
Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Cem Tekin
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Roger Rubio-Sánchez
- 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
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Lorenzo Di Michele
- 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
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
- Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
| |
Collapse
|
13
|
Yutong Huang F, Kumar Lat P, Sen D. Unusual Paradigm for DNA-DNA Recognition and Binding: "Socket-Plug" Complementarity. J Am Chem Soc 2023; 145:3146-3157. [PMID: 36706227 DOI: 10.1021/jacs.2c12514] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA is the key informational polymer in biology by virtue of its precisely defined self-assembling properties. Watson-Crick complementarity, which underlies DNA's self-assembly, is required not only in biology but has also proved powerful in the field of nanoscience, where it has been utilized to assemble complex 2D and 3D architectures and nanodevices built from the DNA double-helix. Aside from Watson-Crick base-pairing, however, DNA also participates in alternative base pairing schemes, giving rise to DNA triplexes and G-quadruplexes. Herein, we describe "sticky-ended" DNA triplex-quadruplex composites that specifically recognize and bind to each other using a wholly different logic, "socket-plug" complementarity, a shape-sensing fitting of guanine "prongs" into guanine-lacking "cavities." A remarkable property of this kind of complementarity is the key role played in it by specific counter-cations: thus, exclusive "self" socket-plug recognition occurs over "other" in sodium salt solutions while precisely the reverse occurs in potassium salt solutions. We have used gel electrophoresis, Förster resonance energy transfer, alkylation protection, and structural modeling to study this remarkable fundamental property of DNA, that we anticipate will find wide practical application.
Collapse
Affiliation(s)
- Fiona Yutong Huang
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Prince Kumar Lat
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
14
|
Zhou S, Ye J, Zhao X, Zhou Z, Dong Y, Shi Q, Liu N, Wu F. A DNA-Schiff base functional nanopore sensing platform for the highly sensitive detection of Al 3+ and Zn 2+ ions. Dalton Trans 2023; 52:1524-1532. [PMID: 36662484 DOI: 10.1039/d2dt03786f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The combination of DNA nanotechnology and nanopore sensing technology has greatly promoted research on target molecule or ion detection. The large solid-state nanopores/nanochannels show better mechanical stability and reproducibility, but metal ion detection in the large nanopores with diameters of hundreds of nanometers or several micrometers is rarely reported. Hence, it is meaningful and urgent to develop a large nanopore-based sensing platform for the detection of metal ions. Herein, we employed a salicylic aldehyde-modified DNA network in conjunction with a glass nanopipette (GN) with a diameter of hundreds of nanometers as a sensing platform for the detection of target metal ions. Upon the addition of different receptors with the amino group, the salicylic aldehyde could in situ specifically recognize and bind with Zn2+ and Al3, forming Schiff base-metal ion complexes at the four vertices of one face per nanocube unit. The steric hindrance effect of multiple Schiff bases and metal ion complexes leads to the blockage of internal structure and decrease of ion current in the GN. Owing to this signal amplification strategy, the detection limit of the target metal ion reaches a level of fM in the GN with a diameter of about 300 nm. In the future, this functional nanopore sensing platform is expected to realize highly sensitive detection for more biological metal ions by choosing appropriate receptors.
Collapse
Affiliation(s)
- Shuailong Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Jianhan Ye
- Department of Chemistry, Renmin University of China, Beijing 100872, China.,Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohuan Zhao
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Zihao Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qian Shi
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Nannan Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
15
|
Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
Collapse
Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| |
Collapse
|
16
|
Hu L, Takezawa Y, Shionoya M. Cu II-mediated DNA base pairing of a triazole-4-carboxylate nucleoside prepared by click chemistry. Chem Commun (Camb) 2023; 59:892-895. [PMID: 36594822 DOI: 10.1039/d2cc06205d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Artificial metal-mediated DNA base pairing is a promising strategy for creating highly functionalized DNA supramolecules. Here we report a novel ligand-type triazole-4-carboxylate (TazC) nucleoside that is readily prepared by the click reaction. TazC nucleosides were found to form a stable TazC-CuII-TazC base pair inside DNA duplexes, resulting in CuII-specific duplex stabilization (ΔTm = +7.7 °C). This study demonstrates that the triazole derivatives are useful in the development of metal-mediated base pairing.
Collapse
Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
17
|
Abstract
Nucleic-acid nanostructures, which have been designed and constructed with atomic precision, have been used as scaffolds for different molecules and proteins, as nanomachines, as computational components, and more. In particular, RNA has garnered tremendous interest as a building block for the self-assembly of sophisticated and functional nanostructures by virtue of its ease of synthesis by in vivo or in vitro transcription, its superior mechanical and thermodynamic properties, and its functional roles in nature. In this Topical Review, we describe recent developments in the use of RNA for the design and construction of nanostructures. We discuss the differences between RNA and DNA that make RNA attractive as a building block for the construction of nucleic-acid nanostructures, and we present the uses of different nanostructures─RNA alone, RNA-DNA, and functional RNA nanostructures.
Collapse
Affiliation(s)
- Ofer I Wilner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Doron Yesodi
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yossi Weizmann
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanotechnology Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| |
Collapse
|
18
|
Zhang P, Ouyang Y, Zhuo Y, Chai Y, Yuan R. Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging. Anal Chem 2023; 95:407-419. [PMID: 36625113 DOI: 10.1021/acs.analchem.2c04540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu Ouyang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China.,Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| |
Collapse
|
19
|
DNA-decorated multilamellar cholesterol assemblies for nucleic acid detection in the micrometer-scale solid-state nanopore. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
20
|
Schuster GB, Hud NV, Alenaizan A. Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions. J Phys Chem B 2022; 126:10758-10767. [PMID: 36502412 DOI: 10.1021/acs.jpcb.2c05934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.
Collapse
Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| |
Collapse
|
21
|
Dong N, Sun Y, Sun G, Zhang L, Sun S. Chiral DNA Nanotubes Self-Assembled from Building Blocks with Tailorable Curvature and Twist. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204996. [PMID: 36287092 DOI: 10.1002/smll.202204996] [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: 08/15/2022] [Revised: 10/04/2022] [Indexed: 06/16/2023]
Abstract
DNA nanotubes with prescribed geometry could allow for nanomaterial organization with designed optical or electrical function. As one of the dominating driving forces for DNA nanotube assembly, intrinsic curvature and twist of building blocks can be induced by bending deformation and twisting deformation. However, it is still unknown that how bending and twisting design on nanoscale building blocks affects the geometry of DNA tubes with micrometer length. Here, through targeted base pair deletion or insertion, the amount of bending deformation in building blocks is modulated by length gradient and the amount of twisting deformation is modulated by average twist density. This work systematically explores the independent effect and synergistic effect of two types of deformation on tube geometry, including diameter, chirality, and helical angles, via a streptavidin-labeling technique. The design rules enable the construction of DNA nanotubes with prescribed chirality and tailored diameters.
Collapse
Affiliation(s)
- Niuniu Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Yishan Sun
- School of Clinical Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Geng Sun
- The College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Sha Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| |
Collapse
|
22
|
Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [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] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
Collapse
Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
| |
Collapse
|
23
|
Liu J, Li M, Zuo X. DNA Nanotechnology-Empowered Live Cell Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204711. [PMID: 36124715 DOI: 10.1002/smll.202204711] [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: 08/01/2022] [Revised: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.
Collapse
Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
24
|
Chandler M, Jain S, Halman J, Hong E, Dobrovolskaia MA, Zakharov AV, Afonin KA. Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204941. [PMID: 36216772 PMCID: PMC9671856 DOI: 10.1002/smll.202204941] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid nanoparticles, or NANPs, rationally designed to communicate with the human immune system, can offer innovative therapeutic strategies to overcome the limitations of traditional nucleic acid therapies. Each set of NANPs is unique in their architectural parameters and physicochemical properties, which together with the type of delivery vehicles determine the kind and the magnitude of their immune response. Currently, there are no predictive tools that would reliably guide the design of NANPs to the desired immunological outcome, a step crucial for the success of personalized therapies. Through a systematic approach investigating physicochemical and immunological profiles of a comprehensive panel of various NANPs, the research team developes and experimentally validates a computational model based on the transformer architecture able to predict the immune activities of NANPs. It is anticipated that the freely accessible computational tool that is called an "artificial immune cell," or AI-cell, will aid in addressing the current critical public health challenges related to safety criteria of nucleic acid therapies in a timely manner and promote the development of novel biomedical tools.
Collapse
Affiliation(s)
- Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| |
Collapse
|
25
|
|
26
|
Sampieri A, Monroy-Contreras R, Asanov A, Vaca L. Design of Hydrogel Silk-Based Microarrays and Molecular Beacons for Reagentless Point-of-Care Diagnostics. Front Bioeng Biotechnol 2022; 10:881679. [PMID: 35957640 PMCID: PMC9361048 DOI: 10.3389/fbioe.2022.881679] [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: 02/22/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
We have developed a novel microarray system based on three technologies: 1) molecular beacons designed to interact with DNA targets at room temperature (25–27°C), 2) tridimensional silk-based microarrays containing the molecular beacons immersed in the silk hydrogel, and 3) shallow angle illumination, which uses separated optical pathways for excitation and emission. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing, and stringency control, and measure only end-point results, our microarray technology provides enhanced signal-to-background ratio (achieved by separating the optical pathways for excitation and emission, resulting in reduced stray light), performs analysis rapidly in one step without the need for labeling DNA targets, and measures the entire course of association kinetics between target DNA and the molecular beacons. To illustrate the benefits of our technology, we conducted microarray assays designed for the identification of influenza viruses. We show that in a single microarray slide, we can identify the virus subtype according to the molecular beacons designed for hemagglutinin (H1, H2, and H3) and neuraminidase (N1, N2). We also show the identification of human and swine influenza using sequence-specific molecular beacons. This microarray technology can be easily implemented for reagentless point-of-care diagnostics of several contagious diseases, including coronavirus variants responsible for the current pandemic.
Collapse
Affiliation(s)
- Alicia Sampieri
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | - Ricardo Monroy-Contreras
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | | | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
- *Correspondence: Luis Vaca,
| |
Collapse
|
27
|
Guselnikova O, Lim H, Kim HJ, Kim SH, Gorbunova A, Eguchi M, Postnikov P, Nakanishi T, Asahi T, Na J, Yamauchi Y. New Trends in Nanoarchitectured SERS Substrates: Nanospaces, 2D Materials, and Organic Heterostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107182. [PMID: 35570326 DOI: 10.1002/smll.202107182] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/23/2022] [Indexed: 06/15/2023]
Abstract
This article reviews recent fabrication methods for surface-enhanced Raman spectroscopy (SERS) substrates with a focus on advanced nanoarchitecture based on noble metals with special nanospaces (round tips, gaps, and porous spaces), nanolayered 2D materials, including hybridization with metallic nanostructures (NSs), and the contemporary repertoire of nanoarchitecturing with organic molecules. The use of SERS for multidisciplinary applications has been extensively investigated because the considerably enhanced signal intensity enables the detection of a very small number of molecules with molecular fingerprints. Nanoarchitecture strategies for the design of new NSs play a vital role in developing SERS substrates. In this review, recent achievements with respect to the special morphology of metallic NSs are discussed, and future directions are outlined for the development of available NSs with reproducible preparation and well-controlled nanoarchitecture. Nanolayered 2D materials are proposed for SERS applications as an alternative to the noble metals. The modern solutions to existing limitations for their applications are described together with the state-of-the-art in bio/environmental SERS sensing using 2D materials-based composites. To complement the existing toolbox of plasmonic inorganic NSs, hybridization with organic molecules is proposed to improve the stability of NSs and selectivity of SERS sensing by hybridizing with small or large organic molecules.
Collapse
Affiliation(s)
- Olga Guselnikova
- JST-ERATO Yamauchi Materials Space Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russian Federation
| | - Hyunsoo Lim
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- New & Renewable Energy Research Center, Korea Electronics Technology Institute (KETI), 25, Saenari-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13509, Republic of Korea
| | - Hyun-Jong Kim
- Surface Technology Group, Korea Institute of Industrial Technology (KITECH), Incheon, 21999, Republic of Korea
| | - Sung Hyun Kim
- New & Renewable Energy Research Center, Korea Electronics Technology Institute (KETI), 25, Saenari-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13509, Republic of Korea
| | - Alina Gorbunova
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russian Federation
| | - Miharu Eguchi
- JST-ERATO Yamauchi Materials Space Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Pavel Postnikov
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russian Federation
| | - Takuya Nakanishi
- Kagami Memorial Research Institute for Materials Science and Technology, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo, 169-0051, Japan
| | - Toru Asahi
- Kagami Memorial Research Institute for Materials Science and Technology, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo, 169-0051, Japan
| | - Jongbeom Na
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- Research and Development (R&D) Division, Green Energy Institute, Mokpo, Jeollanamdo, 58656, Republic of Korea
| | - Yusuke Yamauchi
- JST-ERATO Yamauchi Materials Space Tectonics Project, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- Kagami Memorial Research Institute for Materials Science and Technology, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo, 169-0051, Japan
| |
Collapse
|
28
|
Romero-Sanchez IC, Castellano LE, Laurati M. Tuning the Effective Interactions between Spherical Double-Stranded DNA Brushes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivany C. Romero-Sanchez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
| | - Laura E. Castellano
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
| | - Marco Laurati
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
29
|
Cao D, Xie Y, Song J. DNA Hydrogels in the Perspective of Mechanical Properties. Macromol Rapid Commun 2022; 43:e2200281. [PMID: 35575627 DOI: 10.1002/marc.202200281] [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: 03/26/2022] [Revised: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Tailoring the mechanical properties has always been a key to the field of hydrogels in terms of different applications. Particularly, deoxyribonucleic acid (DNA) hydrogels offer an unambiguous way to precisely tune the mechanical properties, largely on account of their programmable sequences, abundant responding toolbox, and various ligation approaches. In this review, DNA hydrogels from the perspective of mechanical properties, from synthetic standpoint to different applications are introduced. The relationship between the structure and their mechanical properties in DNA hydrogels and the methods of regulating the mechanical properties of DNA hydrogels are specifically summarized. Furthermore, several recent applications of DNA hydrogels in relation to their mechanical properties are discussed. Benefiting from the tunability and flexibility, rational design of mechanical properties in DNA hydrogels provided unheralded interest from fundamental science to extensive applications. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Dengjie Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| |
Collapse
|
30
|
Hu L, Takezawa Y, Shionoya M. Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides. Chem Sci 2022; 13:3977-3983. [PMID: 35440985 PMCID: PMC8985573 DOI: 10.1039/d2sc00926a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (ImOA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The ImOC nucleobases were found to form stable ImOC–CuII–ImOC and ImOC–HgII–ImOC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The ImOC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The ImOC–CuII–ImOC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of CuII. Furthermore, we demonstrated the quantitative assembly of three CuII ions inside a DNA duplex with three consecutive ImOC–ImOC pairs, showing great potential of DNA-template based CuII nanoarray construction. The study of easily-prepared ImOC base pairs will provide a new design strategy for metal-responsive DNA materials. A novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase, which can be easily derived from a commercially available uridine analogue, was found to form stable CuII- and HgII-mediated base pairs in DNA duplexes.![]()
Collapse
Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| |
Collapse
|
31
|
Jia R, Wang Y, Ma W, Huang J, Sun H, Chen B, Cheng H, He X, Wang K. Activatable Dual Cancer-Related RNA Imaging and Combined Gene-Chemotherapy through the Target-Induced Intracellular Disassembly of Functionalized DNA Tetrahedron. Anal Chem 2022; 94:5937-5945. [PMID: 35380798 DOI: 10.1021/acs.analchem.2c00364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The desire for a cancer theranostic system with simultaneously accurate diagnosis and efficient therapy is undeniably interminable. Heretofore, theranostic systems with simple components were designed for cancer theranostics but with confined accuracy of diagnosis and side effects of administered drugs. Here, we report an activatable theranostic system for simultaneously imaging dual cancer-related RNAs, mRNA Bcl-2 and piRNA-36026, and combined gene-chemotherapy through the target-induced intracellular disassembly of DNA tetrahedron. Briefly, five customized oligonucleotides are used to assemble the functionalized DNA tetrahedron. The relevant functional nucleic acids, including the antisequence of mRNA Bcl-2, the antisequence of piRNA-36026, and aptamer AS1411, are designed in the customized oligonucleotides with the signal reporters Cy3 and Cy5. Doxorubicin (DOX) is loaded in the functionalized DNA tetrahedron by inlaying between cytosine and guanine to form the activatable cancer theranostic system. The activatable cancer theranostic system is able to recognize MCF-7 cells by aptamer AS1411 and then enter the cells. In the presence of targets, the antisequences in the activatable cancer theranostic system hybridize with intracellular mRNA Bcl-2 and piRNA-36026, leading to the fluorescence signal recovery of Cy3 and Cy5 and the downregulation of two targets in the cytoplasm as well as the consequent apoptosis of MCF-7 cells in the form of gene therapy. Interestingly, as the antisequences are designed in the assembly strands, the hybridization between targets and the antisequences results in the disassembly of the activatable cancer theranostic system and the release of DOX as well as sequential chemotherapy. Advantageously, the activatable cancer theranostic system can achieve imaging of dual cancer-related RNAs with an imaging time window as long as 15 h and exhibit an obvious therapeutic effect in vivo. Therefore, this work is in furtherance of exploration for activatable cancer theranostic systems with high accuracy and efficiency and sheds new light on the development of precision medicine.
Collapse
Affiliation(s)
- Ruichen Jia
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Yitan Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Wenjie Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Huanhuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Biao Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| |
Collapse
|
32
|
Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
Collapse
|
33
|
Okamura H, Trinh GH, Dong Z, Masaki Y, Seio K, Nagatsugi F. Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface. Nucleic Acids Res 2022; 50:3042-3055. [PMID: 35234916 PMCID: PMC8989583 DOI: 10.1093/nar/gkac140] [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: 10/30/2021] [Revised: 01/27/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Unnatural base pairs (UBPs) which exhibit a selectivity against pairing with canonical nucleobases provide a powerful tool for the development of nucleic acid-based technologies. As an alternative strategy to the conventional UBP designs, which involve utility of different recognition modes at the Watson–Crick interface, we now report that the exclusive base pairing can be achieved through the spatial separation of recognition units. The design concept was demonstrated with the alkynylated purine (NPu, OPu) and pyridazine (NPz, OPz) nucleosides endowed with nucleobase-like 2-aminopyrimidine or 2-pyridone (‘pseudo-nucleobases’) on their major groove side. These alkynylated purines and pyridazines exhibited exclusive and stable pairing properties by the formation of complementary hydrogen bonds between the pseudo-nucleobases in the DNA major groove as revealed by comprehensive Tm measurements, 2D-NMR analyses, and MD simulations. Moreover, the alkynylated purine-pyridazine pairs enabled dramatic stabilization of the DNA duplex upon consecutive incorporation while maintaining a high sequence-specificity. The present study showcases the separation of the recognition interface as a promising strategy for developing new types of UBPs.
Collapse
Affiliation(s)
- Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Giang Hoang Trinh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Zhuoxin Dong
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| |
Collapse
|
34
|
Romero-Sanchez I, Pihlajamaa I, Adžić N, Castellano LE, Stiakakis E, Likos CN, Laurati M. Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes. ACS NANO 2022; 16:2133-2146. [PMID: 35130432 PMCID: PMC8867906 DOI: 10.1021/acsnano.1c07799] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultralong double-stranded DNA (dsDNA) fragments reveal nonmonotonic particle shrinking, aggregation, and re-entrant ordering. Theory and simulations show that aggregation and re-entrant ordering arise from the combined effect of shrinking, which is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes and of a short-range attractive interaction competing with electrostatic repulsion. An unconventional mechanism gives origin to the short-range attraction: blunt-end interactions between stretched dsDNA fragments of neighboring brushes, which become sufficiently intense for dense and packed brushes. The attraction can be tuned by inducing free-end backfolding through the addition of monovalent salt. Our results show that base stacking is a mode parallel to hybridization to steer colloidal assembly in which attractions can be fine-tuned through salinity and, potentially, grafting density and temperature.
Collapse
Affiliation(s)
- Ivany Romero-Sanchez
- Dipartimento
di Chimica & CSGI, Università
di Firenze, 50019 Sesto Fiorentino, Italy
- División
de Ciencias e Ingenierías, Universidad
de Guanajuato, 37150 León, Mexico
| | - Ilian Pihlajamaa
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
- Eindhoven
University of Technology, Department of
Applied Physics, Soft Matter and Biological Physics, Postbus 513, NL-5600 MB Eindhoven, The Netherlands
| | - Natasa Adžić
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
| | - Laura E. Castellano
- División
de Ciencias e Ingenierías, Universidad
de Guanajuato, 37150 León, Mexico
| | - Emmanuel Stiakakis
- Biomacromolecular
Systems and Processes, Institute of Biological Information Processing
(IBI-4), 4 Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
| | - Marco Laurati
- Dipartimento
di Chimica & CSGI, Università
di Firenze, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
35
|
Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
Collapse
Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|
36
|
Abstract
Time efficiency of self-assembly is crucial for many biological processes. Moreover, with the advances of nanotechnology, time efficiency in artificial self-assembly becomes ever more important. While structural determinants and the final assembly yield are increasingly well understood, kinetic aspects concerning the time efficiency, however, remain much more elusive. In computer science, the concept of time complexity is used to characterize the efficiency of an algorithm and describes how the algorithm's runtime depends on the size of the input data. Here we characterize the time complexity of nonequilibrium self-assembly processes by exploring how the time required to realize a certain, substantial yield of a given target structure scales with its size. We identify distinct classes of assembly scenarios, i.e., "algorithms" to accomplish this task, and show that they exhibit drastically different degrees of complexity. Our analysis enables us to identify optimal control strategies for nonequilibrium self-assembly processes. Furthermore, we suggest an efficient irreversible scheme for the artificial self-assembly of nanostructures, which complements the state-of-the-art approach using reversible binding reactions and requires no fine-tuning of binding energies.
Collapse
|
37
|
Gangrade A, Stephanopoulos N, Bhatia D. Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. NANOSCALE 2021; 13:16834-16846. [PMID: 34622910 DOI: 10.1039/d1nr04475c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-based nanotechnology has evolved into an autonomous, highly innovative, and dynamic field of research at the nexus of supramolecular chemistry, nanotechnology, materials science, and biotechnology. DNA-based materials, including origami nanodevices, have started to emerge as an ideal scaffold for use in cellular programming, tissue engineering, and drug delivery applications. We cover herein the applications for DNA as a scaffold for interfacing with, and guiding, the activity of biological systems like cells and tissues. Although DNA is a highly programmable molecular building block, it suffers from a lack of functional capacity for guiding and modulating cells. Coupling DNA to biologically active molecules can bestow bioactivity to these nanodevices. The main goal of such nanodevices is to synthesize systems that can bind to cells and mimic the extracellular environment, and serve as a highly promising toolbox for multiple applications in cellular programming and tissue engineering. DNA-based programmable devices offer a highly promising approach for programming collections of cells, tissue engineering, and regenerative medicine applications.
Collapse
Affiliation(s)
- Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, India
| |
Collapse
|
38
|
Baker Y, Yuan L, Chen J, Belle R, Carlisle R, El-Sagheer A, Brown T. Expanding the chemical functionality of DNA nanomaterials generated by rolling circle amplification. Nucleic Acids Res 2021; 49:9042-9052. [PMID: 34403467 PMCID: PMC8450075 DOI: 10.1093/nar/gkab720] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/01/2021] [Accepted: 08/08/2021] [Indexed: 02/02/2023] Open
Abstract
Rolling circle amplification (RCA) is a powerful tool for the construction of DNA nanomaterials such as hydrogels, high-performance scaffolds and DNA nanoflowers (DNFs), hybrid materials formed of DNA and magnesium pyrophosphate. Such DNA nanomaterials have great potential in therapeutics, imaging, protein immobilisation, and drug delivery, yet limited chemistry is available to expand their functionality. Here, we present orthogonal strategies to produce densely modified RCA products and DNFs. We provide methods to selectively modify the DNA component and/or the protein cargo of these materials, thereby greatly expanding the range of chemical functionalities available to these systems. We have used our methodology to construct DNFs bearing multiple surface aptamers and peptides capable of binding to cancer cells that overexpress the HER2 oncobiomarker, demonstrating their potential for diagnostic and therapeutic applications.
Collapse
Affiliation(s)
- Ysobel R Baker
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Liyiwen Yuan
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jinfeng Chen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Roman Belle
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Robert Carlisle
- Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Chemistry Branch Department of Science and Mathematics, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
39
|
Wong KL, Liu J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol J 2021; 16:e2000338. [PMID: 34411451 DOI: 10.1002/biot.202000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.
Collapse
Affiliation(s)
- Kingsley L Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| |
Collapse
|
40
|
Babi J, Zhu L, Lin A, Uva A, El‐Haddad H, Peloewetse A, Tran H. Self‐assembled free‐floating
nanomaterials from
sequence‐defined
polymers. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jon Babi
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Linglan Zhu
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Angela Lin
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Azalea Uva
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Hana El‐Haddad
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Atang Peloewetse
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Helen Tran
- Department of Chemistry University of Toronto Toronto Ontario Canada
- Department of Chemical Engineering University of Toronto Toronto Ontario Canada
| |
Collapse
|
41
|
Xu J, Qiu X, Hildebrandt N. When Nanoworlds Collide: Implementing DNA Amplification, Nanoparticles, Molecules, and FRET into a Single MicroRNA Biosensor. NANO LETTERS 2021; 21:4802-4808. [PMID: 34041910 DOI: 10.1021/acs.nanolett.1c01351] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Isothermal nucleic acid amplification strategies have been combined with nanotechnology for advanced biosensing, material design, and biomedical applications. However, merging phenomena and materials of different nanoscales with the aim of exploiting all their benefits at once has remained a challenging endeavor. Here, we exemplify the various problems one can encounter when combining the nanodimensions of lanthanide complexes (∼2 nm), Förster resonance energy transfer (FRET, ∼5 nm), quantum dots (QDs, ∼20 nm), and rolling circle amplification (RCA, ∼250 nm) into a single microRNA biosensor and how these challenges can be overcome. Six different approaches, including simple FRET-RCA, enzyme-digesting FRET-RCA, and FRET-hyperbranched-RCA were investigated. We demonstrated specific miR-21 detection with 80 fM limit of detection and multiplexing capability with FRET from a Tb complex to different QDs. The detailed view on the various complex multi-nanodimensional assay systems elucidated the limited clinical translation of such sophisticated multicomponent nanobiosensors.
Collapse
Affiliation(s)
- Jingyue Xu
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Xue Qiu
- School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Niko Hildebrandt
- nanofret.com, Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan Cedex, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| |
Collapse
|
42
|
Johnson MB, Chandler M, Afonin KA. Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects. Adv Drug Deliv Rev 2021; 173:427-438. [PMID: 33857556 PMCID: PMC8178219 DOI: 10.1016/j.addr.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Nucleic acid nanoparticles (NANPs) represent a highly versatile molecular platform for the targeted delivery of various therapeutics. However, despite their promise, further clinical translation of this innovative technology can be hindered by immunological off-target effects. All human cells are equipped with an arsenal of receptors that recognize molecular patterns specific to foreign nucleic acids and understanding the rules that guide this recognition offer the key rationale for the development of therapeutic NANPs with tunable immune stimulation. Numerous recent studies have provided increasing evidence that in addition to NANPs' physicochemical properties and therapeutic effects, their interactions with cells of the immune system can be regulated through multiple independently programmable architectural parameters. The results further suggest that defined immunomodulation by NANPs can either support their immunoquiescent delivery or be used for conditional stimulation of beneficial immunological responses.
Collapse
Affiliation(s)
- M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| |
Collapse
|
43
|
Nakauchi H, Maeda M, Kanayama N. Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5573-5581. [PMID: 33871256 DOI: 10.1021/acs.langmuir.1c00349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force-distance (F-D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3-5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F-D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F-D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl2 solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.
Collapse
Affiliation(s)
- Hiroya Nakauchi
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
| | - Mizuo Maeda
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute of Biomedical Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| |
Collapse
|
44
|
Advances in the Integration of Nucleic Acid Nanotechnology into CRISPR-Cas System. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00180-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
45
|
Berk KL, Blum SM, Funk VL, Sun Y, Yang IY, Gostomski MV, Roth PA, Liem AT, Emanuel PA, Hogan ME, Miklos AE, Lux MW. Rapid Visual Authentication Based on DNA Strand Displacement. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19476-19486. [PMID: 33852293 DOI: 10.1021/acsami.1c02429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.
Collapse
Affiliation(s)
- Kimberly L Berk
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Steven M Blum
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Vanessa L Funk
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Yuhua Sun
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - In-Young Yang
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - Mark V Gostomski
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Pierce A Roth
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Alvin T Liem
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Peter A Emanuel
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Michael E Hogan
- Applied DNA Sciences, Stony Brook, New York 11790, United States
| | - Aleksandr E Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Edgewood, Maryland 21010, United States
| |
Collapse
|
46
|
Bellassai N, D'Agata R, Spoto G. Novel nucleic acid origami structures and conventional molecular beacon-based platforms: a comparison in biosensing applications. Anal Bioanal Chem 2021; 413:6063-6077. [PMID: 33825006 PMCID: PMC8440263 DOI: 10.1007/s00216-021-03309-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022]
Abstract
Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami.
Collapse
Affiliation(s)
- Noemi Bellassai
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.
| |
Collapse
|
47
|
Aksakal R, Mertens C, Soete M, Badi N, Du Prez F. Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004038. [PMID: 33747749 PMCID: PMC7967060 DOI: 10.1002/advs.202004038] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 05/19/2023]
Abstract
In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.
Collapse
Affiliation(s)
- Resat Aksakal
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Chiel Mertens
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Matthieu Soete
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Nezha Badi
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Filip Du Prez
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| |
Collapse
|
48
|
Baral B, Dutta J, Subudhi U. Biophysical interaction between self-assembled branched DNA nanostructures with bovine serum albumin and bovine liver catalase. Int J Biol Macromol 2021; 177:119-128. [PMID: 33609575 DOI: 10.1016/j.ijbiomac.2021.02.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/30/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
Branched DNA (bDNA) nanostructures have emerged as self-assembled biomaterials and are being considered for biomedical applications. Herein, we report the biophysical interaction between self-assembled bDNA nanostructure with circulating protein bovine serum albumin (BSA) and cellular enzyme bovine liver catalase (BLC). The binding between bDNA and BSA or BLC was confirmed through the decrease in fluorescence spectra. The Stern-Volmer data supports for non-covalent bonding with ~1 binding site in case of BSA and BLC thus advocating a static binding. Furthermore, FTIR and ITC study confirmed the binding of bDNAs with proteins through hydrogen bonding and van der Waals interaction. The negative free energy observed in ITC represent spontaneous reaction for BLC-bDNA interaction. The biophysical interaction between bDNA nanostructures and proteins was also supported by DLS and zeta potential measurement. With an increase in bDNA concentrations up to 100 nM, no significant change in absorbance and CD spectra was observed for both BLC and BSA which suggests structural stability and unaffected secondary conformation of proteins in presence of bDNA. Furthermore, the catalytic activity of BLC was unaltered in presence of bDNAscr even with increasing the incubation period from 1 h to 24 h. Interestingly, the time-dependent decrease in activity of BLC was protected by bDNAmix. The thermal melting study suggests a higher Tm value for proteins in presence of bDNAmix which demonstrates that interaction with bDNAmix increases the thermal stability of proteins. Collectively these data suggest that self-assembled DNA nanostructure may bind to BSA for facilitating circulation in plasma or binding to intracellular proteins like BLC for stabilization, however the secondary conformation of protein or catalytic activity of enzyme is unaltered in presence of bDNA nanostructure. Thus, the newly established genomic sequence-driven self-assembled DNA nanostructure can be explored for in vitro or in vivo experimental work in recent future.
Collapse
Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| |
Collapse
|
49
|
Mo F, Jiang K, Zhao D, Wang Y, Song J, Tan W. DNA hydrogel-based gene editing and drug delivery systems. Adv Drug Deliv Rev 2021; 168:79-98. [PMID: 32712197 DOI: 10.1016/j.addr.2020.07.018] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is a promising synthesizer for precisely constructing almost arbitrary geometry in two and three dimensions. Among various DNA-based soft materials, DNA hydrogels are comprised of hydrophilic polymeric networks of crosslinked DNA chains. For their properties of biocompatibility, porosity, sequence programmability and tunable multifunctionality, DNA hydrogels have been widely studied in bioanalysis and biomedicine. In this review, recent developments in DNA hydrogels and their applications in drug delivery systems are highlighted. First, physical and chemical crosslinking methods for constructing DNA hydrogels are introduced. Subsequently, responses of DNA hydrogels to nonbiological and biological stimuli are described. Finally, DNA hydrogel-based delivery platforms for different types of drugs are detailed. With the emergence of gene therapy, this review also gives future prospects for combining DNA hydrogels with the gene editing toolbox.
Collapse
|
50
|
Asefifeyzabadi N, Das PK, Onorimuo AH, Durocher G, Shamsi MH. DNA interfaces with dimensional materials for biomedical applications. RSC Adv 2021; 11:28332-28341. [PMID: 35480758 PMCID: PMC9038036 DOI: 10.1039/d1ra04917h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022] Open
Abstract
DNA interfaces with nano, micro, and macro materials have gained widespread attention for various applications. Such interfaces exhibit distinct functions and properties not only due to the unique properties of interfacing materials but also sequence- and conformation-dependent characteristics of the DNA. Therefore, DNA interfaces with diverse dimensional materials have advanced our understanding of the interaction mechanisms and the properties of such interfaces. The unique interfacial properties of such novel materials have applications in nanotechnology, biophysics, cell biology, biosensing, and bioelectronics. The field is growing rapidly with the frequent emergence of new interfaces carrying remarkable interfacial character. In this review article, we have classified the DNA interfaces into 0D, 1D, 2D, and 3D categories based on the types of dimensional materials. We review the key efforts made in the last five years and focus on types of interfaces, interfacing mechanisms, and their state-of-the-art applications. This review will draw a general interest because of the diversity in the DNA materials science but also the unique applications that will play a cutting-edge role in biomedical and biosensing research. DNA interfaces with 0–3 dimensional materials through physisorption and chemisorption mechanisms acquire unique interfacial character for novel biomedical applications.![]()
Collapse
Affiliation(s)
- Narges Asefifeyzabadi
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Prabhangshu Kumer Das
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | | | - Grace Durocher
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Mohtashim Hassan Shamsi
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| |
Collapse
|