1
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Feng X, Wang X, Liu J, Fu A, Wang Y, Wei S, Chen H, She R, Wang Y, Cui X, Hou H, Xu Y, Wu Y, Meng Q, Zhang L, Wang S, Zhao J. Accelerated Screening of Alternative DNA Base-Organic Molecule-Base Architectures via Integrated Theory and Experiment. Angew Chem Int Ed Engl 2024; 63:e202408003. [PMID: 38771290 DOI: 10.1002/anie.202408003] [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: 04/27/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/22/2024]
Abstract
Organic molecule-mediated noncanonical DNA self-assembly expands the standard DNA base-pairing alphabets. However, only a very limited number of small molecules have been recognized as mediators because of the tedious and complicated experiments like crystallization and microscopy imaging. Here we present an integrative screening protocol incorporating molecular dynamics (MD) for fast theoretical simulation and native polyacrylamide gel electrophoresis for convenient experimental validation. Melamine, the molecule that was confirmed mediating noncanonical DNA base-pairing, and 38 other candidate molecules were applied to demonstrate the feasibility of this protocol. We successfully identified seven stable noncanonical DNA duplex structures, and another eight novel structures with sub-stability. In addition, we discovered that hairpins at both ends can significantly stabilize the noncanonical DNA structures, providing a guideline to design small organic molecule-incorporated DNA structures. Such an efficient screening protocol will accelerate the design of alternative DNA-molecule architectures beyond Watson-Crick pairs. Considering the wide range of potential mediators, it will also facilitate applications such as noncovalent, highly dense loading of drug molecules in DNA-based delivery system and probe design for sensitive detection of certain molecules.
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Affiliation(s)
- Xinyu Feng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xianwen Wang
- School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Jiahe Liu
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Aiting Fu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Ying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Shuheng Wei
- Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Huichao Chen
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Rui She
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yangying Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xiao Cui
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hui Hou
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yuanyuan Xu
- Department of Pediatric Critical Care Medicine, Children's Medical Center of Anhui Medical University, Hefei, Anhui, 230051, China
| | - Yujing Wu
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Qian Meng
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Song Wang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jiemin Zhao
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
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2
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Hu Y, Willner I. Oligo-Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications. Angew Chem Int Ed Engl 2024:e202412106. [PMID: 39183707 DOI: 10.1002/anie.202412106] [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: 06/27/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Oligo-adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter-triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A-motif duplex, A-cyanuric acid triplex, A-coralyne-A duplex, and T ⋅ A-T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli-responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA-derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli-responsiveness and conformational characteristics, advanced material development, such as pH-cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli-responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications.
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Affiliation(s)
- Yuwei Hu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, 138634, Singapore, Republic of Singapore
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
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3
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Ye R, Wang Y, Liu Y, Cai P, Song J. Self-assembled methodologies for the construction of DNA nanostructures and biological applications. Biomater Sci 2024; 12:3712-3724. [PMID: 38912847 DOI: 10.1039/d4bm00584h] [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: 06/25/2024]
Abstract
Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.
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Affiliation(s)
- Rui Ye
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuqi Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Cai
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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4
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Hu Y, Liu J, Ke Y, Wang B, Lim JYC, Dong Z, Long Y, Willner I. Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness. ACS APPLIED MATERIALS & INTERFACES 2024; 16:29235-29247. [PMID: 38769743 DOI: 10.1021/acsami.4c03834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Expanding the functions and applications of DNA by integrating noncanonical bases and structures into biopolymers is a continuous scientific effort. An adenine-rich strand (A-strand) is introduced as functional scaffold revealing, in the presence of the low-molecular-weight cofactor cyanuric acid (CA, pKa 6.9), supramolecular hydrogel-forming efficacies demonstrating multiple pH-responsiveness. At pH 1.2, the A-strand transforms into a parallel A-motif duplex hydrogel cross-linked by AH+-H+A units due to the protonation of adenine (pKa 3.5). At pH 5.2, and in the presence of coadded CA, a helicene-like configuration is formed between adenine and protonated CA, generating a parallel A-CA triplex cross-linked hydrogel. At pH 8.0, the hydrogel undergoes transition into a liquid state by deprotonation of CA cofactor units and disassembly of A-CA triplex into its constituent components. Density functional theory calculations and molecular dynamics simulations, supporting the structural reconfigurations of A-strand in the presence of CA, are performed. The sequential pH-stimulated hydrogel states are rheometrically characterized. The hydrogel framework is loaded with fluorescein-labeled insulin, and the pH-stimulated release of insulin from the hydrogel across the pH barriers present in the gastrointestinal tract is demonstrated. The results provide principles for future application of the hydrogel for oral insulin administration for diabetes.
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Affiliation(s)
- Yuwei Hu
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Jia Liu
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yujie Ke
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jason Y C Lim
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Zhaogang Dong
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
| | - Yi Long
- Electronic Engineering Department, The Chinese University of Hong Kong, Hong Kong 999077, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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5
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Lachance-Brais C, Yao C, Reyes-Valenzuela A, Asohan J, Guettler E, Sleiman HF. Exceptional Nuclease Resistance of DNA and RNA with the Addition of Small-Molecule Nucleobase Mimics. J Am Chem Soc 2024; 146:5811-5822. [PMID: 38387071 DOI: 10.1021/jacs.3c07023] [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: 02/24/2024]
Abstract
Nucleases present a formidable barrier to the application of nucleic acids in biology, significantly reducing the lifetime of nucleic acid-based drugs. Here, we develop a novel methodology to protect DNA and RNA from nucleases by reconfiguring their supramolecular structure through the addition of a nucleobase mimic, cyanuric acid. In the presence of cyanuric acid, polyadenine strands assemble into triple helical fibers known as the polyA/CA motif. We report that this motif is exceptionally resistant to nucleases, with the constituent strands surviving for up to 1 month in the presence of serum. The conferred stability extends to adjacent non-polyA sequences, albeit with diminishing returns relative to their polyA sections due to hypothesized steric clashes. We introduce a strategy to regenerate stability through the introduction of free polyA strands or positively charged amino side chains, enhancing the stability of sequences of varied lengths. The proposed protection mechanism involves enzyme failure to recognize the unnatural polyA/CA motif, coupled with the motif's propensity to form long, bundling supramolecular fibers. The methodology provides a fundamentally new mechanism to protect nucleic acids from degradation using a supramolecular approach and increases lifetime in serum to days, weeks, or months.
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Affiliation(s)
| | - Chihyu Yao
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | | | - Jathavan Asohan
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Elizabeth Guettler
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Hanadi F Sleiman
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
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6
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Lachance‐Brais C, Rammal M, Asohan J, Katolik A, Luo X, Saliba D, Jonderian A, Damha MJ, Harrington MJ, Sleiman HF. Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205713. [PMID: 36752390 PMCID: PMC10131789 DOI: 10.1002/advs.202205713] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/18/2022] [Indexed: 05/31/2023]
Abstract
Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 103 Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 105 Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.
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Affiliation(s)
| | - Mostafa Rammal
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Jathavan Asohan
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Adam Katolik
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Xin Luo
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Antranik Jonderian
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | | | - Hanadi F. Sleiman
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
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7
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Peng S, Chang Y, Zeng X, Lai R, Yang M, Wang D, Zhou X, Shao Y. Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy. Anal Chim Acta 2023; 1241:340777. [PMID: 36657870 DOI: 10.1016/j.aca.2022.340777] [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: 10/05/2022] [Revised: 12/04/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.
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Affiliation(s)
- Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
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8
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Schuster GB, Hud NV, Alenaizan A. Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions. J Phys Chem B 2022; 126:10758-10767. [PMID: 36502412 DOI: 10.1021/acs.jpcb.2c05934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
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9
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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10
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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11
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Alenaizan A. Structural Analysis of the Poly(thymidine)-Melamine Assembly. J Phys Chem B 2022; 126:6948-6954. [PMID: 36027577 DOI: 10.1021/acs.jpcb.2c04665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia 31261
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12
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Zheng B, Dong H, Zhu J, Zhang Q, Yang S, Yao D. A rational design of a cascaded DNA circuit for nanoparticle assembly and its application in the discrimination of single-base changes. J Mater Chem B 2022; 10:4561-4567. [PMID: 35621087 DOI: 10.1039/d2tb00155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the field of dynamic DNA nanotechnology, a designable DNA assembly circuit based on the toehold-mediated strand displacement reaction has demonstrated its ability to program the self-assembly of nanoparticles. However, the laborious work for the modification of nanoparticles with oligonucleotides, the long assembly time, and the circuit leakage prevent its further and scalable applications. To this end, cascaded circuits composed of two recycling circles are rationally designed in this study. Through the pre-initiation of the autonomous reaction, nanoparticles as sensing elements and no additionally exposed bases on the substrate hybridized with fuel strand, the real assembly time and signal leakage for diagnostic application can be effectively reduced and eliminated, thus offering a promising methodology for future point-of-care testing.
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Affiliation(s)
- Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Huaze Dong
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Jinmiao Zhu
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Shiwei Yang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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Hennecker CD, Lachance-Brais C, Sleiman H, Mittermaier A. Using transient equilibria (TREQ) to measure the thermodynamics of slowly assembling supramolecular systems. SCIENCE ADVANCES 2022; 8:eabm8455. [PMID: 35385301 PMCID: PMC8985918 DOI: 10.1126/sciadv.abm8455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Supramolecular chemistry involves the noncovalent assembly of monomers into materials with unique properties and wide-ranging applications. Thermal analysis is a key analytical tool in this field, as it provides quantitative thermodynamic information on both the structural stability and nature of the underlying molecular interactions. However, there exist many supramolecular systems whose kinetics are so slow that the thermodynamic methods currently applied are unreliable or fail completely. We have developed a simple and rapid spectroscopic method for extracting accurate thermodynamic parameters from these systems. It is based on repeatedly raising and lowering the temperature during assembly and identifying the points of transient equilibrium as they are passed on the up- and down-scans. In a proof-of-principle application to the coassembly of polydeoxyadenosine (polyA) containing 15 adenosines and cyanuric acid (CA), we found that roughly 30% of the CA binding sites on the polyA chains were unoccupied, with implications for high-valence systems.
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Fabricating functionalized fibres. Nat Rev Chem 2021; 6:5. [PMID: 37117621 DOI: 10.1038/s41570-021-00357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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