51
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Stasi M, Monferrer A, Babl L, Wunnava S, Dirscherl CF, Braun D, Schwille P, Dietz H, Boekhoven J. Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle. J Am Chem Soc 2022; 144:21939-21947. [PMID: 36442850 PMCID: PMC9732876 DOI: 10.1021/jacs.2c08463] [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] [Indexed: 11/30/2022]
Abstract
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.
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Affiliation(s)
- Michele Stasi
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany
| | - Alba Monferrer
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Leon Babl
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Sreekar Wunnava
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | | | - Dieter Braun
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Hendrik Dietz
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Job Boekhoven
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany,
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52
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Minkner R, Boonyakida J, Park EY, Wätzig H. Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks? Electrophoresis 2022; 43:2402-2427. [PMID: 36285667 DOI: 10.1002/elps.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.
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Affiliation(s)
- Robert Minkner
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jirayu Boonyakida
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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53
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Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
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Affiliation(s)
- Xiuhai Mao
- 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
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- 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
| | - Chunhai Fan
- 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
| | - 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
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54
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Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. SCIENCE ADVANCES 2022; 8:eadd1830. [PMID: 36223466 PMCID: PMC9555772 DOI: 10.1126/sciadv.add1830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Membrane dynamics in living organisms can arise from proteins adhering to, assembling on, and exerting force on cell membranes. Programmable synthetic materials, such as self-assembled DNA nanostructures, offer the capability to drive membrane-remodeling events that resemble protein-mediated dynamics but with user-defined outcomes. An illustrative example is the tubular deformation of liposomes by DNA nanostructures with purposely designed shapes, surface modifications, and self-assembling properties. However, stimulus-responsive membrane tubulation mediated by DNA reconfiguration remains challenging. Here, we present the triggered formation of membrane tubes in response to specific DNA signals that actuate membrane-bound DNA clamps from an open state to various predefined closed states, releasing prestored energy to activate membrane deformation. We show that the timing and efficiency of vesicle tubulation, as well as the membrane tube widths, are modulated by the conformational change of DNA clamps, marking a solid step toward spatiotemporal control of membrane dynamics in an artificial system.
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Affiliation(s)
- Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chun Xie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Laboratoire de Physique de l’Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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55
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Mirzaiebadizi A, Ravan H, Dabiri S, Mohammadi P, Shahba A, Ziasistani M, Khatami M. An intelligent DNA nanorobot for detection of MiRNAs cancer biomarkers using molecular programming to fabricate a logic-responsive hybrid nanostructure. Bioprocess Biosyst Eng 2022; 45:1781-1797. [PMID: 36125526 DOI: 10.1007/s00449-022-02785-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022]
Abstract
Herein, we designed a DNA framework-based intelligent nanorobot using toehold-mediated strand displacement reaction-based molecular programming and logic gate operation for the selective and synchronous detection of miR21 and miR125b, which are known as significant cancer biomarkers. Moreover, to investigate the applicability of our design, DNA nanorobots were implemented as capping agents onto the pores of MSNs. These agents can develop a logic-responsive hybrid nanostructure capable of specific drug release in the presence of both targets. The prosperous synthesis steps were verified by FTIR, XRD, BET, UV-visible, FESEM-EDX mapping, and HRTEM analyses. Finally, the proper release of the drug in the presence of both target microRNAs was studied. This Hybrid DNA Nanostructure was designed with the possibility to respond to any target oligonucleotides with 22 nucleotides length.
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Affiliation(s)
- Amin Mirzaiebadizi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.,Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Shahriar Dabiri
- Department of Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Pourya Mohammadi
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Arezoo Shahba
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Ziasistani
- Department of Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrdad Khatami
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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56
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Colorimetric detection of viral RNA fragments based on an integrated logic-operated three-dimensional DNA walker. Biosens Bioelectron 2022; 217:114714. [PMID: 36116222 DOI: 10.1016/j.bios.2022.114714] [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: 07/20/2022] [Revised: 08/28/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Timely and accurate detection of virus is crucial for preventing spread of disease and early treatment of the infected cases. Herein we design an integrated logic-operated three-dimensional DNA walker for colorimetric detection of viral RNA fragments, by taking SARS-CoV-2 as an example. The DNA walker is composed of small amounts of dually-blocked walking strands and large amounts of dual-stem-loop track strands on gold nanoparticles. The walking strand contains a swing arm domain and a DNAzyme domain blocked at both sides of catalytic core, while the track strand contains a substrate domain located at the peripheral larger loop. Only the presence of both ORF1ab and N RNA fragments can fully de-block the walking strand, which then continuously hybridizes with track strands and cleaves them by DNAzyme-catalyzed hydrolysis. As the cleavage of track strands from long-stranded, double stem-loop structure to short-stranded, linear sequence, the DNA walker shows much lowered stability due to decreased negative charge density and diminished steric repulsion, which then gets aggregated at high salt concentration, accompanied by a visible color change. The colorimetric DNA walker detects RNA fragments down to 1 nM, responds dual viral genes in a "AND" logic way, and shows high specificity to target sequence. It can further detect large nucleic acids containing ORF1ab and N sequences, and reach 200 copies/mL detection limit by coupling a simple upstream amplification of sample. The method may provide a convenient way for reliable detection of viral RNA.
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57
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Rodgers MT, Seidu YS, Israel E. Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1697-1715. [PMID: 35921530 DOI: 10.1021/jasms.2c00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2'-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.
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Affiliation(s)
- M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Yakubu S Seidu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - E Israel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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58
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McCarte B, Yeung OT, Speakman AJ, Elfick A, Dunn KE. Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures. Biochem Biophys Rep 2022; 31:101293. [PMID: 35677630 PMCID: PMC9167695 DOI: 10.1016/j.bbrep.2022.101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/21/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes. Ultraviolet absorption spectroscopy can probe non-canonical DNA structures. Absorbance at 295 nm tends to increase as G-quadruplexes form. Four G-quartets are needed to form a quadruplex with less than 1 mM potassium. Formation of DNA triplexes can also yield a small change in UV spectra. UV absorption is a cheap label-free method for studying DNA nanoswitches.
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59
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Urso M, Pumera M. Micro‐ and Nanorobots Meet DNA. ADVANCED FUNCTIONAL MATERIALS 2022; 32. [DOI: 10.1002/adfm.202200711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 09/02/2023]
Abstract
AbstractDNA, the well‐known molecule that carries the genetic information of almost all forms of life, represents a pivotal element in formulating intelligent and versatile micro/nanorobotic systems. DNA‐functionalized micro/nanorobots have opened new and exciting opportunities in many research areas due to the synergistic combination of self‐propulsion at the micro/nanoscale and the high specificity and programmability of DNA interactions. Here, their designs and applications are critically reviewed, which span from the use of DNA as the fuel to chemotactically power nanorobots toward cancer cells to DNA as the main building block for sophisticated phototactic biorobots, DNA nanodevices to self‐monitor microrobots’ activity status, DNA and RNA sensing, nucleic acids isolation, gene therapy, and water purification. The perspective on future directions of the field is also shared, envisioning DNA‐mediated reconfigurable assemblies of nanorobotic swarms.
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Affiliation(s)
- Mario Urso
- Future Energy and Innovation Lab Central European Institute of Technology Brno University of Technology Purkyňova 656/123 612 00 Brno Czech Republic
| | - Martin Pumera
- Future Energy and Innovation Lab Central European Institute of Technology Brno University of Technology Purkyňova 656/123 612 00 Brno Czech Republic
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60
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Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chem Soc Rev 2022; 51:7631-7661. [PMID: 35975685 DOI: 10.1039/d2cs00317a] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO2 nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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61
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022; 61:e202208367. [DOI: 10.1002/anie.202208367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Nada Farag
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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62
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Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
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63
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Han LT, Sun GG, Ruan LS, Li X. Structured Aptamers: A Flourishing Nanomaterial for Tumor Targeting. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structured aptamers are nucleic acid systems produced using DNA nano self-assembly technology and can be constructed in a programmable manner. These aptamers are widely used in biomedical fields because of their low biological toxicity, weak immunogenicity, good cytocompatibility and
biocompatibility, stability, and facile modification ability. Additionally, structured aptamers achieve nano precision in spatial configuration and can be directly internalized into targets without the assistance of transfection reagents. They exhibit higher stability, rigidity, and binding
efficiency than aptamers alone. Therefore, structured aptamers have been universally applied in the tumor-targeting field and have emerged as a current research hotspot. Here, we introduce the assembly principle, assembly methods, and characterization methods of structured aptamers. Moreover,
the application status of structured aptamers for tumor detection and targeted therapy is summarized to provide new research directions for early diagnosis and drug research in the field of oncology.
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Affiliation(s)
- Li-Ting Han
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ge-Ge Sun
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Luo-Shan Ruan
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xin Li
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
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64
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A modular spring-loaded actuator for mechanical activation of membrane proteins. Nat Commun 2022; 13:3182. [PMID: 35902570 PMCID: PMC9334261 DOI: 10.1038/s41467-022-30745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells. Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.
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65
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Bai T, Zhang J, Huang K, Wang W, Chen B, Li Y, Zhao M, Zhang S, Zhu C, Liu D, Wei B. Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment. Nucleic Acids Res 2022; 50:8392-8398. [PMID: 35880584 PMCID: PMC9371897 DOI: 10.1093/nar/gkac606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Enzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration. A careful calibration of ligation efficiency is performed on structures with programmable nicks. Systematic investigation using comparative agarose gel electrophoresis enables quantitative assessment of enhanced survivability with ligation treatment on a number of unique structures. The solid ligation performance sets up the foundation for the ligation-based structural reconfiguration. With the capability of switching base pairing status between permanent and transient (ON and OFF) by a simple round of enzymatic treatment, ligation induced reconfiguration can be engineered for DNA nanostructures accordingly.
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Affiliation(s)
- Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Kai Huang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Bowen Chen
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mengyao Zhao
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Suoyu Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chenyou Zhu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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66
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Paluzzi V, Zhang C, Mao C. Assembly of Two-Dimensional DNA Arrays Could Influence the Formation of Their Component Tiles. Chembiochem 2022; 23:e202200306. [PMID: 35802389 PMCID: PMC9543644 DOI: 10.1002/cbic.202200306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Indexed: 11/07/2022]
Abstract
Tile-based DNA self-assembly is a powerful approach for nano-constructions. In this approach, individual DNA single strands first assemble into well-defined structural tiles, which, then, further associate with each other into final nanostructures. It is a general assumption that the lower-level structures (tiles) determines the higher-level, final structures. In this study, we present concrete experimental data to show that higher-level structures could, at least in the current example, also impact on the formation of lower-level structures. This study prompts questions such as: how general does this phenomenon exist in programmed DNA self-assembly and can we turn it into a useful tool for fine tuning DNA self-assembly?
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Affiliation(s)
| | | | - Chengde Mao
- Purdue University, Chemistry, 560 Oval Drive, 47907, West Lafayette, UNITED STATES
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67
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Hou S, Hasnat M, Chen Z, Liu Y, Faran Ashraf Baig MM, Liu F, Chen Z. Application Perspectives of Nanomedicine in Cancer Treatment. Front Pharmacol 2022; 13:909526. [PMID: 35860027 PMCID: PMC9291274 DOI: 10.3389/fphar.2022.909526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer is a disease that seriously threatens human health. Based on the improvement of traditional treatment methods and the development of new treatment modes, the pattern of cancer treatment is constantly being optimized. Nanomedicine plays an important role in these evolving tumor treatment modalities. In this article, we outline the applications of nanomedicine in three important tumor-related fields: chemotherapy, gene therapy, and immunotherapy. According to the current common problems, such as poor targeting of first-line chemotherapy drugs, easy destruction of nucleic acid drugs, and common immune-related adverse events in immunotherapy, we discuss how nanomedicine can be combined with these treatment modalities, provide typical examples, and summarize the advantages brought by the application of nanomedicine.
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Affiliation(s)
- Shanshan Hou
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
| | - Muhammad Hasnat
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ziwei Chen
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
| | - Yinong Liu
- Hospital Laboratory of Nangjing Lishui People’s Hospital, Nangjing, China
| | - Mirza Muhammad Faran Ashraf Baig
- Laboratory of Biomedical Engineering for Novel Bio-functional, and Pharmaceutical Nanomaterials, Prince Philip Dental Hospital, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fuhe Liu
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
- *Correspondence: Zelong Chen, ; Fuhe Liu,
| | - Zelong Chen
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Province Engineering Research Center of Artificial Intelligence and Internet of Things Wise Medical, Zhengzhou, China
- *Correspondence: Zelong Chen, ; Fuhe Liu,
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68
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Zheng M, Li Z, Zhang C, Seeman NC, Mao C. Powering ≈50 µm Motion by a Molecular Event in DNA Crystals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200441. [PMID: 35389546 DOI: 10.1002/adma.202200441] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/04/2022] [Indexed: 06/14/2023]
Abstract
A major challenge in material design is to couple nanoscale molecular and supramolecular events into desired chemical, physical, and mechanical properties at the macroscopic scale. Here, a novel self-assembled DNA crystal actuator is reported, which has reversible, directional expansion and contraction for over 50 μm in response to versatile stimuli, including temperature, ionic strength, pH, and redox potential. The macroscopic actuation is powered by cooperative dissociation or cohesion of thousands of DNA sticky ends at the designed crystal contacts. The increase in crystal porosity and cavity in the expanded state dramatically enhances the crystal capability to accommodate/encapsulate nanoparticles/proteins, while the contraction enables a "sponge squeezing" motion for releasing nanoparticles. This crystal actuator is envisioned to be useful for a wide range of applications, including powering self-propelled robotics, sensing subtle environmental changes, constructing functional hybrid materials, and working in drug controlled-release systems.
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Affiliation(s)
- Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhe Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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69
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Abstract
To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6-8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9-12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.
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70
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nada Farag
- Universita degli Studi di Roma Tor Vergata Chemistry ITALY
| | | | | | - Francesco Ricci
- University of Rome, Tor Vergata Department of Chemistry Via della Ricerca Scientifica 00133 Rome ITALY
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71
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Unksov IN, Korosec CS, Surendiran P, Verardo D, Lyttleton R, Forde NR, Linke H. Through the Eyes of Creators: Observing Artificial Molecular Motors. ACS NANOSCIENCE AU 2022; 2:140-159. [PMID: 35726277 PMCID: PMC9204826 DOI: 10.1021/acsnanoscienceau.1c00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
![]()
Inspired by molecular
motors in biology, there has been significant
progress in building artificial molecular motors, using a number of
quite distinct approaches. As the constructs become more sophisticated,
there is also an increasing need to directly observe the motion of
artificial motors at the nanoscale and to characterize their performance.
Here, we review the most used methods that tackle those tasks. We
aim to help experimentalists with an overview of the available tools
used for different types of synthetic motors and to choose the method
most suited for the size of a motor and the desired measurements,
such as the generated force or distances in the moving system. Furthermore,
for many envisioned applications of synthetic motors, it will be a
requirement to guide and control directed motions. We therefore also
provide a perspective on how motors can be observed on structures
that allow for directional guidance, such as nanowires and microchannels.
Thus, this Review facilitates the future research on synthetic molecular
motors, where observations at a single-motor level and a detailed
characterization of motion will promote applications.
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Affiliation(s)
- Ivan N. Unksov
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Chapin S. Korosec
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | | | - Damiano Verardo
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
- AlignedBio AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Roman Lyttleton
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Nancy R. Forde
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | - Heiner Linke
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
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72
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Zhou K, Mei Z, Lei Y, Guan Z, Mao C, Li Y. Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement. Chembiochem 2022; 23:e202200138. [PMID: 35676202 DOI: 10.1002/cbic.202200138] [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: 03/10/2022] [Revised: 06/08/2022] [Indexed: 11/11/2022]
Abstract
Cations such as divalent magnesium ion (Mg2+ ) play an essential role in DNA self-assembly. However, the strong electrostatic shielding effect of Mg2+ would be disadvantageous in some situations that require relatively weak interactions to allow a highly reversible error-correcting mechanism in the process of assembly. Herein, by substituting the conventional divalent Mg2+ with monovalent sodium ion (Na+ ), we have achieved one-pot high-yield assembly of tile-based DNA polyhedra at micromolar concentration of tiles, at least 10 times higher than the DNA concentrations reported previously. This strategy takes advantage of coexisting counterions and is expected to surmount the major obstacle to potential applications of such DNA nanostructures: large-scale production.
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Affiliation(s)
- Kaixuan Zhou
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhichao Mei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Yunxiang Lei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhen Guan
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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73
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Hübner K, Raab M, Bohlen J, Bauer J, Tinnefeld P. Salt-induced conformational switching of a flat rectangular DNA origami structure. NANOSCALE 2022; 14:7898-7905. [PMID: 35587049 DOI: 10.1039/d1nr07793g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A rectangular DNA origami structure is one of the most studied and often used motif for applications in DNA nanotechnology. Here, we present two assays to study structural changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA origami structure induced by bivalent cations such as magnesium or calcium. First, we applied one-color and two-color superresolution DNA-PAINT with protruding strands along the long edges of the DNA origami rectangle. At increasing salt concentration, a single line instead of two lines is observed as a first indicator of rolling-up. Two-color measurements also revealed different conformations with parallel and angled edges. Second, we placed a gold nanoparticle and a dye molecule at different positions on the DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle reports on dynamic transitions as well as it provides evidence that the rolling-up occurs preferentially along the diagonal of the DNA origami rectangle. The results will be helpful to test DNA structural models and the assays presented will be useful to study further structural transitions in DNA nanotechnology.
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Affiliation(s)
- Kristina Hübner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Mario Raab
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
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74
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Cao S, Wang F, Wang L, Fan C, Li J. DNA nanotechnology-empowered finite state machines. NANOSCALE HORIZONS 2022; 7:578-588. [PMID: 35502877 DOI: 10.1039/d2nh00060a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A finite state machine (FSM, or automaton) is an abstract machine that can switch among a finite number of states in response to temporally ordered inputs, which allows storage and processing of information in an order-sensitive manner. In recent decades, DNA molecules have been actively exploited to develop information storage and nanoengineering materials, which hold great promise for smart nanodevices and nanorobotics under the framework of FSM. In this review, we summarize recent progress in utilizing DNA self-assembly and DNA nanostructures to implement FSMs. We describe basic principles for representative DNA FSM prototypes and highlight their advantages and potential in diverse applications. The challenges in this field and future directions have also been discussed.
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Affiliation(s)
- Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- 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.
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200127, China
| | - Chunhai Fan
- 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.
| | - Jiang Li
- 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.
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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75
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Tian T, Li Y, Lin Y. Prospects and challenges of dynamic DNA nanostructures in biomedical applications. Bone Res 2022; 10:40. [PMID: 35606345 PMCID: PMC9125017 DOI: 10.1038/s41413-022-00212-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 02/08/2023] Open
Abstract
The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yanjing Li
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin, 300070, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China.
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76
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Rothenbühler S, Gonzalez A, Iacovache I, Langenegger SM, Zuber B, Häner R. Tetraphenylethylene-DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles. Org Biomol Chem 2022; 20:3703-3707. [PMID: 35262542 PMCID: PMC9092531 DOI: 10.1039/d2ob00357k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow monitoring the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology. The supramolecular assembly of tetraphenylethylene (TPE)–DNA conjugates is presented. The length of the TPE sticky ends exerts a pronounced effect on the formation of aggregation-induced emission (AIE)-active vesicles.![]()
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Affiliation(s)
- Simon Rothenbühler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Adrian Gonzalez
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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77
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Majikes JM, Zwolak M, Liddle JA. Best practice for improved accuracy: a critical reassessment of van't Hoff analysis of melt curves. Biophys J 2022; 121:1986-2001. [PMID: 35546781 DOI: 10.1016/j.bpj.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Biomolecular thermodynamics, particularly for DNA, are frequently determined via van't Hoff analysis of optically-measured melt curves. Accurate and precise values of thermodynamic parameters are essential for the modelling of complex systems involving cooperative effects, such as RNA tertiary structure and DNA origami because the uncertainties associated with each motif in a folding energy landscape can compound, significantly reducing the power of predictive models. We follow the sources of uncertainty as they propagate through a typical van't Hoff analysis to derive best practices for melt experiments and subsequent data analysis, assuming perfect signal baseline correction. With appropriately designed experiments and analysis, a van't Hoff approach can provide surprisingly high precision, e.g., enthalpies may be determined with a precision as low as a 10-2 kJ∙mol-1 for an 8 base DNA oligomer.
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Affiliation(s)
- Jacob M Majikes
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Michael Zwolak
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J Alexander Liddle
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland.
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78
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Hao P, Niu L, Luo Y, Wu N, Zhao Y. Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology. Chempluschem 2022; 87:e202200074. [PMID: 35604011 DOI: 10.1002/cplu.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Pengyan Hao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Liqiong Niu
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Yuanyuan Luo
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Na Wu
- Xi'an Jiaotong University School of Life Science and Technology No.28, West Xianning Road 710049 Xi'an CHINA
| | - Yongxi Zhao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
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79
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Ahn SY, Kim J, Vellampatti S, Oh S, Lim YT, Park SH, Luo D, Chung J, Um SH. Protein-Encoding Free-Standing RNA Hydrogel for Sub-Compartmentalized Translation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2110424. [PMID: 35263477 DOI: 10.1002/adma.202110424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/20/2022] [Indexed: 06/14/2023]
Abstract
RNA can self-fold into complex structures that can serve as major biological regulators in protein synthesis and in catalysis. Due to the abundance of structural primitives and functional diversity, RNA has been utilized for designing nature-defined goals despite its intrinsic chemical instability and lack of technologies. Here, a robust, free-standing RNA hydrogel is developed through a sequential process involving both ligation and rolling circle transcription to form RNA G-quadruplexes, capable of both catalytic activity and enhancing expression of several proteins in sub-compartmentalized, phase-separated translation environments. The observations suggest that this hydrogel will expand RNA research and impact practical RNA principles and applications.
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Affiliation(s)
- So Yeon Ahn
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | - Jeonghun Kim
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | | | - Sung Oh
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | - Yong Taik Lim
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
| | - Sung Ha Park
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Department of Physics, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Soong Ho Um
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
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80
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Programming a DNA tetrahedral nanomachine as an integrative tool for intracellular microRNA biosensing and stimulus-unlocked target regulation. Mater Today Bio 2022; 15:100276. [PMID: 35711289 PMCID: PMC9194454 DOI: 10.1016/j.mtbio.2022.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/22/2022]
Abstract
The synchronous detection and regulation of microRNAs (miRNAs) are essential for the early tumor diagnosis and treatment but remains a challenge. An integrative DNA tetrahedral nanomachine was self-assembled for sensitive detection and negative feedback regulation of intracellular miRNAs. This nanomachine comprised a DNA tetrahedron nanostructure as the framework, and a miRNA inhibitor-controlled allosteric DNAzyme as the core. The DNA tetrahedron brought the DNAzyme and the substrate in spatial proximity and facilitated the cellular uptake of DNAzyme. In allosteric regulation of DNAzyme, the locked tetrahedral DNAzyme (L-tetra-D) and active tetrahedral DNAzyme (A-Tetra-D) were controlled by miRNA inhibitor. The combination of miRNA inhibitor and target could trigger the conformational change from L-tetra-D to A-Tetra-D. A-Tetra-D cleaved the substrate and released fluorescence for intracellular miRNA biosensing. The DNA tetrahedral nanomachine showed excellent sensitivity (with detection limit down to 0.77 pM), specificity (with one-base mismatch discrimination), biocompatibility and stability. Simultaneously, miRNA stimulus-unlocked inhibitor introduced by our nanomachine exhibited the synchronous regulation of target cells, of which regulatory performance has been verified by the upregulated levels of downstream genes/proteins and the increased cellular apoptosis. Our study demonstrated that the DNA tetrahedral nanomachine is a promising biosense-and-treat tool for the synchronous detection and regulation of intracellular miRNA, and is expected to be applied in the early diagnosis and tailored management of cancers.
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81
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Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [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: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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82
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Dong J, Ouyang Y, Wang J, O’Hagan MP, Willner I. Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks. ACS NANO 2022; 16:6153-6164. [PMID: 35294174 PMCID: PMC9047661 DOI: 10.1021/acsnano.1c11631] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Michael P. O’Hagan
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
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83
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Courbet A, Hansen J, Hsia Y, Bethel N, Park YJ, Xu C, Moyer A, Boyken S, Ueda G, Nattermann U, Nagarajan D, Silva D, Sheffler W, Quispe J, Nord A, King N, Bradley P, Veesler D, Kollman J, Baker D. Computational design of mechanically coupled axle-rotor protein assemblies. Science 2022; 376:383-390. [PMID: 35446645 PMCID: PMC10712554 DOI: 10.1126/science.abm1183] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo-electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.
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Affiliation(s)
- A. Courbet
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Hansen
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Y. Hsia
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - N. Bethel
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - YJ. Park
- Department of Biochemistry, University of Washington, Seattle, USA
| | - C. Xu
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - A. Moyer
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - S.E. Boyken
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - G. Ueda
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - U. Nattermann
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Nagarajan
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - D. Silva
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Monod Bio, Inc, Seattle, USA
| | - W. Sheffler
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - J. Quispe
- Department of Biochemistry, University of Washington, Seattle, USA
| | - A. Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - N. King
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - P. Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - D. Veesler
- Department of Biochemistry, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
| | - J. Kollman
- Department of Biochemistry, University of Washington, Seattle, USA
| | - D. Baker
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, USA
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84
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Jiang C, Lu B, Zhang W, Ohayon YP, Feng F, Li S, Seeman NC, Xiao SJ. Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist. J Am Chem Soc 2022; 144:6759-6769. [PMID: 35385657 DOI: 10.1021/jacs.1c13601] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The overwinding and underwinding of DNA duplexes between junctions have been used in designing left- and right-handed DNA origami nanostructures, respectively. For DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the tiles has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile's intrinsic curvature in DNA nanostructures have so far never been addressed. In this work, we designed three types of tile cores built around a circular scaffold using three- and four-branched junctions. Joining the tile cores with arms having two kinds of inter-tile distances, an odd and an even number of DNA half-turns, tended to form planar 2D lattices and tubes, respectively. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the tubes and thereby the tile conformation of dihedrals with addressable faces. DNA tubes with either right- or left-handed chirality were obtained by the coupling of the intrinsic curvature of the tiles with the arm twist. We were able to assign the chiral indices (n,m) to a tube with its structure resolved by AFM at the single-tile level and therefore to estimate the global curvature of the tube (or its component tile) using a regular polygon model that approximated its transverse section. A deeper understanding of the integrated actions of different types of twisting forces on DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.
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Affiliation(s)
- Chuan Jiang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shijie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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85
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Zhao J, Guo Y, Li Q, Chen J, Niu D, Liu J. Reconstruction of a Cofactor Self-Sufficient Whole-Cell Biocatalyst System for Efficient Biosynthesis of Allitol from d-Glucose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3775-3784. [PMID: 35298165 DOI: 10.1021/acs.jafc.2c00440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The combined catalysis of glucose isomerase (GI), d-psicose 3-epimerase (DPEase), ribitol dehydrogenase (RDH), and formate dehydrogenase (FDH) provides a convenient route for the biosynthesis of allitol from d-glucose; however, the low catalytic efficiency restricts its industrial applications. Here, the supplementation of 0.32 g/L NAD+ significantly promoted the cell catalytic activity by 1.18-fold, suggesting that the insufficient intracellular NAD(H) content was a limiting factor in allitol production. Glucose dehydrogenase (GDH) with 18.13-fold higher activity than FDH was used for reconstructing a cofactor self-sufficient system, which was combined with the overexpression of the rate-limiting genes involved in NAD+ salvage metabolic flow to expand the available intracellular NAD(H) pool. Then, the multienzyme self-assembly system with SpyTag and SpyCatcher effectively channeled intermediates, leading to an 81.1% increase in allitol titer to 15.03 g/L from 25 g/L d-glucose. This study provided a facilitated strategy for large-scale and efficient biosynthesis of allitol from a low-cost substrate.
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Affiliation(s)
- Jingyi Zhao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yan Guo
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Qiufeng Li
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jing Chen
- South Subtropical Agricultural Scientific Research Institute of Guangxi, Longzhou, Guangxi 532415, China
| | - Debao Niu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jidong Liu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
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86
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Chang X, Yang Q, Lee J, Zhang F. Self-Assembled Nucleic Acid Nanostructures for Biomedical Applications. Curr Top Med Chem 2022; 22:652-667. [PMID: 35319373 DOI: 10.2174/1568026622666220321140729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Structural DNA nanotechnology has been developed into a powerful method for creating self-assembled nanomaterials. Their compatibility with biosystems, nanoscale addressability, and programmable dynamic features make them appealing candidates for biomedical research. This review paper focuses on DNA self-assembly strategies and designer nanostructures with custom functions for biomedical applications. Specifically, we review the development of DNA self-assembly methods, from simple DNA motifs consisting of a few DNA strands to complex DNA architectures assembled by DNA origami. Three advantages are discussed using structural DNA nanotechnology for biomedical applications: (1) precise spatial control, (2) molding and guiding other biomolecules, and (3) using reconfigurable DNA nanodevices to overcome biomedical challenges. Finally, we discuss the challenges and opportunities of employing DNA nanotechnology for biomedical applications, emphasizing diverse assembly strategies to create a custom DNA nanostructure with desired functions.
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Affiliation(s)
- Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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87
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Chen X, Cui W, Liu Z, Ma W, Yang X, Tian T, Yang Y, Xie Y, Liu Y, Lin Y. Positive Neuroplastic Effect of DNA Framework Nucleic Acids on Neuropsychiatric Diseases. ACS MATERIALS LETTERS 2022. [DOI: 10.1021/acsmaterialslett.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xingyu Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weitong Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xiao Yang
- Psychiatric Laboratory and Mental Health Centre, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuting Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yu Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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88
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An X, Meng Z, Wang Y, Sun J. Design of a Single-Channel Chaotic Secure Communication System Implemented by DNA Strand Displacement. ACS Synth Biol 2022; 11:843-854. [PMID: 35089690 DOI: 10.1021/acssynbio.1c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA strand displacement (DSD) is regarded as a foundation for the construction of biological computing systems because of the predictability of DNA molecular behaviors. Some complex system dynamics can be approximated by cascading DSD reaction modules with different functions. In this paper, four DSD reaction modules are used to realize chaotic secure communication based on drive-response synchronization of four-dimensional chaotic systems. The system adopts the communication technology of chaos masking and uses a single-channel synchronization scheme to achieve high accuracy. The simulation results demonstrate that encryption and decryption of the signal are achieved by the design. Moreover, the system is robust to noise signals and interference during the DNA reactions. This work provides a method for the application of DNA molecular computation in the communication field.
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Affiliation(s)
- Xiaoyu An
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Zijie Meng
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yanfeng Wang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Junwei Sun
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
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89
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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90
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Fabrini G, Minard A, Brady RA, Di Antonio M, Di Michele L. Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures. NANO LETTERS 2022; 22:602-611. [PMID: 35026112 PMCID: PMC8796241 DOI: 10.1021/acs.nanolett.1c03314] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.
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Affiliation(s)
- Giacomo Fabrini
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Aisling Minard
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Ryan A. Brady
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Marco Di Antonio
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Lorenzo Di Michele
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
- Department
of Physics—Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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91
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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.
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92
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Xiang Z, Zhao J, Qu J, Song J, Li L. A Multivariate‐Gated DNA Nanodevice for Spatioselective Imaging of Pro‐metastatic Targets in Extracellular Microenvironment. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhichu Xiang
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Junle Qu
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
| | - Jun Song
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
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93
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DNA-Based Molecular Engineering of the Cell Membrane. MEMBRANES 2022; 12:membranes12020111. [PMID: 35207033 PMCID: PMC8876765 DOI: 10.3390/membranes12020111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 01/27/2023]
Abstract
The cell membrane serves as a barrier and gatekeeper to regulate the cellular transportation of substances and information. It plays a significant role in protecting the cell from the extracellular environment, maintaining intracellular homeostasis, and regulating cellular function and behaviors. The capability to engineer the cell membrane with functional modules that enable dynamic monitoring and manipulating the cell-surface microenvironment would be critical for studying molecular mechanisms underlying various biological processes. To meet this goal, DNA, with intrinsic advantages of high versatility, programmability, and biocompatibility, has gained intense attention as a molecular tool for cell-surface engineering. The past three decades have witnessed the rapid advances of diverse nucleic acid materials, including functional nucleic acids (FNAs), dynamic DNA circuits, and exquisite DNA nanostructures. In this mini review, we have summarized the recent progress of DNA technology for cell membrane engineering, particularly focused on their applications for molecular sensing and imaging, precise cell identification, receptor activity regulation, and artificial membrane structures. Furthermore, we discussed the challenge and outlook on using nucleic acid materials in this specific research area.
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94
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Zhang C, Yuan Y, Wu K, Wang Y, Zhu S, Shi J, Wang L, Li Q, Zuo X, Fan C, Chang C, Li J. Driving DNA Origami Assembly with a Terahertz Wave. NANO LETTERS 2022; 22:468-475. [PMID: 34968055 DOI: 10.1021/acs.nanolett.1c04369] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Terahertz (THz) waves show nontrivial interactions with living systems, but the underlying molecular mechanisms have yet to be explored. Here, we employ DNA origami as a model system to study the interactions between THz waves and DNA structures. We find that a 3-min THz illumination (35.2 THz) can drive the unwinding of DNA duplexes at ∼10 °C below their melting point. Computational study reveals that the THz wave can resonate with the vibration of DNA bases, provoking the hydrogen bond breaking. The cooperation of thermal and nonthermal effects allows the unfolding of undesired secondary structures and the THz illumination can generate diverse DNA origami assemblies with the yield (>80%) ∼ 4-fold higher than that by the contact heating at similar temperatures. We also demonstrate the in situ assembly of DNA origami in cell lysate. This method enables remotely controllable assembly of intact biomacromolecules, providing new insight into the bioeffects of THz waves.
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Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yifang Yuan
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 700071, China
| | - Kaijie Wu
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shitai Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics, Peking University, Beijing 100084, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
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95
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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96
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Chen L, Zhang J, Lin Z, Zhang Z, Mao M, Wu J, Li Q, Zhang Y, Fan C. Pharmaceutical applications of framework nucleic acids. Acta Pharm Sin B 2022; 12:76-91. [PMID: 35127373 PMCID: PMC8799870 DOI: 10.1016/j.apsb.2021.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023] Open
Abstract
DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.
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Affiliation(s)
- Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziyan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qian Li
- 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
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chunhai Fan
- 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
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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97
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Li K, Carroll M, Vafabakhsh R, Wang XA, Wang JP. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3142-3154. [PMID: 35288750 PMCID: PMC8989542 DOI: 10.1093/nar/gkac162] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.
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Affiliation(s)
- Keren Li
- Department of Statistics, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Matthew Carroll
- Weinberg College IT Solutions (WITS), Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaozhong A Wang
- Correspondence may also be addressed to Xiaozhong A. Wang. Tel: +1 847 467 4897;
| | - Ji-Ping Wang
- To whom correspondence should be addressed. Tel: +1 847 467 6896;
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98
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Zhai T, Sun C, Ye D, Xia K, Liu X, Fan C, Li Q, Shen J. Electrochemically driven assembly of framework nucleic acids. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2021.115901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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99
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Engelen W, Sigl C, Kadletz K, Willner EM, Dietz H. Antigen-Triggered Logic-Gating of DNA Nanodevices. J Am Chem Soc 2021; 143:21630-21636. [PMID: 34927433 PMCID: PMC8719334 DOI: 10.1021/jacs.1c09967] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Synthetic nanoscale
devices that reconfigure dynamically in response
to physiological stimuli could offer new avenues for diagnostics and
therapy. Here, we report a strategy for controlling the state of DNA
nanodevices based on sensing antigens with IgG antibodies. To this
end, we use IgG antibodies as structural elements to kinetically trap
reconfigurable DNA origami structures in metastable states. Addition
of soluble antigens displace the IgGs from the objects and triggers
reconfiguration. We demonstrate this mechanism by antigen-triggered
disassembly of DNA origami shells for two different IgGs and their
cognate antigens, and we determined the corresponding dose response
curves. We also describe the logic-gated actuation of DNA objects
with combinations of antigens, as demonstrated with AND-type shells
that disassemble only when two different antigens are detected simultaneously.
We apply our system for the antigen-triggered release of molecular
payload as exemplified by the release of virus particles that we loaded
into the DNA origami shells. We expect our approach to be applicable
in many types of DNA nanostructures and with many other IgG-antigen
combinations.
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Affiliation(s)
- Wouter Engelen
- Laboratory for Biomolecular Nanotechnology, Physics Department, Technical University of Munich, Garching near Munich 85748, Germany.,Munich Institute of Biomedical Engineering, Technical University of Munich, Garching near Munich 85748, Germany
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Physics Department, Technical University of Munich, Garching near Munich 85748, Germany.,Munich Institute of Biomedical Engineering, Technical University of Munich, Garching near Munich 85748, Germany
| | - Karoline Kadletz
- Laboratory for Biomolecular Nanotechnology, Physics Department, Technical University of Munich, Garching near Munich 85748, Germany.,Munich Institute of Biomedical Engineering, Technical University of Munich, Garching near Munich 85748, Germany
| | - Elena M Willner
- Laboratory for Biomolecular Nanotechnology, Physics Department, Technical University of Munich, Garching near Munich 85748, Germany.,Munich Institute of Biomedical Engineering, Technical University of Munich, Garching near Munich 85748, Germany
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Physics Department, Technical University of Munich, Garching near Munich 85748, Germany.,Munich Institute of Biomedical Engineering, Technical University of Munich, Garching near Munich 85748, Germany
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100
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Lee JY, Kim M, Lee C, Kim DN. Characterizing and Harnessing the Mechanical Properties of Short Single-Stranded DNA in Structured Assemblies. ACS NANO 2021; 15:20430-20441. [PMID: 34870958 DOI: 10.1021/acsnano.1c08861] [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: 06/13/2023]
Abstract
Precise engineering of DNA structures is of growing interest to solve challenging problems in biomolecular applications and beyond. The introduction of single-stranded DNA (ssDNA) into the DNA structure can play a pivotal role in providing high controllability of critical structural features. Herein, we present a computational model of ssDNA with structural applications to harness its characteristics. The nonlinear properties of nucleotide gaps are systematically characterized to construct a structural model of the ssDNA across length scales with the incorporation of a finite element framework. The proposed method shows the programmability of structural bending, twisting, and persistence length by implementing the ssDNA in various DNA structures with experimental validation. Our results have significant implications for DNA nanotechnology in expanding the boundary of design and analysis of structural shape and stiffness.
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Affiliation(s)
- Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Myoungseok Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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