1
|
Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
Collapse
Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
2
|
Hooe SL, Smith AD, Dean SN, Breger JC, Ellis GA, Medintz IL. Multienzymatic Cascades and Nanomaterial Scaffolding-A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309963. [PMID: 37944537 DOI: 10.1002/adma.202309963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Indexed: 11/12/2023]
Abstract
Synthetic biology is touted as the next industrial revolution as it promises access to greener biocatalytic syntheses to replace many industrial organic chemistries. Here, it is shown to what synthetic biology can offer in the form of multienzyme cascades for the synthesis of the most basic of new materials-chemicals, including especially designer chemical products and their analogs. Since achieving this is predicated on dramatically expanding the chemical space that enzymes access, such chemistry will probably be undertaken in cell-free or minimalist formats to overcome the inherent toxicity of non-natural substrates to living cells. Laying out relevant aspects that need to be considered in the design of multi-enzymatic cascades for these purposes is begun. Representative multienzymatic cascades are critically reviewed, which have been specifically developed for the synthesis of compounds that have either been made only by traditional organic synthesis along with those cascades utilized for novel compound syntheses. Lastly, an overview of strategies that look toward exploiting bio/nanomaterials for accessing channeling and other nanoscale materials phenomena in vitro to direct novel enzymatic biosynthesis and improve catalytic efficiency is provided. Finally, a perspective on what is needed for this field to develop in the short and long term is presented.
Collapse
Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, Washington, DC, 20001, USA
| | - Aaron D Smith
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Scott N Dean
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| |
Collapse
|
3
|
Kannappan S, Jo K, Kim KK, Lee JH. Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review. Int J Biol Macromol 2024; 256:128427. [PMID: 38016615 DOI: 10.1016/j.ijbiomac.2023.128427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023]
Abstract
Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.
Collapse
Affiliation(s)
- Shrute Kannappan
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Mapo-gu, Seoul 04107, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| |
Collapse
|
4
|
Bekkouche I, Kuznetsova MN, Rejepov DT, Vetcher AA, Shishonin AY. Recent Advances in DNA Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2449. [PMID: 37686956 PMCID: PMC10490369 DOI: 10.3390/nano13172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.
Collapse
Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Maria N. Kuznetsova
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Dovlet T. Rejepov
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| |
Collapse
|
5
|
Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
Collapse
Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
| |
Collapse
|
6
|
Ban Ž, Barišić A, Crnolatac I, Kazazić S, Škulj S, Savini F, Bertoša B, Barišić I, Piantanida I. Highly selective preparation of N-terminus Horseradish peroxidase-DNA conjugate with fully retained enzymatic activity: HRP-DNA structure - activity relation. Enzyme Microb Technol 2023; 168:110257. [PMID: 37209508 DOI: 10.1016/j.enzmictec.2023.110257] [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: 01/24/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Within the last decade, the field of bio-nanoengineering has achieved significant advances allowing us to generate, e.g., nanoscaled molecular machineries with arbitrary shapes. To unleash the full potential of novel methods such as DNA origami technology, it is important to functionalise complex molecules and nanostructures precisely. Thus, considerable attention has been given to site-selective modifications of proteins allowing further incorporation of various functionalities. Here, we describe a method for the covalent attachment of oligonucleotides to the glycosylated horseradish peroxidase protein (HRP) with high N-terminus selectivity and significant yield while conserving the enzymatic activity. This two-step process includes a pH-controlled metal-free diazotransfer reaction using imidazole-1-sulfonyl azide hydrogen sulfate, which at pH 8.5 results in an N-terminal azide-functionalized protein, followed by the Cu-free click SPAAC reaction to dibenzocyclooctyne- (DBCO) modified oligonucleotides. The reaction conditions were optimised to achieve maximum yield and the best performance. The resulting protein-oligonucleotide conjugates (HRP-DNA) were characterised by electrophoresis and mass spectrometry (MS). Native-PAGE experiments demonstrated different migration patterns for HRP-DNA and the azido-modified protein allowing zymogram experiments. Structure-activity relationships of novel HRP-DNA conjugates were assessed using molecular dynamics simulations, characterising the molecular interactions that define the structural and dynamical properties of the obtained protein-oligonucleotide conjugates (POC).
Collapse
Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Saša Kazazić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Ivan Barišić
- AIT Austrian Institute of Technology,Vienna, Austria.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
7
|
Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
Collapse
Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| |
Collapse
|
8
|
Adamczyk AK, Huijben TAPM, Sison M, Di Luca A, Chiarelli G, Vanni S, Brasselet S, Mortensen KI, Stefani FD, Pilo-Pais M, Acuna GP. DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation. ACS NANO 2022; 16:16924-16931. [PMID: 36065997 DOI: 10.1021/acsnano.2c06936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.
Collapse
Affiliation(s)
- Aleksandra K Adamczyk
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Teun A P M Huijben
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Miguel Sison
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Germán Chiarelli
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Kim I Mortensen
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQDCiudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHACiudad Autónoma de Buenos Aires, Argentina
| | - Mauricio Pilo-Pais
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| |
Collapse
|
9
|
Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
Collapse
|
10
|
Sheng J, Pi Y, Zhao S, Wang B, Chen M, Chang K. Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics. Trends Biotechnol 2022; 41:653-668. [PMID: 36117022 DOI: 10.1016/j.tibtech.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.
Collapse
Affiliation(s)
- Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Yan Pi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; College of Pharmacy and Laboratory Medicine, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
| |
Collapse
|
11
|
Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
Collapse
Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| |
Collapse
|
12
|
Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging.
Collapse
Affiliation(s)
- Anastasia A. Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, 141701, Russia
| | - Victor M. Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Valeria A. Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Georgiy Yu. Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| |
Collapse
|
13
|
The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
Collapse
|
14
|
Mariconti M, Morel M, Baigl D, Rudiuk S. Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density. Biomacromolecules 2021; 22:3431-3439. [PMID: 34260203 DOI: 10.1021/acs.biomac.1c00501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.
Collapse
Affiliation(s)
- Marina Mariconti
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| |
Collapse
|
15
|
Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
Collapse
Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| |
Collapse
|
16
|
Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020; 4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.
Collapse
Affiliation(s)
- Weitao Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - D. Sebastian Arias
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | |
Collapse
|
17
|
Lombardo D, Calandra P, Kiselev MA. Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments. Molecules 2020; 25:E5624. [PMID: 33260426 PMCID: PMC7730346 DOI: 10.3390/molecules25235624] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.
Collapse
Affiliation(s)
- Domenico Lombardo
- CNR-IPCF, Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- CNR-ISMN, Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Mikhail A. Kiselev
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980 Moscow, Russia;
| |
Collapse
|
18
|
Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
Collapse
Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
| |
Collapse
|
19
|
Abstract
Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.
Collapse
Affiliation(s)
- Sami Nummelin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| |
Collapse
|
20
|
Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
Collapse
Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| |
Collapse
|
21
|
Cross-linkage urease nanoparticles: a high-efficiency signal-generation tag for portable pH meter-based electrochemical immunoassay of lipocalin-2 protein diagnostics. Mikrochim Acta 2020; 187:485. [DOI: 10.1007/s00604-020-04466-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/25/2020] [Indexed: 12/20/2022]
|
22
|
Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
| |
Collapse
|
23
|
McCluskey JB, Clark DS, Glover DJ. Functional Applications of Nucleic Acid-Protein Hybrid Nanostructures. Trends Biotechnol 2020; 38:976-989. [PMID: 32818445 DOI: 10.1016/j.tibtech.2020.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/09/2023]
Abstract
Combining the diverse chemical functionality of proteins with the predictable structural assembly of nucleic acids has enabled the creation of hybrid nanostructures for a range of biotechnology applications. Through the attachment of proteins onto or within nucleic acid nanostructures, materials with dynamic capabilities can be created that include switchable enzyme activity, targeted drug delivery, and multienzyme cascades for biocatalysis. Investigations of difficult-to-study biological mechanisms have also been aided by using DNA-protein assemblies that mimic natural processes in a controllable manner. Furthermore, advances that enable the recombinant production and intracellular assembly of hybrid nanostructures have the potential to overcome the significant manufacturing cost that has limited the use of DNA and RNA nanotechnology.
Collapse
Affiliation(s)
- Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| |
Collapse
|
24
|
Lombardo D, Calandra P, Pasqua L, Magazù S. Self-assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E1048. [PMID: 32110877 PMCID: PMC7084717 DOI: 10.3390/ma13051048] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
In this paper, we survey recent advances in the self-assembly processes of novel functional platforms for nanomaterials and biomaterials applications. We provide an organized overview, by analyzing the main factors that influence the formation of organic nanostructured systems, while putting into evidence the main challenges, limitations and emerging approaches in the various fields of nanotechology and biotechnology. We outline how the building blocks properties, the mutual and cooperative interactions, as well as the initial spatial configuration (and environment conditions) play a fundamental role in the construction of efficient nanostructured materials with desired functional properties. The insertion of functional endgroups (such as polymers, peptides or DNA) within the nanostructured units has enormously increased the complexity of morphologies and functions that can be designed in the fabrication of bio-inspired materials capable of mimicking biological activity. However, unwanted or uncontrollable effects originating from unexpected thermodynamic perturbations or complex cooperative interactions interfere at the molecular level with the designed assembly process. Correction and harmonization of unwanted processes is one of the major challenges of the next decades and requires a deeper knowledge and understanding of the key factors that drive the formation of nanomaterials. Self-assembly of nanomaterials still remains a central topic of current research located at the interface between material science and engineering, biotechnology and nanomedicine, and it will continue to stimulate the renewed interest of biologist, physicists and materials engineers by combining the principles of molecular self-assembly with the concept of supramolecular chemistry.
Collapse
Affiliation(s)
- Domenico Lombardo
- Consiglio Nazionale delle Ricerche, Istituto per i Processi Chimico-Fisici, 98158 Messina, Italy
| | - Pietro Calandra
- Consiglio Nazionale delle Ricerche, Istituto Studio Materiali Nanostrutturati, 00015 Roma, Italy;
| | - Luigi Pasqua
- Department of Environmental and Chemical Engineering, University of Calabria, 87036 Rende, Italy;
| | - Salvatore Magazù
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, 98166 Messina, Italy;
| |
Collapse
|
25
|
At the Dawn of Applied DNA Nanotechnology. Molecules 2020; 25:molecules25030639. [PMID: 32028556 PMCID: PMC7036935 DOI: 10.3390/molecules25030639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 11/25/2022] Open
|