1
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Jampani VSR, Škarabot M, Mur U, Baigl D, Jonas U, Lagerwall JPF, Ravnik M, Anyfantakis M. Water-Templated Growth of Interfacial Superglue Polymers for Tunable Thin Films and In Situ Fluid Encapsulation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2408243. [PMID: 39188202 DOI: 10.1002/adma.202408243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/02/2024] [Indexed: 08/28/2024]
Abstract
Thin polymer films (TPFs) are indispensable elements in numerous technologies ranging from liquid encapsulation to biotechnology to electronics. However, their production typically relies on wet chemistry involving organic solvents or chemical vapor deposition, necessitating elaborate equipment and often harsh conditions. Here, an eco-friendly, fast, and facile synthesis of water-templated interfacial polymers based on cyanoacrylates (superglues, CAs) that yield thin films with tailored properties is demonstrated. Specifically, by exposing a cationic surfactant-laden water surface to cyanoacrylate vapors, surfactant-modulated anionic polymerization produces a manipulable thin polymer film with a thickness growth rate of 8 nm min-1. Furthermore, the shape and color of the film are precisely controlled by the polymerization kinetics, wetting conditions, and/or exposure to patterned light. Using various interfaces as templates for film growth, including the free surface of drops and soap bubbles, the developed method advantageously enables in situ packaging of chemical and biological cargos in liquid phase as well as the encapsulation of gases within solidified bubbles. Simple, versatile, and biocompatible, this technology constitutes a potent platform for programmable coating and soft/smart encapsulation of fluids.
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Affiliation(s)
- Venkata S R Jampani
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg, L-1511, Luxembourg
- Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, 1000, Slovenia
| | - Miha Škarabot
- Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, 1000, Slovenia
| | - Urban Mur
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Ulrich Jonas
- Department of Chemistry and Biology, University of Siegen, D-57076, Siegen, Germany
| | - Jan P F Lagerwall
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg, L-1511, Luxembourg
| | - Miha Ravnik
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Manos Anyfantakis
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg, L-1511, Luxembourg
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2
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Maiti A, Daschakraborty S. Investigating the Influence of Photoswitchable Lipids on the Structure and Dynamics of Lipid Membranes: Fundamentals and Potential Applications. J Phys Chem B 2024. [PMID: 39066711 DOI: 10.1021/acs.jpcb.4c03004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In this work, we delve into the impact of photoisomerization of photoswitchable lipids (PSLs) on the membrane structure and dynamics at a molecular level. Through all-atom molecular dynamics simulations, we explore how UV irradiation-induced trans-to-cis isomerization of these lipids, particularly the azobenzene-derivatized phosphatidylcholine (AzoPC) lipid, influences the structure and dynamics of a simplified lipid membrane, mimicking those of E. coli bacteria across different temperatures. Our findings align with previous experimental observations regarding membrane properties and offer insights into localized effects and microscopic heterogeneity. Additionally, we estimate the relaxation time scale of the lipid membrane following AzoPC photoisomerization. Moreover, we demonstrate the feasibility of photoactivated drug release, exemplified by the controlled liberation of doxorubicin, an anticancer agent, through the membrane, suggesting the potential of PSLs in engineering photoactivated liposomes, coined as photoazosomes, for precise targeted drug delivery applications.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801106, India
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3
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Okamura H, Yao T, Nagatsugi F. Reversible Control of Gene Expression by Guest-Modified Adenosines in a Cell-Free System via Host-Guest Interaction. J Am Chem Soc 2024; 146:18513-18523. [PMID: 38941287 PMCID: PMC11240562 DOI: 10.1021/jacs.4c04262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/30/2024]
Abstract
Gene expression technology has become an indispensable tool for elucidating biological processes and developing biotechnology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host-guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand using a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility was fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled tight and reversible control of in vitro transcription and protein expression in the CFE system. This study marks the first utility of the host-guest interaction for gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nanotechnology.
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Affiliation(s)
- Hidenori Okamura
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Takeyuki Yao
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Fumi Nagatsugi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
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4
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Kumar A, Maiti A, Verma S, Daschakraborty S. How do Photoswitchable Lipids Influence the Intercalation of Anticancer Drug in Lipid Membrane? Investigation using Molecular Dynamics Simulation. Chem Asian J 2024:e202400416. [PMID: 38949780 DOI: 10.1002/asia.202400416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
Photoswitchable lipids, particularly azobenzene-derivatized phosphatidylcholine (azoPC) lipids, offer a unique mechanism for reversible modification of membrane properties upon exposure to ultraviolet (UV) radiation. Through all-atom molecular dynamics simulations, we explore how UV irradiation-induced trans-to-cis photoisomerization (TCPI) of AzoPC lipid influences the structure and dynamics of a lipid membrane, composed of dipalmitoylphosphatidylcholine (DPPC) and cholesterol with similar composition to that of the DOXIL®. Structural and dynamical analyses of two states of the membrane, 'dark' state (containing cis-azoPC lipid) and 'bright' state (containing 85 % cis-azoPC and 15 % trans-azoPC lipids) reveal that the TCPI reduces membrane packing density and increases diffusivity of lipids. We have demonstrated an enhanced intercalation of doxorubicin (DOX), an anticancer drug, in the 'bright' state of the membrane compared to that in the 'dark' state. This study - elucidating the complex interplay between lipid composition, photoswitching, and lipid-drug interactions - contributes to the design of lipid-based systems for targeted drug delivery and biomedical applications.
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Affiliation(s)
- Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India
| | - Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India
| | - Sahil Verma
- Department of Chemistry, Indian Institute of Technology Patna, Bihar, 801106, India
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5
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Abodja O, Touati N, Morel M, Rudiuk S, Baigl D. ATP/azobenzene-guanidinium self-assembly into fluorescent and multi-stimuli-responsive supramolecular aggregates. Commun Chem 2024; 7:142. [PMID: 38918507 PMCID: PMC11199595 DOI: 10.1038/s42004-024-01226-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Building stimuli-responsive supramolecular systems is a way for chemists to achieve spatio-temporal control over complex systems as well as a promising strategy for applications ranging from sensing to drug-delivery. For its large spectrum of biological and biomedical implications, adenosine 5'-triphosphate (ATP) is a particularly interesting target for such a purpose but photoresponsive ATP-based systems have mainly been relying on covalent modification of ATP. Here, we show that simply mixing ATP with AzoDiGua, an azobenzene-guanidium compound with photodependent nucleotide binding affinity, results in the spontaneous self-assembly of the two non-fluorescent compounds into photoreversible, micrometer-sized and fluorescent aggregates. Obtained in water at room temperature and physiological pH, these supramolecular structures are dynamic and respond to several chemical, physical and biological stimuli. The presence of azobenzene allows a fast and photoreversible control of their assembly. ATP chelating properties to metal dications enable ion-triggered disassembly and fluorescence control with valence-selectivity. Finally, the supramolecular aggregates are disassembled by alkaline phosphatase in a few minutes at room temperature, resulting in enzymatic control of fluorescence. These results highlight the interest of using a photoswitchable nucleotide binding partner as a self-assembly brick to build highly responsive supramolecular entities involving biological targets without the need to covalently modify them.
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Affiliation(s)
- Olivier Abodja
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Nadia Touati
- Chimie ParisTech, Université PSL, CNRS, Institut de Recherche de Chimie-Paris, PCMTH, 75005, Paris, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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6
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Ishii Y, Fukunaga K, Cooney A, Yokobayashi Y, Matsuura T. Switchable and orthogonal gene expression control inside artificial cells by synthetic riboswitches. Chem Commun (Camb) 2024; 60:5972-5975. [PMID: 38767578 DOI: 10.1039/d4cc00965g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Here we report two novel synthetic riboswitches that respond to ASP2905 and theophylline and function in reconstituted cell-free protein synthesis (CFPS) system. We encapsulated the CFPS system as well as DNA-templated encoding reporter genes regulated by these orthogonal riboswitches inside liposomes, and achieved switchable and orthogonal control over gene expression by external stimulation with the cognate ligands.
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Affiliation(s)
- Yuta Ishii
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Keisuke Fukunaga
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
| | - Aileen Cooney
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
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7
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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8
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Dohno C, Kimura M, Fujiwara Y, Nakatani K. Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme. Nucleic Acids Res 2023; 51:9533-9541. [PMID: 37615580 PMCID: PMC10570050 DOI: 10.1093/nar/gkad690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Single-stranded RNA folds into a variety of secondary and higher-order structures. Distributions and dynamics of multiple RNA conformations are responsible for the biological function of RNA. We here developed a photoswitchable molecular glue for RNA, which could reversibly control the association of two unpaired RNA regions in response to light stimuli. The photoswitchable molecular glue, NCTA, is an RNA-binding ligand possessing a photoisomerizable azobenzene moiety. Z-NCTA is an active ligand for the target RNA containing 5'-WGG-3'/5'-WGG-3' (W = U or A) site and stabilizes its hybridized state, while its isomer E-NCTA is not. Photoreversible isomerization of NCTA enabled control of the secondary and tertiary structure of the target RNA. The RNA-cleaving activity of hammerhead ribozyme, where appropriate RNA folding is necessary, could be reversibly regulated by photoirradiation in cells treated with NCTA, demonstrating precise photocontrol of RNA structure and function by the photoswitchable molecular glue.
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Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Maki Kimura
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yusuke Fujiwara
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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9
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Chaix A, Cueto-Diaz E, Dominguez-Gil S, Spiteri C, Lichon L, Maynadier M, Dumail X, Aggad D, Delalande A, Bessière A, Pichon C, Chiappini C, Sailor MJ, Bettache N, Gary-Bobo M, Durand JO, Nguyen C, Cunin F. Two-Photon Light Trigger siRNA Transfection of Cancer Cells Using Non-Toxic Porous Silicon Nanoparticles. Adv Healthc Mater 2023; 12:e2301052. [PMID: 37499629 DOI: 10.1002/adhm.202301052] [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: 04/06/2023] [Revised: 07/23/2023] [Indexed: 07/29/2023]
Abstract
The concept of using two-photon excitation in the NIR for the spatiotemporal control of biological processes holds great promise. However, its use for the delivery of nucleic acids has been very scarcely described and the reported procedures are not optimal as they often involve potentially toxic materials and irradiation conditions. This work prepares a simple system made of biocompatible porous silicon nanoparticles (pSiNP) for the safe siRNA photocontrolled delivery and gene silencing in cells upon two-photon excitation. PSiNP are linked to an azobenzene moiety, which possesses a lysine group (pSiNP@ICPES-azo@Lys) to efficiently complex siRNA. Non-linear excitation of the two-photon absorber system (pSiNP) followed by intermolecular energy transfer (FRET) to trans azobenzene moiety, result in the photoisomerization of the azobenzene from trans to cis and in the destabilization of the azobenzene-siRNA complex, thus inducing the delivery of the cargo siRNA to the cytoplasm of cells. Efficient silencing in MCF-7 expressing stable firefly luciferase with siRNAluc against luciferase is observed. Furthermore, siRNA against inhibitory apoptotic protein (IAP) leads to over 70% of MCF-7 cancer cell death. The developed technique using two-photon light allows a unique high spatiotemporally controlled and safe siRNA delivery in cells in few seconds of irradiation.
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Affiliation(s)
- Arnaud Chaix
- ICGM, CNRS, ENSCM, University of Montpellier, Montpellier, 34293, France
| | - Eduardo Cueto-Diaz
- ICGM, CNRS, ENSCM, University of Montpellier, Montpellier, 34293, France
| | | | - Chantelle Spiteri
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
- London Centre for Nanotechnology, King's College London, London, WC2R 2LS, UK
| | - Laure Lichon
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34093, France
| | - Marie Maynadier
- NanoMedSyn Avenue Charles Flahault, Montpellier Cedex 05, 34093, France
| | - Xavier Dumail
- ICGM, CNRS, ENSCM, University of Montpellier, Montpellier, 34293, France
| | - Dina Aggad
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34093, France
| | - Anthony Delalande
- Centre de Biophysique Moléculaire, CNRS UPR4301, Orléans cedex 02, F-45071, France
- Inserm UMS 55, ART ARNm and University of Orléans, Orléans, F-45100, France
- Institut Universitaire de France, 1 rue Descartes, Paris, F-75035, France
| | - Aurélie Bessière
- ICGM, CNRS, ENSCM, University of Montpellier, Montpellier, 34293, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Orléans cedex 02, F-45071, France
- Inserm UMS 55, ART ARNm and University of Orléans, Orléans, F-45100, France
- Institut Universitaire de France, 1 rue Descartes, Paris, F-75035, France
| | - Ciro Chiappini
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
- London Centre for Nanotechnology, King's College London, London, WC2R 2LS, UK
| | - Michael J Sailor
- University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, m/c 0358, La Jolla, CA, 92093, USA
| | - Nadir Bettache
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34093, France
| | - Magali Gary-Bobo
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34093, France
| | | | | | - Frédérique Cunin
- ICGM, CNRS, ENSCM, University of Montpellier, Montpellier, 34293, France
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10
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Zhang L, Liu Y, Wang K, Zhang G, Du Q, Liang Q, Wu Z. Azobenzene-containing surfactant directs small features of DNA thermotropic liquid crystals via bottom-up and top-down strategies. Acta Biomater 2023; 166:147-154. [PMID: 37207742 DOI: 10.1016/j.actbio.2023.05.023] [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: 02/05/2023] [Revised: 04/03/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Compared to classical block copolymers, the self-assembly of small molecules shows an advantage in addressing small features. As a new type of solvent-free ionic complexes, azobenzene-containing DNA thermotropic liquid crystals (TLCs) form an assembly as block copolymers when using small DNA. However, the self-assembly behavior of such biomaterials has not been fully investigated. In this study, photoresponsive DNA TLCs are fabricated by employing an azobenzene-containing surfactant with double flexible chains. For these DNA TLCs, the self-assembly behavior of DNA and surfactants could be guided by the factors of the molar ratio of azobenzene-containing surfactant, dsDNA/ssDNA, and presence or absence of water, which addresses the bottom-up control on domain spacing of mesophase. Meanwhile, such DNA TLCs also gain top-down control on morphology via photoinduced phase change. This work would provide a strategy for regulating the small features of solvent-free biomaterials, facilitating the development of patterning templates based on photoresponsive biomaterials. STATEMENT OF SIGNIFICANCE: The relationship between nanostructure and function is attractive in the science of biomaterials. With biocompatibility and degradability, photoresponsive DNA materials in solutions have been widely studied in biological and medical areas, but they are still hard to obtain in a condensed state. The complex created with designed azobenzene-containing surfactants paves the way for obtaining condensed photoresponsive DNA materials. However, fine control of the small features of such biomaterials has not yet been achieved. In this study, we present a bottom-up strategy of controlling the small features of such DNA materials and, simultaneously, the top-down control of morphology via photoinduced phase change. This work provides a bi-directional approach to controlling the small features of condensed biomaterials.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yun Liu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang 524023, China
| | - Kang Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Guoqiang Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qianyao Du
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qikai Liang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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11
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Halder S, Paul M, Dyagala S, Aggrawal R, Aswal VK, Biswas S, Saha SK. Role of Gemini Surfactants with Variable Spacers and SiO 2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/ In Vivo Gene Delivery. ACS APPLIED BIO MATERIALS 2023. [PMID: 37277159 DOI: 10.1021/acsabm.3c00256] [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: 06/07/2023]
Abstract
Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO2 nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO2 NPs. While 50% ct-DNA compaction in the presence of SiO2 NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO2 NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO2 NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO2 NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO2 has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO2 NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.
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Affiliation(s)
- Sayantan Halder
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Milan Paul
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Shalini Dyagala
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Rishika Aggrawal
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, Maharashtra 400085, India
| | - Swati Biswas
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Subit K Saha
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
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12
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Jacková B, Mottet G, Rudiuk S, Morel M, Baigl D. DNA-Encoded Immunoassay in Picoliter Drops: A Minimal Cell-Free Approach. Adv Biol (Weinh) 2023; 7:e2200266. [PMID: 36750732 DOI: 10.1002/adbi.202200266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Immunoassays have emerged as indispensable bioanalytical tools but necessitate long preliminary steps for the selection, production, and purification of the antibody(ies) to be used. Here is explored the paradigm shift of creating a rapid and purification-free assay in picoliter drops where the antibody is expressed from coding DNA and its binding to antigens concomitantly characterized in situ. Efficient synthesis in bulk of various functional variable domains of heavy-chain only antibodies (VHH) using reconstituted cell-free expression media, including an anti-green fluorescent protein VHH, is shown first. A microfluidic device is then used to generate monodisperse drops (30 pL) containing all the assay components, including a capture scaffold, onto which the accumulation of VHH:antigen produces a specific fluorescent signal. This allows to assess, in parallel or sequentially at high throughput (500 Hz), the VHH-antigen binding and its specificity in less than 3 h, directly from a VHH-coding DNA, for multiple VHH sequences, various antigens and down to DNA concentrations as low as 12 plasmids per drop. It is anticipated that the ultraminiaturized format, robustness, and programmability of this novel cell-free immunoassay concept will constitute valuable assets in fields as diverse as antibody discovery, point-of-care diagnostics, synthetic biology, and/or bioanalytical assays.
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Affiliation(s)
- Barbara Jacková
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
- Large Molecules Research Platform, Sanofi, Vitry-sur-Seine, 94400, France
| | - Guillaume Mottet
- Large Molecules Research Platform, Sanofi, Vitry-sur-Seine, 94400, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
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13
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Zheng T, Fu J, Xiong Q, Shen X, Li B, Zhao X, Yu Z. Photo-regulated genetic encoding of dibenzo[ c,g][1,2]diazocine on proteins via configuration switching. Chem Commun (Camb) 2023; 59:1201-1204. [PMID: 36629150 DOI: 10.1039/d2cc06738b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report two evolved Methanosarcina mazei pyrrolysine tRNA synthetases to genetically incorporate the isomers of dibenzo[c,g][1,2]diazocine-alanine (DBDAA) into proteins either in the dark or under regulation of 405 nm photo-stimulation. The genetic-encoded DBDAA realizes photo-tuning of enzymatic activity via the host-guest recognition of cucurbit[7]uril.
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Affiliation(s)
- Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
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14
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Zhang L, Gu J, Luo X, Tang Z, Qu Y, Zhang C, Liu H, Liu J, Xie C, Wu Z. Photoregulative phase change biomaterials showing thermodynamic and mchanical stabilities. NANOSCALE 2022; 14:976-983. [PMID: 34989736 DOI: 10.1039/d1nr06000g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Azobenzenes are great photochromic molecules for switching the physical properties of various materials via trans-cis isomerization. However, the UV light resulted cis-azobenzene is metastable and thermodynamically gets back to trans-azobenzene after ceasing UV irradiation, which causes an unwanted property change of azobenzene-containing materials. Additionally, thermal and mechanical conditions would accelerate this process dramatically. In this present work, a new type of azobenzene-containing surfactant is designed for the fabrication of photoresponsive phase change biomaterials. With a "locked" cis-azobenzene conformation, the resulting biomaterials could maintain their disordered state after ceasing UV light, which exhibit great resistance to thermal and piezo conditions. Interestingly, the "locked" cis-azobenzene could be unlocked by Vis light in high efficiency, which opens a new way for the design of phase change materials only responding to light. By showing stable cis-azobenzene maintained physical state, the newly fabricated biomaterials provide new potential for the construction of advanced materials, like self-healing materials, with less use of long time UV irradiation for maintaining their disordered states.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Jingjing Gu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Zhenyu Tang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Yang Qu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Chenghao Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Han Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Jishuai Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Congxia Xie
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Zhongtao Wu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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15
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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16
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Doroudgar M, Morstein J, Becker-Baldus J, Trauner D, Glaubitz C. How Photoswitchable Lipids Affect the Order and Dynamics of Lipid Bilayers and Embedded Proteins. J Am Chem Soc 2021; 143:9515-9528. [PMID: 34133158 DOI: 10.1021/jacs.1c03524] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Altering the properties of phospholipid membranes by light is an attractive option for the noninvasive manipulation of membrane proteins and cellular functions. Lipids with an azobenzene group within their acyl chains such as AzoPC are suitable tools for manipulating lipid order and dynamics through a light-induced trans-to-cis isomerization. However, the action of these photoswitchable lipids at the atomic level is still poorly understood. Here, liposomes containing AzoPC, POPE, and POPG have been characterized by solid-state NMR through chemical shift and dipolar CH order parameter measurements. Upon UV-light illumination, an efficient trans-to-cis conversion can be achieved resulting in a localized reduction of the CH order parameter within the bulk lipid acyl chains. This effect is even more pronounced in liposomes containing the integral membrane protein E. coli diacylglycerol kinase. The protein responds to the light-induced trans-to-cis isomerization by a site-specific increase in the molecular dynamics as observed by altered cross peak intensities in NCA spectra. This study represents a proof-of-concept demonstration for the use of photoswitchable lipids to modulate membrane properties by light for inducing dynamic changes within an embedded membrane protein.
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Affiliation(s)
- Mahmoudreza Doroudgar
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Johannes Morstein
- Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003, United States
| | - Johanna Becker-Baldus
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Dirk Trauner
- Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003, United States
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt, Germany
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17
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Prakash K. Laser-free super-resolution microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200144. [PMID: 33896204 DOI: 10.1098/rsta.2020.0144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We report that high-density single-molecule super-resolution microscopy can be achieved with a conventional epifluorescence microscope set-up and a mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM) is an extension of single-molecule localization microscopy (SMLM) techniques and allows single molecules to be switched on and off (a phenomenon termed as 'blinking'), detected and localized. The use of a short burst of deep blue excitation (350-380 nm) can be further used to reactivate the blinking, once the blinking process has slowed or stopped. A resolution of 90 nm is achieved on test specimens (mouse and amphibian meiotic chromosomes). Finally, we demonstrate that stimulated emission depletion and LFSM can be performed on the same biological sample using a simple commercial mounting medium. It is hoped that this type of correlative imaging will provide a basis for a further enhanced resolution. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kirti Prakash
- National Physical Laboratory, TW11 0LW Teddington, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
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18
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Nishio T, Yoshikawa Y, Yoshikawa K, Sato SI. Longer DNA exhibits greater potential for cell-free gene expression. Sci Rep 2021; 11:11739. [PMID: 34083658 PMCID: PMC8175755 DOI: 10.1038/s41598-021-91243-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
Cell-free gene expression systems have been valuable tools for understanding how transcription/translation can be regulated in living cells. Many studies have investigated the determining factors that affect gene expression. Here we report the effect of the length of linearized reporter DNAs encoding the firefly luciferase gene so as to exclude the influence of supercoiling. It is found that longer DNA molecules exhibit significantly greater potency in gene expression; for example, the expression level for DNA with 25.7 kbp is 1000-times higher than that for DNA of 1.7 kbp. AFM observation of the DNA conformation indicates that longer DNA takes shrunken conformation with a higher segment density in the reaction mixture for gene expression, in contrast to the stiff conformation of shorter DNA. We propose an underlying mechanism for the favorable effect of longer DNA on gene expression in terms of the enhancement of access of RNA polymerase to the shrunken conformation. It is expected that the enhancement of gene expression efficiency with a shrunken DNA conformation would also be a rather general mechanism in living cellular environments.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan.
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19
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Hartmann D, Smith JM, Mazzotti G, Chowdhry R, Booth MJ. Controlling gene expression with light: a multidisciplinary endeavour. Biochem Soc Trans 2020; 48:1645-1659. [PMID: 32657338 PMCID: PMC7458398 DOI: 10.1042/bst20200014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.
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Affiliation(s)
- Denis Hartmann
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Jefferson M. Smith
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Giacomo Mazzotti
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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20
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Abstract
Coacervate micro-droplets produced by liquid-liquid phase separation are increasingly used to emulate the dynamical organization of membraneless organelles found in living cells. Designing synthetic coacervates able to be formed and disassembled with improved spatiotemporal control is still challenging. In this chapter, we describe the design of photoswitchable coacervate droplets produced by phase separation of short double stranded DNA in the presence of an azobenzene cation. The droplets can be reversibly dissolved with light, which provides a new approach for the spatiotemporal regulation of coacervation. Significantly, the dynamics of light-actuated droplet formation and dissolution correlates with the capture and release of guest solutes. The reported system can find applications for the dynamic photocontrol of biomolecule compartmentalization, paving the way to the light-activated regulation of signaling pathways in artificial membraneless organelles.
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21
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Preußke N, Moormann W, Bamberg K, Lipfert M, Herges R, Sönnichsen FD. Visible-light-driven photocontrol of the Trp-cage protein fold by a diazocine cross-linker. Org Biomol Chem 2020; 18:2650-2660. [PMID: 32207764 DOI: 10.1039/c9ob02442e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Diazocines are characterized by extraordinary photochemical properties rendering them of particular interest for switching the conformation of biomolecules with visible light. Current developments afford synthetic access to unprecedented diazocine derivatives promising particular opportunities in photocontrol of proteins and biological systems. In this work, the well-established approach of photocontrolling the secondary structure of α-helices was exploited using a diazocine to reversibly fold and unfold the tertiary structure of a small protein. The protein of choice was the globulary folded Trp-cage, a widely used model system for the elucidation of protein folding pathways. A specifically designed, short and rigid dicarboxy-functionalized diazocine-based cross-linker was attached to two solvent-exposed side chains at the α-helix of the miniprotein through the use of a primary amine-selective active ester. This cross-linking strategy is orthogonal to the common cysteine-based chemistry. The cross-linked Trp-cage was successfully photoisomerized and exhibited a strong correlation between protein fold and diazocine isomeric state. As determined by NMR spectroscopy, the cis-isomer stabilized the fold, while the trans-isomer led to complete protein unfolding. The successful switching of the protein fold in principle demonstrates the ability to control protein function, as the activity depends on their structural integrity.
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Affiliation(s)
- Nils Preußke
- Otto-Diels-Institute for Organic Chemistry, Christian-Albrechts-University of Kiel, Otto-Hahn-Platz 4, 24118 Kiel, Germany.
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22
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Ji W, Li W, Wang Y, Lan D. Tunable Spreading and Shrinking on Photocontrolled Liquid Substrate. ACS OMEGA 2019; 4:21967-21974. [PMID: 31891076 PMCID: PMC6933795 DOI: 10.1021/acsomega.9b03039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/25/2019] [Indexed: 05/28/2023]
Abstract
Droplets of n-hexadecane were observed to shrink under ultraviolet (365 nm) and spread under blue light (475 nm) irradiation on an aqueous solution of photosensitive surfactant AzoTAB. We demonstrate that the change of wettability of n-hexadecane droplet on the solution depends on the change of oil-water interface tension. According to the addition of ethanol into the substrate, the change of relative diameter ΔD/D exceeds 20%, much larger than the system without ethanol. With light-emitting diode (LED) light as a sole power source, without any other triggers, we provide a contactless and isothermal method to realize photocontrolled alternative spreading and shrinking of a droplet on a liquid surface, which provides a basis for a chromocapillary-based optical zoom liquid lens.
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Affiliation(s)
- Wenjie Ji
- Key
Laboratory of Microgravity (National Microgravity Laboratory), Institute
of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
- School
of Engineering Science, University of Chinese
Academy of Sciences, 100049 Beijing, China
| | - Weibin Li
- Key
Laboratory of Microgravity (National Microgravity Laboratory), Institute
of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
- School
of Engineering Science, University of Chinese
Academy of Sciences, 100049 Beijing, China
| | - Yuren Wang
- Key
Laboratory of Microgravity (National Microgravity Laboratory), Institute
of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
- School
of Engineering Science, University of Chinese
Academy of Sciences, 100049 Beijing, China
| | - Ding Lan
- Key
Laboratory of Microgravity (National Microgravity Laboratory), Institute
of Mechanics, Chinese Academy of Sciences, 100190 Beijing, China
- School
of Engineering Science, University of Chinese
Academy of Sciences, 100049 Beijing, China
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23
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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24
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Martin N, Tian L, Spencer D, Coutable-Pennarun A, Anderson JLR, Mann S. Photoswitchable Phase Separation and Oligonucleotide Trafficking in DNA Coacervate Microdroplets. Angew Chem Int Ed Engl 2019; 58:14594-14598. [PMID: 31408263 DOI: 10.1002/anie.201909228] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 01/01/2023]
Abstract
Coacervate microdroplets produced by liquid-liquid phase separation have been used as synthetic protocells that mimic the dynamical organization of membrane-free organelles in living systems. Achieving spatiotemporal control over droplet condensation and disassembly remains challenging. Herein, we describe the formation and photoswitchable behavior of light-responsive coacervate droplets prepared from mixtures of double-stranded DNA and an azobenzene cation. The droplets disassemble and reassemble under UV and blue light, respectively, due to azobenzene trans/cis photoisomerisation. Sequestration and release of captured oligonucleotides follow the dynamics of phase separation such that light-activated transfer, mixing, hybridization, and trafficking of the oligonucleotides can be controlled in binary populations of the droplets. Our results open perspectives for the spatiotemporal control of DNA coacervates and provide a step towards the dynamic regulation of synthetic protocells.
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Affiliation(s)
- Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 Avenue du Dr. Albert Schweitzer, 33600, Pessac, France.,Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Liangfei Tian
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Dan Spencer
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Angélique Coutable-Pennarun
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK.,School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - J L Ross Anderson
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK.,School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
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25
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Martin N, Tian L, Spencer D, Coutable‐Pennarun A, Anderson JLR, Mann S. Photoswitchable Phase Separation and Oligonucleotide Trafficking in DNA Coacervate Microdroplets. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909228] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Martin
- Univ. Bordeaux CNRS Centre de Recherche Paul Pascal, UMR5031 115 Avenue du Dr. Albert Schweitzer 33600 Pessac France
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Liangfei Tian
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building University of Bristol Tyndall Avenue Bristol BS8 1TQ UK
| | - Dan Spencer
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Angélique Coutable‐Pennarun
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building University of Bristol Tyndall Avenue Bristol BS8 1TQ UK
- School of Biochemistry University of Bristol University Walk Bristol BS8 1TD UK
| | - J. L. Ross Anderson
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building University of Bristol Tyndall Avenue Bristol BS8 1TQ UK
- School of Biochemistry University of Bristol University Walk Bristol BS8 1TD UK
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building University of Bristol Tyndall Avenue Bristol BS8 1TQ UK
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26
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Zhou L, Retailleau P, Morel M, Rudiuk S, Baigl D. Photoswitchable Fluorescent Crystals Obtained by the Photoreversible Coassembly of a Nucleobase and an Azobenzene Intercalator. J Am Chem Soc 2019; 141:9321-9329. [PMID: 31117648 DOI: 10.1021/jacs.9b02836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-assembled nucleobases, such as G-quartets or quadruplexes, have numerous applications, but light-responsive structures are limited to small, noncrystalline motifs. In addition, the assembly of the widely exploited azobenzene photochromic compounds can produce fluorescent crystals of extended dimensions but at the prize of sacrificing their photoswitchability. Here, we overcome inherent limitations of self-assembly with a new concept of supramolecular coassembly leading to materials with unprecedented properties. We show that the coassembly of guanosine monophosphate (GMP) with an azobenzene-containing DNA intercalator produces supramolecular crystals arranged through a combination of π-π, electrostatic, and hydrogen-bond interactions. The resulting crystals are 100 μm long, pH-sensitive, fluorescent, and can be photoreversibly disassembled/reassembled upon UV/blue irradiation. This allows us to perform operations such as dynamic photocontrol of a single-crystal growth, light-gated permeability in membrane-like materials, and photoswitchable fluorescence. We believe this concept critically expands the breadth of multifunctional materials attainable by self-assembly.
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Affiliation(s)
- Li Zhou
- PASTEUR, Department of Chemistry , Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles , CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay , 1 av. de la Terrasse , Gif-sur-Yvette 91198 , France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry , Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry , Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Damien Baigl
- PASTEUR, Department of Chemistry , Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
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27
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Xie W, Yin T, Chen YL, Zhu DM, Zan MH, Chen B, Ji LW, Chen L, Guo SS, Huang HM, Zhao XZ, Wang Y, Wu Y, Liu W. Capture and "self-release" of circulating tumor cells using metal-organic framework materials. NANOSCALE 2019; 11:8293-8303. [PMID: 30977474 DOI: 10.1039/c8nr09071h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Capturing circulating tumor cells (CTCs) from peripheral blood for subsequent analyses has shown potential in precision medicine for cancer patients. Broad as the prospect is, there are still some challenges that hamper its clinical applications. One of the challenges is to maintain the viability of the captured cells during the capturing and releasing processes. Herein, we have described a composite material that could encapsulate a magnetic Fe3O4 core in a MIL-100 shell (MMs), which could respond to pH changes and modify the anti-EpCAM antibody (anti-EpCAM-MMs) on the surface of MIL-100. After the anti-EpCAM-MMs captured the cells, there was no need for additional conditions but with the acidic environment during the cell culture process, MIL-100 could realize automatic degradation, leading to cell self-release. This self-release model could not only improve the cell viability, but could also reduce the steps of the release process and save human and material resources simultaneously. In addition, we combined clinical patients' case diagnosis with the DNA sequencing and next generation of RNA sequencing technologies in the hope of precision medicine for patients in the future.
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Affiliation(s)
- Wei Xie
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.
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28
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Pardatscher G, Schwarz-Schilling M, Sagredo S, Simmel FC. Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography. J Vis Exp 2018. [PMID: 30417873 DOI: 10.3791/58634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Immobilization of genes on lithographically structured surfaces allows the study of compartmentalized gene expression processes in an open microfluidic bioreactor system. In contrast to other approaches towards artificial cellular systems, such a setup allows for a continuous supply with gene expression reagents and simultaneous draining of waste products. This facilitates the implementation of cell-free gene expression processes over extended periods of time, which is important for the realization of dynamic gene regulatory feedback systems. Here we provide a detailed protocol for the fabrication of genetic biochips using a simple-to-use lithographic technique based on DNA strand displacement reactions, which exclusively uses commercially available components. We also provide a protocol on the integration of compartmentalized genes with a polydimethylsiloxane (PDMS)-based microfluidic system. Furthermore, we show that the system is compatible with total internal reflection fluorescence (TIRF) microscopy, which can be used for the direct observation of molecular interactions between DNA and molecules contained in the expression mix.
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29
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Georgiev VN, Grafmüller A, Bléger D, Hecht S, Kunstmann S, Barbirz S, Lipowsky R, Dimova R. Area Increase and Budding in Giant Vesicles Triggered by Light: Behind the Scene. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800432. [PMID: 30128249 PMCID: PMC6096984 DOI: 10.1002/advs.201800432] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/18/2018] [Indexed: 06/08/2023]
Abstract
Biomembranes are constantly remodeled and in cells, these processes are controlled and modulated by an assortment of membrane proteins. Here, it is shown that such remodeling can also be induced by photoresponsive molecules. The morphological control of giant vesicles in the presence of a water-soluble ortho-tetrafluoroazobenzene photoswitch (F-azo) is demonstrated and it is shown that the shape transformations are based on an increase in membrane area and generation of spontaneous curvature. The vesicles exhibit budding and the buds can be retracted by using light of a different wavelength. In the presence of F-azo, the membrane area can increase by more than 5% as assessed from vesicle electrodeformation. To elucidate the underlying molecular mechanism and the partitioning of F-azo in the membrane, molecular dynamics simulations are employed. Comparison with theoretically calculated shapes reveals that the budded shapes are governed by curvature elasticity, that the spontaneous curvature can be decomposed into a local and a nonlocal contribution, and that the local spontaneous curvature is about 1/(2.5 µm). The results show that exo- and endocytotic events can be controlled by light and that these photoinduced processes provide an attractive method to change membrane area and morphology.
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Affiliation(s)
- Vasil N. Georgiev
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park Golm14424PotsdamGermany
| | - Andrea Grafmüller
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park Golm14424PotsdamGermany
| | - David Bléger
- Department of Chemistry & IRIS AdlershofHumboldt‐Universität zu BerlinBrook‐Taylor‐Str. 212489BerlinGermany
| | - Stefan Hecht
- Department of Chemistry & IRIS AdlershofHumboldt‐Universität zu BerlinBrook‐Taylor‐Str. 212489BerlinGermany
| | - Sonja Kunstmann
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park Golm14424PotsdamGermany
- Physikalische BiochemieUniversität PotsdamKarl‐Liebknecht‐Str. 24‐2514476PotsdamGermany
| | - Stefanie Barbirz
- Physikalische BiochemieUniversität PotsdamKarl‐Liebknecht‐Str. 24‐2514476PotsdamGermany
| | - Reinhard Lipowsky
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park Golm14424PotsdamGermany
| | - Rumiana Dimova
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesScience Park Golm14424PotsdamGermany
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30
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Kasyanenko N, Unksov I, Bakulev V, Santer S. DNA Interaction with Head-to-Tail Associates of Cationic Surfactants Prevents Formation of Compact Particles. Molecules 2018; 23:E1576. [PMID: 29958479 PMCID: PMC6100511 DOI: 10.3390/molecules23071576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022] Open
Abstract
Cationic azobenzene-containing surfactants are capable of condensing DNA in solution with formation of nanosized particles that can be employed in gene delivery. The ratio of surfactant/DNA concentration and solution ionic strength determines the result of DNA-surfactant interaction: Complexes with a micelle-like surfactant associates on DNA, which induces DNA shrinkage, DNA precipitation or DNA condensation with the emergence of nanosized particles. UV and fluorescence spectroscopy, low gradient viscometry and flow birefringence methods were employed to investigate DNA-surfactant and surfactant-surfactant interaction at different NaCl concentrations, [NaCl]. It was observed that [NaCl] (or the Debye screening radius) determines the surfactant-surfactant interaction in solutions without DNA. Monomers, micelles and non-micellar associates of azobenzene-containing surfactants with head-to-tail orientation of molecules were distinguished due to the features of their absorption spectra. The novel data enabled us to conclude that exactly the type of associates (together with the concentration of components) determines the result of DNA-surfactant interaction. Predomination of head-to-tail associates at 0.01 M < [NaCl] < 0.5 M induces DNA aggregation and in some cases DNA precipitation. High NaCl concentration (higher than 0.8 M) prevents electrostatic attraction of surfactants to DNA phosphates for complex formation. DAPI dye luminescence in solutions with DNA-surfactant complexes shows that surfactant tails overlap the DNA minor groove. The addition of di- and trivalent metal ions before and after the surfactant binding to DNA indicate that the bound surfactant molecules are located on DNA in islets.
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Affiliation(s)
- Nina Kasyanenko
- Department of Physics, Saint Petersburg State University, 199034 St Petersburg, Russia.
| | - Ivan Unksov
- Department of Physics, Saint Petersburg State University, 199034 St Petersburg, Russia.
| | - Vladimir Bakulev
- Department of Physics, Saint Petersburg State University, 199034 St Petersburg, Russia.
| | - Svetlana Santer
- Experimental Physics, Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
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31
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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32
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Drożdż W, Bessin Y, Gervais V, Cao XY, Lehn JM, Stefankiewicz AR, Ulrich S. Switching Multivalent DNA Complexation using Metal-Controlled Cationic Supramolecular Self-Assemblies. Chemistry 2018; 24:1518-1521. [DOI: 10.1002/chem.201705630] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Wojciech Drożdż
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c 61-614 Poznań Poland
| | - Yannick Bessin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier; Ecole Nationale Supérieure de Chimie de Montpellier; 8 rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Virginie Gervais
- CNRS; Institut de Pharmacologie et de Biologie Structurale (IPBS); Université de Toulouse, UPS; 205 route de Narbonne 31077 Toulouse France
| | - Xiao-Yu Cao
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), UMR 7006, CNRS; Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), UMR 7006, CNRS; Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Artur R. Stefankiewicz
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c 61-614 Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier; Ecole Nationale Supérieure de Chimie de Montpellier; 8 rue de l'Ecole Normale 34296 Montpellier cedex 5 France
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33
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Booth MJ, Restrepo Schild V, Box SJ, Bayley H. Light-patterning of synthetic tissues with single droplet resolution. Sci Rep 2017; 7:9315. [PMID: 28839174 PMCID: PMC5570938 DOI: 10.1038/s41598-017-09394-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022] Open
Abstract
Synthetic tissues can be generated by forming networks of aqueous droplets in lipid-containing oil. Each droplet contains a cell-free expression system and is connected to its neighbor through a lipid bilayer. In the present work, we have demonstrated precise external control of such networks by activating protein expression within single droplets, by using light-activated DNA to encode either a fluorescent or a pore-forming protein. By controlling the extent of activation, synthetic tissues were generated with graded levels of protein expression in patterns of single droplets. Further, we have demonstrated reversible activation within individual compartments in synthetic tissues by turning a fluorescent protein on-and-off. This is the first example of the high-resolution patterning of droplet networks, following their formation. Single-droplet control will be essential to power subsets of compartments within synthetic tissues or to stimulate subsets of cells when synthetic tissues are interfaced with living tissues.
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Affiliation(s)
- Michael J Booth
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | | | - Stuart J Box
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
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34
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Zhou L, Morel M, Rudiuk S, Baigl D. Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700706. [PMID: 28561941 DOI: 10.1002/smll.201700706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/11/2017] [Indexed: 06/07/2023]
Abstract
DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization).
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Affiliation(s)
- Li Zhou
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
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35
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Pardatscher G, Bracha D, Daube SS, Vonshak O, Simmel FC, Bar-Ziv RH. DNA condensation in one dimension. NATURE NANOTECHNOLOGY 2016; 11:1076-1081. [PMID: 27501315 DOI: 10.1038/nnano.2016.142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
DNA can be programmed to assemble into a variety of shapes and patterns on the nanoscale and can act as a template for hybrid nanostructures such as conducting wires, protein arrays and field-effect transistors. Current DNA nanostructures are typically in the sub-micrometre range, limited by the sequence space and length of the assembled strands. Here we show that on a patterned biochip, DNA chains collapse into one-dimensional (1D) fibres that are 20 nm wide and around 70 µm long, each comprising approximately 35 co-aligned chains at its cross-section. Electron beam writing on a photocleavable monolayer was used to immobilize and pattern the DNA molecules, which condense into 1D bundles in the presence of spermidine. DNA condensation can propagate and split at junctions, cross gaps and create domain walls between counterpropagating fronts. This system is inherently adept at solving probabilistic problems and was used to find the possible paths through a maze and to evaluate stochastic switching circuits. This technique could be used to propagate biological or ionic signals in combination with sequence-specific DNA nanotechnology or for gene expression in cell-free DNA compartments.
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Affiliation(s)
- Günther Pardatscher
- Systems Biophysics and Bionanotechnology - E14, Physics-Department and ZNN, Technische Universität München, 85748 Garching, Germany
| | - Dan Bracha
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirley S Daube
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ohad Vonshak
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Friedrich C Simmel
- Systems Biophysics and Bionanotechnology - E14, Physics-Department and ZNN, Technische Universität München, 85748 Garching, Germany
- Nanosystems Initiative Munich, 80539 Munich, Germany
| | - Roy H Bar-Ziv
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Lv SW, Liu Y, Xie M, Wang J, Yan XW, Li Z, Dong WG, Huang WH. Near-Infrared Light-Responsive Hydrogel for Specific Recognition and Photothermal Site-Release of Circulating Tumor Cells. ACS NANO 2016; 10:6201-10. [PMID: 27299807 DOI: 10.1021/acsnano.6b02208] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Isolation of single circulating tumor cells (CTCs) from patients is a very challenging technique that may promote the process of individualized antitumor therapies. However, there exist few systems capable of highly efficient capture and release of single CTCs with high viability for downstream analysis and culture. Herein, we designed a near-infrared (NIR) light-responsive substrate for highly efficient immunocapture and biocompatible site-release of CTCs by a combination of the photothermal effect of gold nanorods (GNRs) and a thermoresponsive hydrogel. The substrate was fabricated by imprinting target cancer cells on a GNR-pre-embedded gelatin hydrogel. Micro/nanostructures generated by cell imprinting produce artificial receptors for cancer cells to improve capture efficiency. Temperature-responsive gelatin dissolves rapidly at 37 °C; this allows bulk recovery of captured CTCs at physiological temperature or site-specific release of single CTCs by NIR-mediated photothermal activation of embedded GNRs. Furthermore, the system has been applied to capture, individually release, and genetically analyze CTCs from the whole blood of cancer patients. The multifunctional NIR-responsive platform demonstrates excellent performance in capture and site-release of CTCs with high viability, which provides a robust and versatile means toward individualized antitumor therapies and also shows promising potential for dynamically manipulating cell-substrate interactions in vitro.
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Affiliation(s)
- Song-Wei Lv
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Ya Liu
- Renmin Hospital of Wuhan University , Wuhan 430060, China
| | - Min Xie
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Jing Wang
- Renmin Hospital of Wuhan University , Wuhan 430060, China
| | - Xue-Wei Yan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Zhen Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Wei-Guo Dong
- Renmin Hospital of Wuhan University , Wuhan 430060, China
| | - Wei-Hua Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
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37
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Deiana M, Pokladek Z, Olesiak-Banska J, Młynarz P, Samoc M, Matczyszyn K. Photochromic switching of the DNA helicity induced by azobenzene derivatives. Sci Rep 2016; 6:28605. [PMID: 27339811 PMCID: PMC4919647 DOI: 10.1038/srep28605] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ziemowit Pokladek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Młynarz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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38
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Tongu C, Kenmotsu T, Yoshikawa Y, Zinchenko A, Chen N, Yoshikawa K. Divalent cation shrinks DNA but inhibits its compaction with trivalent cation. J Chem Phys 2016; 144:205101. [DOI: 10.1063/1.4950749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Chika Tongu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0321, Japan
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0321, Japan
| | - Yuko Yoshikawa
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Ning Chen
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0321, Japan
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39
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McCoy TM, Liu ACY, Tabor RF. Light-controllable dispersion and recovery of graphenes and carbon nanotubes using a photo-switchable surfactant. NANOSCALE 2016; 8:6969-6974. [PMID: 26973013 DOI: 10.1039/c6nr00075d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aqueous dispersibility of carbon-based nanomaterials, namely graphene oxide (GO), reduced graphene oxide (rGO) and carbon nanotubes (CNTs), can be controlled by light via the photoisomerisation of a photoswitchable surfactant molecule adsorbed to the surface of these materials. By incorporating a cationic azobenzene photosurfactant into these systems, GO, rGO and CNT dispersions can be separated and redispersed on command utilising UV radiation at 365 nm, whereby the surfactant molecules change from the trans to the cis isomer. This increases their aqueous solubility and in turn, alters their adsorption affinity for the GO and rGO sheets such that the ratio of free to adsorbed surfactant molecules changes significantly, allowing for reversible phase separation of the colloids. These effects present a unique method for controlling the dispersion behaviour of two-dimensional nanomaterials using light as a clean and low energy external stimulus.
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Affiliation(s)
- Thomas M McCoy
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia.
| | - Amelia C Y Liu
- Monash Centre for Electron Microscopy and School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
| | - Rico F Tabor
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia.
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40
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Booth MJ, Schild VR, Graham AD, Olof SN, Bayley H. Light-activated communication in synthetic tissues. SCIENCE ADVANCES 2016; 2:e1600056. [PMID: 27051884 PMCID: PMC4820383 DOI: 10.1126/sciadv.1600056] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/25/2016] [Indexed: 05/17/2023]
Abstract
We have previously used three-dimensional (3D) printing to prepare tissue-like materials in which picoliter aqueous compartments are separated by lipid bilayers. These printed droplets are elaborated into synthetic cells by using a tightly regulated in vitro transcription/translation system. A light-activated DNA promoter has been developed that can be used to turn on the expression of any gene within the synthetic cells. We used light activation to express protein pores in 3D-printed patterns within synthetic tissues. The pores are incorporated into specific bilayer interfaces and thereby mediate rapid, directional electrical communication between subsets of cells. Accordingly, we have developed a functional mimic of neuronal transmission that can be controlled in a precise way.
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41
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Tian T, Song Y, Wang J, Fu B, He Z, Xu X, Li A, Zhou X, Wang S, Zhou X. Small-Molecule-Triggered and Light-Controlled Reversible Regulation of Enzymatic Activity. J Am Chem Soc 2016; 138:955-61. [DOI: 10.1021/jacs.5b11532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tian Tian
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Yanyan Song
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Jiaqi Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Boshi Fu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Zhiyong He
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xianqun Xu
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Anling Li
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xin Zhou
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Shaoru Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
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42
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Bergen A, Rudiuk S, Morel M, Le Saux T, Ihmels H, Baigl D. Photodependent Melting of Unmodified DNA Using a Photosensitive Intercalator: A New and Generic Tool for Photoreversible Assembly of DNA Nanostructures at Constant Temperature. NANO LETTERS 2016; 16:773-80. [PMID: 26652690 DOI: 10.1021/acs.nanolett.5b04762] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
External control of DNA melting and hybridization, a key step in bio- and DNA nanotechnology, is commonly achieved with temperature. The use of light to direct this process is a challenging alternative, which has been only possible with a DNA modification, such as covalent grafting or mismatch introduction, so far. Here we describe the first photocontrol of DNA melting that relies on the addition of a molecule that noncovalently interacts with unmodified DNA and affects its melting properties in a photoreversible and highly robust manner, without any prerequisite in the length or sequence of the target DNA molecule. We synthesize azobenzene-containing guanidinium derivatives and show that a bivalent molecule with a conformation-dependent binding mode, AzoDiGua, strongly increases the melting temperature (Tm) of DNA under dark conditions because its trans isomer intercalates in the DNA double helix. Upon UV irradiation at 365 nm, the trans-cis isomerization induced the ejection of AzoDiGua from the intercalation binding sites, resulting in a decrease in Tm up to 18 °C. This illumination-dependent Tm shift is observed on many types of DNA, from self-complementary single-stranded or double-stranded oligonucleotides to long genomic duplex DNA molecules. Finally, we show that simply adding AzoDiGua allows us to photoreversibly control the assembly/disassembly of a DNA nanostructure at constant temperature, as demonstrated here with a self-hybridized DNA hairpin. We anticipate that this strategy will be the key ingredient in a new and generic way of placing DNA-based bio- and nanotechnologies under dynamic control by light.
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Affiliation(s)
- Anna Bergen
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Mathieu Morel
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen , Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
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43
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Nurdin L, Venancio-Marques A, Rudiuk S, Morel M, Baigl D. High-throughput photocontrol of water drop generation, fusion, and mixing in a dual flow-focusing microfluidic device. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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44
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Díaz-Lobo M, Garcia-Amorós J, Fita I, Velasco D, Guinovart JJ, Ferrer JC. Selective photoregulation of the activity of glycogen synthase and glycogen phosphorylase, two key enzymes in glycogen metabolism. Org Biomol Chem 2015; 13:7282-8. [PMID: 26055498 DOI: 10.1039/c5ob00796h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Glycogen is a polymer of α-1,4- and α-1,6-linked glucose units that provides a readily available source of energy in living organisms. Glycogen synthase (GS) and glycogen phosphorylase (GP) are the two enzymes that control, respectively, the synthesis and degradation of this polysaccharide and constitute adequate pharmacological targets to modulate cellular glycogen levels, by means of inhibition of their catalytic activity. Here we report on the synthesis and biological evaluation of a selective inhibitor that consists of an azobenzene moiety glycosidically linked to the anomeric carbon of a glucose molecule. In the ground state, the more stable (E)-isomer of the azobenzene glucoside had a slight inhibitory effect on rat muscle GP (RMGP, IC50 = 4.9 mM) and Escherichia coli GS (EcGS, IC50 = 1.6 mM). After irradiation and subsequent conversion to the (Z)-form, the inhibitory potency of the azobenzene glucoside did not significantly change for RMGP (IC50 = 2.4 mM), while its effect on EcGS increased 50-fold (IC50 = 32 μM). Sucrose synthase 4 from potatoes, a glycosyltransferase that does not operate on glycogen, was only slightly inhibited by the (E)-isomer (IC50 = 0.73 mM). These findings could be rationalized on the basis of kinetic and computer-aided docking analysis, which indicated that both isomers of the azobenzene glucoside mimic the EcGS acceptor substrate and exert their inhibitory effect by binding to the glycogen subsite in the active center of the enzyme. The ability to selectively photoregulate the catalytic activity of key enzymes of glycogen metabolism may represent a new approach for the treatment of glycogen metabolism disorders.
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Affiliation(s)
- Mireia Díaz-Lobo
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain.
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45
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Knežević NŽ, Durand J. Targeted Treatment of Cancer with Nanotherapeutics Based on Mesoporous Silica Nanoparticles. Chempluschem 2015. [DOI: 10.1002/cplu.201402369] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikola Ž. Knežević
- Faculty of Pharmacy, European University, Trg mladenaca 5, 21000 Novi Sad (Serbia)
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS‐UM2‐ENSCM‐UM1, CC1701 Equipe Chimie Moléculaire et Organisation du Solide, Place Eugène Bataillon, 34095 Montpellier Cedex 05 (France)
| | - Jean‐Olivier Durand
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS‐UM2‐ENSCM‐UM1, CC1701 Equipe Chimie Moléculaire et Organisation du Solide, Place Eugène Bataillon, 34095 Montpellier Cedex 05 (France)
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46
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Tabor RF, Tan DD, Han SS, Young SA, Seeger ZLE, Pottage MJ, Garvey CJ, Wilkinson BL. Reversible pH‐ and Photocontrollable Carbohydrate‐Based Surfactants. Chemistry 2014; 20:13881-4. [DOI: 10.1002/chem.201404945] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Rico F. Tabor
- School of Chemistry, Monash University, Victoria 3800 (Australia)
| | - David D. Tan
- School of Chemical and Life Sciences, Nanyang Polytechnic, Singapore 569830 (Singapore)
| | - Sean S. Han
- School of Chemical and Life Sciences, Nanyang Polytechnic, Singapore 569830 (Singapore)
| | - Scott A. Young
- School of Chemistry, Monash University, Victoria 3800 (Australia)
| | - Zoe L. E. Seeger
- School of Chemistry, Monash University, Victoria 3800 (Australia)
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47
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Venancio-Marques A, Bergen A, Rossi-Gendron C, Rudiuk S, Baigl D. Photosensitive polyamines for high-performance photocontrol of DNA higher-order structure. ACS NANO 2014; 8:3654-3663. [PMID: 24580129 DOI: 10.1021/nn500266b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Polyamines are small, ubiquitous, positively charged molecules that play an essential role in numerous biological processes such as DNA packaging, gene regulation, neuron activity, and cell proliferation. Here, we synthesize the first series of photosensitive polyamines (PPAs) and demonstrate their ability to photoreversibly control nanoscale DNA higher-order structure with high efficiency. We show with fluorescence microscopy imaging that the efficiency of the PPAs as DNA-compacting agents is directly correlated to their molecular charge. Micromolar concentration of the most efficient molecule described here, a PPA containing three charges at neutral pH, compacts DNA molecules from a few kilobase pairs to a few hundred kilobase pairs, while subsequent 3 min UV illuminations at 365 nm triggers complete unfolding of DNA molecules. Additional application of blue light (440 nm for 3 min) induces the refolding of DNA into the compact state. Atomic force microscopy reveals that the compaction involves a global folding of the whole DNA molecule, whereas UV-induced unfolding is a modification initiated from the periphery of the compacted DNA, resulting in the occurrence of intermediate flower-like structures prior to the fully unfolded state.
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Affiliation(s)
- Anna Venancio-Marques
- Ecole Normale Supérieure-PSL Research University , Department of Chemistry, 24 Rue Lhomond, F-75005, Paris, France
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48
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Bracha D, Bar-Ziv RH. Dendritic and Nanowire Assemblies of Condensed DNA Polymer Brushes. J Am Chem Soc 2014; 136:4945-53. [DOI: 10.1021/ja410960w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Dan Bracha
- Department
of Materials and
Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roy H. Bar-Ziv
- Department
of Materials and
Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
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49
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Jafari MR, Deng L, Kitov PI, Ng S, Matochko WL, Tjhung KF, Zeberoff A, Elias A, Klassen JS, Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. ACS Chem Biol 2014; 9:443-50. [PMID: 24195775 DOI: 10.1021/cb4006722] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light-responsive ligands are useful tools in biochemistry and cell biology because the function of these ligands can be spatially and temporally controlled. Conventional design of such ligands relies on previously available data about the structure of both the ligand and the receptor. In this paper, we describe de novo discovery of light-responsive ligands through screening of a genetically encoded light-responsive library. We ligated a photoresponsive azobenzene core to a random CX7C peptide library displayed on the coat protein of M13 phage. A one-pot alkylation/reduction of the cysteines yielded a photoresponsive library of random heptapeptide macrocycles with over 2 × 10(8) members. We characterized the reaction on-phage and optimized the yield of the modifications in phage libraries. Screening of the library against streptavidin yielded three macrocycles that bind to streptavidin in the dark and cease binding upon irradiation with 370 nm light. All ligands restored their binding properties upon thermal relaxation and could be turned ON and OFF for several cycles. We measured dissociation constants, Kd, by electrospray ionization mass spectrometry (ESI-MS) binding assay. For ligand ACGFERERTCG, the Kd of cis and trans isomers differed by 22-fold; an incomplete isomerization (85%), however, resulted in the apparent difference of 4.5-fold between the dark and the irradiated state. We anticipate that the selection strategy described in this report can be used to find light-responsive ligands for many targets that do not have known natural ligands.
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Affiliation(s)
- Mohammad R. Jafari
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lu Deng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Simon Ng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wadim L. Matochko
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anthony Zeberoff
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anastasia Elias
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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50
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Liu YJ, Hansen GPR, Venancio-Marques A, Baigl D. Cell-free preparation of functional and triggerable giant proteoliposomes. Chembiochem 2013; 14:2243-7. [PMID: 24115581 DOI: 10.1002/cbic.201300501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Indexed: 01/15/2023]
Abstract
Heat, we leak: We express a membrane protein outside well-defined giant liposomes obtained by gravity-transferred sucrose-in-oil droplets into a cell-free, reconstituted expression system. We show that the presence of the liposome is necessary during expression for efficient protein insertion into the membrane and that temperature can trigger the resulting membrane function.
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Affiliation(s)
- Yan-Jun Liu
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France) http://www.baigllab.com/; Université Pierre et Marie Curie Paris 6, 4 place Jussieu, 75005 Paris (France); UMR 8640, CNRS, 3 rue Michel-Ange, 75016 Paris (France)
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