1
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Lauzon D, Vallée-Bélisle A. Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies. Angew Chem Int Ed Engl 2024; 63:e202313944. [PMID: 37975629 DOI: 10.1002/anie.202313944] [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: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.
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Affiliation(s)
- Dominic Lauzon
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
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2
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Zheng LL, Li JZ, Wen M, Xi D, Zhu Y, Wei Q, Zhang XB, Ke G, Xia F, Gao ZF. Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption. SCIENCE ADVANCES 2023; 9:eadf5868. [PMID: 37196083 DOI: 10.1126/sciadv.adf5868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A+/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A+/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pKa, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.
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Affiliation(s)
- Lin Lin Zheng
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jin Ze Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yanxi Zhu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Central Laboratory of Linyi People's Hospital, Linyi 276003, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 388 Lumo Road, Wuhan 430074, P. R. China
| | - Zhong Feng Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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3
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Périllat VJ, Del Grosso E, Berton C, Ricci F, Pezzato C. Controlling DNA nanodevices with light-switchable buffers. Chem Commun (Camb) 2023; 59:2146-2149. [PMID: 36727426 PMCID: PMC9933455 DOI: 10.1039/d2cc06525h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Control over synthetic DNA-based nanodevices can be achieved with a variety of physical and chemical stimuli. Actuation with light, however, is as advantageous as difficult to implement without modifying DNA strands with photo-switchable groups. Herein, we show that DNA nanodevices can be controlled using visible light in photo-switchable aqueous buffer solutions in a reversible and highly programmable fashion. The strategy presented here is non-invasive and allows the remote control with visible light of complex operations of DNA-based nanodevices such as the reversible release/loading of cargo molecules.
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Affiliation(s)
- Valentin Jean Périllat
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cesare Berton
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cristian Pezzato
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,Department of Chemical Sciences, University of Padua Via Marzolo 1, 35131 Padua, Italy.
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4
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Mariottini D, Idili A, Ercolani G, Ricci F. Thermo-Programmed Synthetic DNA-Based Receptors. ACS NANO 2023; 17:1998-2006. [PMID: 36689298 PMCID: PMC9933611 DOI: 10.1021/acsnano.2c07039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Herein, we present a generalizable and versatile strategy to engineer synthetic DNA ligand-binding devices that can be programmed to load and release a specific ligand at a defined temperature. We do so by re-engineering two model DNA-based receptors: a triplex-forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an ATP-binding aptamer. The temperature at which these receptors load/release their ligands can be finely modulated by controlling the entropy associated with the linker connecting the two ligand-binding domains. The availability of a set of receptors with tunable and reversible temperature dependence allows achieving complex load/release behavior such as sustained ligand release over a wide temperature range. Similar programmable thermo-responsive synthetic ligand-binding devices can be of utility in applications such as drug delivery and production of smart materials.
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Affiliation(s)
- Davide Mariottini
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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5
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Wang GA, Wu X, Chen F, Shen C, Yang Q, Li F. Toehold-Exchange-Based Activation of Aptamer Switches Enables High Thermal Robustness and Programmability. J Am Chem Soc 2023; 145:2750-2753. [PMID: 36701187 DOI: 10.1021/jacs.2c10928] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aptamer switches are attractive nature-inspired tools for developing smart materials and nanodevices. However, the thermal robustness and programmability of current aptamer switches are often limited by their activation processes that are coupled with high reaction enthalpy. Here, we present an enthalpy-independent activation approach that harnesses toehold-exchange as a general framework to design aptamer switches. We demonstrate mathematically and experimentally that this approach is highly effective in improving thermal robustness and thus leads to better analytical performances of aptamer switches. Enhanced programmability is also demonstrated through fine-grained and dynamic tuning of effective affinities and dynamic ranges, as well as the construction of a synthetic DNA network that resembled biological signaling cascades. Our study not only enriches the current toolbox for engineering and controlling synthetic molecular switches but also offers new insights into their thermodynamic basis, which is critical for diverse synthetic biological designs and applications.
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Affiliation(s)
- Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Xinghong Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Fangfang Chen
- College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, China, 710127
| | - Chenlan Shen
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Qianfan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario, Canada, L2S 3A1.,Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
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6
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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7
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Lin PY, Chi R, Wu YL, Ho JAA. Applications of triplex DNA nanostructures in sensor development. Anal Bioanal Chem 2022; 414:5217-5237. [PMID: 35469098 DOI: 10.1007/s00216-022-04058-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Triplex DNA nanostructures are one of the most emerging and fascinating self-assembled nanostructures due to their unique nanoparticle-like organization and inherit characteristics. They have attracted numerous interests recently because of their versatile and powerful utility in diverse areas of science and technology, such as clinical or disease diagnosis and stimuli-based drug delivery. This review addresses particularly the utilization of DNA triplexes in the development of biosensors for detecting nucleic acid; strategies in sensing pH, protein activity, ions, or molecules. Finally, an outlook for potential applications of triplex DNA nanoswitches is provided.
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Affiliation(s)
- Pei-Ying Lin
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Rong Chi
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Ling Wu
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Ja-An Annie Ho
- BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Biotechnology, National Taiwan University, Taipei, 10617, Taiwan.
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8
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Mariottini D, Del Giudice D, Ercolani G, Di Stefano S, Ricci F. Dissipative operation of pH-responsive DNA-based nanodevices. Chem Sci 2021; 12:11735-11739. [PMID: 34659709 PMCID: PMC8442697 DOI: 10.1039/d1sc03435a] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022] Open
Abstract
We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We have employed such low-to-high pH cycles to control in a dissipative way the operation of two model DNA-based nanodevices: a DNA nanoswitch undergoing time-programmable open–close–open cycles of motion, and a DNA-based receptor able to release-uptake a DNA cargo strand. The kinetics of the transient operation of both systems can be easily modulated by varying the concentration of the acid fuel added to the solution and both acid fuels show an efficient reversibility which further supports their versatility. We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices.![]()
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Affiliation(s)
- Davide Mariottini
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy
| | - Daniele Del Giudice
- Dipartimento di Chimica, Università di Roma La Sapienza, ISB-CNR Sede Secondaria di Roma-Meccanismi di Reazione P.le A. Moro 5 00185 Roma Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università di Roma La Sapienza, ISB-CNR Sede Secondaria di Roma-Meccanismi di Reazione P.le A. Moro 5 00185 Roma Italy
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy
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9
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Zheng LL, Li JZ, Li YX, Gao JB, Dong JX, Gao ZF. pH-Responsive DNA Motif: From Rational Design to Analytical Applications. Front Chem 2021; 9:732770. [PMID: 34458239 PMCID: PMC8385663 DOI: 10.3389/fchem.2021.732770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022] Open
Abstract
pH-responsive DNA motifs have attracted substantial attention attributed to their high designability and versatility of DNA chemistry. Such DNA motifs typically exploit DNA secondary structures that exhibit pH response properties because of the presence of specific protonation sites. In this review, we briefly summarized second structure-based pH-responsive DNA motifs, including triplex DNA, i-motif, and A+-C mismatch base pair-based DNA devices. Finally, the challenges and prospects of pH-responsive DNA motifs are also discussed.
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Affiliation(s)
- Lin Lin Zheng
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, Collaborative Innovation Center of Tumor Marker Detection Technology, School of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi, China
| | - Jin Ze Li
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, Collaborative Innovation Center of Tumor Marker Detection Technology, School of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi, China
| | - Ying Xu Li
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, Collaborative Innovation Center of Tumor Marker Detection Technology, School of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi, China
| | - Jian Bang Gao
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, Collaborative Innovation Center of Tumor Marker Detection Technology, School of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi, China
| | - Jiang Xue Dong
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology, Hebei University, Baoding, China
| | - Zhong Feng Gao
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, Collaborative Innovation Center of Tumor Marker Detection Technology, School of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi, China
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10
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Tang Q, Lai W, Wang P, Xiong X, Xiao M, Li L, Fan C, Pei H. Multi-Mode Reconfigurable DNA-Based Chemical Reaction Circuits for Soft Matter Computing and Control. Angew Chem Int Ed Engl 2021; 60:15013-15019. [PMID: 33893703 DOI: 10.1002/anie.202102169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/31/2021] [Indexed: 01/17/2023]
Abstract
Developing smart material systems for performing different tasks in diverse environments remains challenging. Here, we show that by integrating stimuli-responsive soft materials with multi-mode reconfigurable DNA-based chemical reaction circuits (D-CRCs), it can control size change of microgels with multiple reaction pathways and adapt expansion behaviors to meet diverse environments. We first use pH-responsive intramolecular conformational switches for regulating DNA strand displacement reactions (SDRs). The ability to regulate SDRs with tunable pH-dependence allows to build dynamic chemical reaction networks with diverse reaction pathways. We confirm that the designed DNA switching circuits are reconfigurable at different pH and perform different logic operations, and the swelling of DNA switching circuit-integrated microgel systems can be programmably directed by D-CRCs. Our approach provides insight into building smart responsive materials and fabricating autonomous soft robots.
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Affiliation(s)
- Qian Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Peipei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
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11
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Tang Q, Lai W, Wang P, Xiong X, Xiao M, Li L, Fan C, Pei H. Multi‐Mode Reconfigurable DNA‐Based Chemical Reaction Circuits for Soft Matter Computing and Control. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qian Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Peipei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 China
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12
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Del Giudice D, Spatola E, Valentini M, Bombelli C, Ercolani G, Di Stefano S. Time-programmable pH: decarboxylation of nitroacetic acid allows the time-controlled rising of pH to a definite value. Chem Sci 2021; 12:7460-7466. [PMID: 34163836 PMCID: PMC8171335 DOI: 10.1039/d1sc01196k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/21/2021] [Indexed: 12/24/2022] Open
Abstract
In this report it is shown that nitroacetic acid 1 (O2NCH2CO2H) can be conveniently used to control the pH of a water solution over time. Time-programmable sequences of the kind pH1(high)-pH2(low)-pH3(high) can be achieved, where both the extent of the initial pH jump (pH1(high)-pH2(low)) and the time required for the subsequent pH rising (pH2(low)-pH3(high)) can be predictably controlled by a judicious choice of the absolute and relative concentrations of the reagents (acid 1 and NaOH). Successive pH1(high)-pH2(low)-pH3(high) sequences can be obtained by subsequent additions of acid 1. As a proof of concept, the method is applied to control over time the pH-dependent host-guest interaction between alpha-cyclodextrin and p-aminobenzoic acid.
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Affiliation(s)
- Daniele Del Giudice
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Emanuele Spatola
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Matteo Valentini
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Cecilia Bombelli
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
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13
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding-upon-Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021; 60:7283-7289. [PMID: 33415794 PMCID: PMC8783695 DOI: 10.1002/anie.202016223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 09/28/2023]
Abstract
We present a new class of DNA-based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding-upon-repair DNA nanoswitches are synthetic DNA sequences containing O6 -methyl-guanine (O6 -MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of the O6 -MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding-upon-repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors.
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Affiliation(s)
- Nada Farag
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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14
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Sorrentino D, Ranallo S, Ricci F. Rational Control of the Activity of a Cu 2+-Dependent DNAzyme by Re-engineering Purely Entropic Intrinsically Disordered Domains. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9300-9305. [PMID: 33001621 DOI: 10.1021/acsami.0c09472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The function and activity of many proteins is finely controlled by the modulation of the entropic contribution of intrinsically disordered domains that are not directly involved in any recognition event. Inspired by this mechanism, we demonstrate here that we could finely regulate the catalytic activity of a model DNAzyme (i.e., a synthetic DNA sequence with enzyme-like properties) by rationally introducing intrinsically disordered nucleic acid portions in its original sequence. More specifically, we have re-engineered here the well-characterized Cu2+-dependent DNAzyme that catalyzes a self-cleavage reaction by introducing a poly(T) linker domain in its sequence. The linker is not directly involved in the recognition event and connects the two domains that fold to form the catalytic core. We demonstrate that the enzyme-like activity of this re-engineered DNAzyme can be modulated in a predictable and fine way by changing the length, and thus entropy, of such a linker domain. Given these attributes, the rational design of intrinsically disordered domains could expand the available toolbox to achieve a control of the activity of DNAzymes and, in analogy, ribozymes through a purely entropic contribution.
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Affiliation(s)
- Daniela Sorrentino
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Simona Ranallo
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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15
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nada Farag
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Giulia Palermo
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
- Department of Chemistry University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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16
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Zhou Z, Fan D, Wang J, Sohn YS, Nechushtai R, Willner I. Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007355. [PMID: 33470517 DOI: 10.1002/smll.202007355] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/06/2020] [Indexed: 05/21/2023]
Abstract
The reversible and switchable triggered reconfiguration of tetrahedra nanostructures from monomer tetrahedra structures into dimer or trimer structures is introduced. The triggered bridging of monomer tetrahedra by K+ -ion-stabilized G-quadruplexes or T-A•T triplexes leads to dimer or trimer tetrahedra structures that are separated by crown ether or basic pH conditions, respectively. The signal-triggered dimerization/trimerization of DNA tetrahedra structures is used to develop multiplexed miRNA-sensing platforms, and the tetrahedra mixture is used for intracellular sensing and imaging of miRNAs.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Daoqing Fan
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yang Sung Sohn
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Nechushtai
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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17
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Inda ME, Almada JC, Vazquez DB, Bortolotti A, Fernández A, Ruysschaert JM, Cybulski LE. Driving the catalytic activity of a transmembrane thermosensor kinase. Cell Mol Life Sci 2020; 77:3905-3912. [PMID: 31802141 PMCID: PMC11104839 DOI: 10.1007/s00018-019-03400-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
DesK is a Bacillus thermosensor kinase that is inactive at high temperatures but turns activated when the temperature drops below 25 °C. Surprisingly, the catalytic domain (DesKC) lacking the transmembrane region is more active at higher temperature, showing an inverted regulation regarding DesK. How does the transmembrane region control the catalytic domain, repressing activity at high temperatures, but allowing activation at lower temperatures? By designing a set of temperature minimized sensors that share the same catalytic cytoplasmic domain but differ in number and position of hydrogen-bond (H-bond) forming residues along the transmembrane helix, we are able to tune, invert or disconnect activity from the input signal. By favoring differential H-bond networks, the activation peak could be moved towards lower or higher temperatures. This principle may be involved in regulation of other sensors as environmental physicochemical changes or mutations that modify the transmembrane H-bond pattern can tilt the equilibrium favoring alternative conformations.
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Affiliation(s)
- María Eugenia Inda
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Argentine National Research Council-CONICET, Suipacha 531, 2000, Rosario, Argentina
| | - Juan Cruz Almada
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Argentine National Research Council-CONICET, Suipacha 531, 2000, Rosario, Argentina
| | - Daniela Belén Vazquez
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Argentine National Research Council-CONICET, Suipacha 531, 2000, Rosario, Argentina
| | - Ana Bortolotti
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Argentine National Research Council-CONICET, Suipacha 531, 2000, Rosario, Argentina
| | - Ariel Fernández
- Argentine Mathematics Institute-IAM/CONICET, 1053, Buenos Aires, Argentina
- Chemistry Institute-INQUISUR/UNS, National Research Council-CONICET, 8000, Bahía Blanca, Argentina
| | - Jean Marie Ruysschaert
- Structure et Fonction des Membranes Biologiques (SFMB) Campus de la Plaine, Boulevard du Triomphe, CP206/02, 1050, Brussels, Belgium
| | - Larisa Estefanía Cybulski
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Argentine National Research Council-CONICET, Suipacha 531, 2000, Rosario, Argentina.
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