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Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
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2
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Xu L, Hu Y, Zhao D, Zhang W, Wang H. A Versatile Assembly Approach toward Multifunctional Supramolecular Poly(Ionic Liquid) Nanoporous Membranes in Water. Macromol Rapid Commun 2023; 44:e2300189. [PMID: 37248809 DOI: 10.1002/marc.202300189] [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: 04/03/2023] [Revised: 05/25/2023] [Indexed: 05/31/2023]
Abstract
Hydrogen (H)-bonding-integration of multiple ingredients into supramolecular polyelectrolyte nanoporous membranes in water, thereby achieving tailor-made porous architectures, properties, and functionalities, remains one of the foremost challenges in materials chemistry due to the significantly opposing action of water molecules against H-bonding. Herein, a strategy is described that allows direct fusing of the functional attributes of small additives into water-involved hydrogen bonding assembled supramolecular poly(ionic liquid) (PIL) nanoporous membranes (SPILMs) under ambient conditions. It discloses that the pore size distributions and mechanical properties of SPILMs are rationally controlled by tuning the H-bonding interactions between small additives and homo-PIL. It demonstrates that, benefiting from the synergy of multiple noncovalent interactions, small dye additives/homo-PIL solutions can be utilized as versatile inks for yielding colorful light emitting films with robust underwater adhesion strength, excellent stretchability, and flexibility on diverse substrates, including both hydrophilic and hydrophobic surfaces. This system provides a general platform for integrating the functional attributes of a diverse variety of additives into SPILMs to create multifunctional and programmable materials in water.
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Affiliation(s)
- Luyao Xu
- Key Laboratory of Functional Polymer Materials of the Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yingyi Hu
- Key Laboratory of Functional Polymer Materials of the Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Dongbing Zhao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Wangqing Zhang
- Key Laboratory of Functional Polymer Materials of the Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Hong Wang
- Key Laboratory of Functional Polymer Materials of the Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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3
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [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: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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4
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Roche TP, Nedumpurath PJ, Karunakaran SC, Schuster GB, Hud NV. One-Pot Formation of Pairing Proto-RNA Nucleotides and Their Supramolecular Assemblies. Life (Basel) 2023; 13:2200. [PMID: 38004340 PMCID: PMC10672710 DOI: 10.3390/life13112200] [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: 10/09/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Most contemporary theories for the chemical origins of life include the prebiotic synthesis of informational polymers, including strong interpretations of the RNA World hypothesis. Existing challenges to the prebiotic emergence of RNA have encouraged exploration of the possibility that RNA was preceded by an ancestral informational polymer, or proto-RNA, that formed more easily on the early Earth. We have proposed that the proto-nucleobases of proto-RNA would have readily formed glycosides with ribose and that these proto-nucleosides would have formed base pairs as monomers in aqueous solution, two properties not exhibited by the extant nucleosides or nucleotides. Here we demonstrate that putative proto-nucleotides of the model proto-nucleobases barbituric acid and melamine can be formed in the same one-pot reaction with ribose-5-phosphate. Additionally, the proto-nucleotides formed in these reactions spontaneously form assemblies that are consistent with the presence of Watson-Crick-like base pairs. Together, these results provide further support for the possibility that heterocycles closely related to the extant bases of RNA facilitated the prebiotic emergence of RNA-like molecules, which were eventually replaced by RNA over the course of chemical and biological evolution.
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Affiliation(s)
| | | | | | | | - Nicholas V. Hud
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (T.P.R.); (P.J.N.); (S.C.K.); (G.B.S.)
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5
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González-Sánchez M, Mayoral MJ, Vázquez-González V, Paloncýová M, Sancho-Casado I, Aparicio F, de Juan A, Longhi G, Norman P, Linares M, González-Rodríguez D. Stacked or Folded? Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers. J Am Chem Soc 2023; 145:17805-17818. [PMID: 37531225 PMCID: PMC10436278 DOI: 10.1021/jacs.3c04773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 08/04/2023]
Abstract
Self-assembled nanotubes exhibit impressive biological functions that have always inspired supramolecular scientists in their efforts to develop strategies to build such structures from small molecules through a bottom-up approach. One of these strategies employs molecules endowed with self-recognizing motifs at the edges, which can undergo either cyclization-stacking or folding-polymerization processes that lead to tubular architectures. Which of these self-assembly pathways is ultimately selected by these molecules is, however, often difficult to predict and even to evaluate experimentally. We show here a unique example of two structurally related molecules substituted with complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway taken is determined by chelate cooperativity, that is, by their propensity to assemble in specific cyclic structures through Watson-Crick pairing. Because of chelate cooperativities that differ in several orders of magnitude, these molecules exhibit distinct supramolecular scenarios prior to their polymerization that generate self-assembled nanotubes with different internal monomer arrangements, either stacked or coiled, which lead at the same time to opposite helicities and chiroptical properties.
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Affiliation(s)
- Marina González-Sánchez
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María J. Mayoral
- Department
of Inorganic Chemistry, Universidad Complutense
de Madrid, 28040 Madrid, Spain
| | - Violeta Vázquez-González
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Markéta Paloncýová
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký
University Olomouc, 779 00 Olomouc, Czech Republic
| | - Irene Sancho-Casado
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fátima Aparicio
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alberto de Juan
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Giovanna Longhi
- Department
of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Patrick Norman
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Mathieu Linares
- Laboratory
of Organic Electronics and Scientific Visualization Group, ITN, Campus
Norrköping; Swedish e-Science Research Centre (SeRC), Linköping University, 58183 Linköping, Sweden
| | - David González-Rodríguez
- Nanostructured
Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
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6
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Merz GE, Chalkley MJ, Tan SK, Tse E, Lee J, Prusiner SB, Paras NA, DeGrado WF, Southworth DR. Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments. Nat Commun 2023; 14:3048. [PMID: 37236970 PMCID: PMC10220082 DOI: 10.1038/s41467-023-38537-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Accumulation of filamentous aggregates of tau protein in the brain is a pathological hallmark of Alzheimer's disease (AD) and many other neurodegenerative tauopathies. The filaments adopt disease-specific cross-β amyloid conformations that self-propagate and are implicated in neuronal loss. Development of molecular diagnostics and therapeutics is of critical importance. However, mechanisms of small molecule binding to the amyloid core is poorly understood. We used cryo-electron microscopy to determine a 2.7 Å structure of AD patient-derived tau paired-helical filaments bound to the PET ligand GTP-1. The compound is bound stoichiometrically at a single site along an exposed cleft of each protofilament in a stacked arrangement matching the fibril symmetry. Multiscale modeling reveals pi-pi aromatic interactions that pair favorably with the small molecule-protein contacts, supporting high specificity and affinity for the AD tau conformation. This binding mode offers critical insight into designing compounds to target different amyloid folds found across neurodegenerative diseases.
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Affiliation(s)
- Gregory E Merz
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew J Chalkley
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Joanne Lee
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Nick A Paras
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - William F DeGrado
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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7
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Revignas D, Ferrarini A. Spontaneous Twisting of Achiral Hard Rod Nematics. PHYSICAL REVIEW LETTERS 2023; 130:028102. [PMID: 36706401 DOI: 10.1103/physrevlett.130.028102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/25/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Since Onsager's seminal work, hard rods have been taken as a prototype of nematic liquid crystals, characterized by uniaxial order and a uniform director field as a ground state. Here, using Onsager theory to calculate the free energy in the presence of arbitrary deformations, we find that hard rod nematics have an intrinsic tendency to twist around their ordering axis (double twist), driven by a mechanism in which the orientational fluctuations of particles play a key role. The anisotropic hard core potential used here is arguably the simplest form of interaction able to originate spontaneous breaking of mirror symmetry in a 3D fluid. Our results are discussed in relation to the recent discovery of a double twisted ground state in cylindrically confined lyotropic chromonic liquid crystals.
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Affiliation(s)
- Davide Revignas
- Department of Chemical Sciences, University of Padova Via Marzolo 1, 35131 Padova, Italy
| | - Alberta Ferrarini
- Department of Chemical Sciences, University of Padova Via Marzolo 1, 35131 Padova, Italy
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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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Zhang J, Xu S, Zhang L, Wang X, Bian Y, Tang S, Zhang R, Tao Y, Huang W, Chen R. Highly Efficient and Robust Full-Color Organic Afterglow through 2D Superlattices Embedment. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2206712. [PMID: 36086873 DOI: 10.1002/adma.202206712] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Purely organic afterglow (POA) originating from the slow radiative decay of stabilized triplet excited states has shown amazing potential in many fields. However, achieving highly stable POA with high phosphorescent quantum yield (PhQY) and long lifetime is still a formidable challenge owing to the intrinsically active and sensitive nature of triplet excitons. Here, triplet excitons of phosphors are protected and stabilized by embedding in tricomponent trihapto self-assembled 2D hydrogen-bonded superlattices, which not only enables deep-blue POA with high PhQY (up to 65%), ultralong lifetime (over 1300 ms) and the highest figure-of-merit at room temperature, but also achieves excellent stability capable of resisting quenching effects of oxygen, solvent, pressure, light, and heat. In addition, the POA color is tuned from deep-blue to red via efficient Förster resonance energy transfer from the deep-blue POA emitters to the fluorophores. Moreover, with the high-performance, robust, and full-color POA materials, flexible anti-counterfeit displays and direct-current (DC)-driven lifetime-encrypted color Morse Code applications are facilely realized.
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Affiliation(s)
- Jingyu Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Shen Xu
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Longyan Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Xin Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Yanfang Bian
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Senlin Tang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Runqi Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Ye Tao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Wei Huang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
- Frontiers Science Center for Flexible Electronics (FSCFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Shaanxi Key Laboratory of Flexible Electronics, Xi'an Key Laboratory of Flexible Electronics, Xi'an Key Laboratory of Biomedical Materials & Engineering, Xi'an Institute of Flexible Electronics, Institute of Flexible Electronics (IFE), Northwestern Polytechnical University, Xi'an, Shanxi, 710072, China
| | - Runfeng Chen
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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10
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Prebiotic synthesis of noncanonical nucleobases under plausible alkaline hydrothermal conditions. Sci Rep 2022; 12:15140. [PMID: 36071125 PMCID: PMC9452575 DOI: 10.1038/s41598-022-19474-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Herein, the potential of alkaline hydrothermal environments for the synthesis of possible ancestral pre-RNA nucleobases using cyanide as a primary source of carbon and nitrogen is described. Water cyanide polymerizations were assisted by microwave radiation to obtain high temperature and a relatively high pressure (MWR, 180 °C, 15 bar) and were also carried out using a conventional thermal system (CTS, 80 °C, 1 bar) to simulate subaerial and aerial hydrothermal conditions, respectively, on the early Earth. For these syntheses, the initial concentration of cyanide and the diffusion effects were studied. In addition, it is well known that hydrolysis conditions are directly related to the amount and diversity of organic molecules released from cyanide polymers. Thus, as a first step, we studied the effect of several hydrolysis procedures, generally used in prebiotic chemistry, on some of the potential pre-RNA nucleobases of interest, together with some of their isomers and/or deamination products, also presumably formed in these complex reactions. The results show that the alkaline hydrothermal scenarios with a relatively constant pH are good geological scenarios for the generation of noncanonical nucleobases using cyanide as a prebiotic precursor.
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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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Hassenkam T, Deamer D. Visualizing RNA polymers produced by hot wet-dry cycling. Sci Rep 2022; 12:10098. [PMID: 35739144 PMCID: PMC9226162 DOI: 10.1038/s41598-022-14238-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/03/2022] [Indexed: 11/24/2022] Open
Abstract
It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet-dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers and polymers. The aim of the study reported here was to verify this claim and visualize the products prepared from solutions composed of single mononucleotides and 1:1 mixture of two mononucleotides. Therefore, we designed experiments that allowed comparisons of all such mixtures representing six combinations of the four mononucleotides of RNA. We observed irregular stringy patches and crystal strands when wet-dry cycling was performed at room temperature (20 °C). However, when the same solutions were exposed to wet-dry cycles at 80 °C, we observed what appeared to be true polymers. Their thickness was consistent with RNA-like products composed of covalently bonded monomers, while irregular strings and crystal segments of mononucleotides dried or cycled at room temperature were consistent with structures assembled and stabilized by weak hydrogen bonds. In a few instances we observed rings with short polymer attachments. These observations are consistent with previous claims of polymerization during wet-dry cycling. We conclude that RNA-like polymers and rings could have been synthesized non-enzymatically in freshwater hot springs on the prebiotic Earth with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.
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Affiliation(s)
- Tue Hassenkam
- Globe Institute, University of Copenhagen, 1350, Copenhagen, Denmark.
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
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13
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Arsenie LV, Semsarilar M, Brendel JC, Lacroix-Desmazes P, Ladmiral V, Catrouillet S. Supramolecular co-assembly of water-soluble nucleobase-containing copolymers: bioinspired synthetic platforms towards new biomimetic materials. Polym Chem 2022. [DOI: 10.1039/d2py00872f] [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
This study presents the development of new co-assembled copolymers architectures at physiological pH (pH=7.4) formed via H-bonds between complementary nucleobase-containing copolymers. Well-defined hydrophilic copolymers were synthesised by RAFT polymerisation: statistical...
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Arsenie LV, Ladmiral V, Lacroix-Desmazes P, Catrouillet S. Nucleobase-containing polymer architectures controlled by supramolecular interactions: the key to achieve biomimetic platforms with various morphologies. Polym Chem 2022. [DOI: 10.1039/d2py00920j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Challenges and opportunities in supramolecular self-assembly of synthetic nucleobase-containing copolymers.
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Kovalenko SP. On the Origin of Genetically Coded Protein Synthesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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