1
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Gonçalves D. Rethinking life and predicting its origin. Theory Biosci 2024:10.1007/s12064-024-00420-9. [PMID: 38922566 DOI: 10.1007/s12064-024-00420-9] [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: 06/15/2021] [Accepted: 06/24/2024] [Indexed: 06/27/2024]
Abstract
The definition, origin and recreation of life remain elusive. As others have suggested, only once we put life into reductionist physical terms will we be able to solve those questions. To that end, this work proposes the phenomenon of life to be the product of two dissipative mechanisms. From them, one characterises extant biological life and deduces a testable scenario for its origin. The proposed theory of life allows its replication, reinterprets ecological evolution and creates new constraints on the search for life.
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Affiliation(s)
- Diogo Gonçalves
- Centro de Química Estrutural and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001, Lisbon, Portugal.
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2
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Sánchez IE, Galpern EA, Ferreiro DU. Solvent constraints for biopolymer folding and evolution in extraterrestrial environments. Proc Natl Acad Sci U S A 2024; 121:e2318905121. [PMID: 38739787 PMCID: PMC11127021 DOI: 10.1073/pnas.2318905121] [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: 10/29/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets.
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Affiliation(s)
- Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
| | - Ezequiel A. Galpern
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
| | - Diego U. Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
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3
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [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: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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4
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Grefenstette N, Chou L, Colón-Santos S, Fisher TM, Mierzejewski V, Nural C, Sinhadc P, Vidaurri M, Vincent L, Weng MM. Chapter 9: Life as We Don't Know It. ASTROBIOLOGY 2024; 24:S186-S201. [PMID: 38498819 DOI: 10.1089/ast.2021.0103] [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: 03/20/2024]
Abstract
While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.
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Affiliation(s)
- Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Georgetown University, Washington, DC, USA
| | | | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Arizona, USA
| | | | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Monica Vidaurri
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Howard University, DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
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5
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Randolph-Flagg NG, Ely T, Som SM, Shock EL, German CR, Hoehler TM. Phosphate availability and implications for life on ocean worlds. Nat Commun 2023; 14:2388. [PMID: 37185347 PMCID: PMC10130162 DOI: 10.1038/s41467-023-37770-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Several moons in the outer solar system host liquid water oceans. A key next step in assessing the habitability of these ocean worlds is to determine whether life's elemental and energy requirements are also met. Phosphorus is required by all known life and is often limited to biological productivity in Earth's oceans. This raises the possibility that its availability may limit the abundance or productivity of Earth-like life on ocean worlds. To address this potential problem, here we calculate the equilibrium dissolved phosphate concentrations associated with the reaction of water and rocks-a key driver of ocean chemical evolution-across a broad range of compositional inputs and reaction conditions. Equilibrium dissolved phosphate concentrations range from 10-11 to 10-1 mol/kg across the full range of carbonaceous chondrite compositions and reaction conditions considered, but are generally > 10-5 mol/kg for most plausible scenarios. Relative to the phosphate requirements and uptake kinetics of microorganisms in Earth's oceans, such concentrations would be sufficient to support initially rapid cell growth and construction of global ocean cell populations larger than those observed in Earth's deep oceans.
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Affiliation(s)
- Noah G Randolph-Flagg
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA.
- NASA Postdoctoral Program, Universities Space Research Association, Columbia, MD, USA.
- Blue Marble Space Institute of Science, Seattle, WA, USA.
| | - Tucker Ely
- NASA Postdoctoral Program, Universities Space Research Association, Columbia, MD, USA
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, USA
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - Sanjoy M Som
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Everett L Shock
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - Christopher R German
- Dept. Geology and Geophysics, Woods Hole Oceanographic Institution Woods Hole, Falmouth, MA, USA
| | - Tori M Hoehler
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
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6
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Dujardin A, Himbert S, Pudritz R, Rheinstädter MC. The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010112. [PMID: 36676060 PMCID: PMC9860743 DOI: 10.3390/life13010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/04/2023]
Abstract
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.
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Affiliation(s)
- Alix Dujardin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Ralph Pudritz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
- Correspondence: ; Tel.: +1-(905)-525-9140-23134; Fax: +1-(905)-546-1252
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7
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Špaček J, Benner SA. Agnostic Life Finder (ALF) for Large-Scale Screening of Martian Life During In Situ Refueling. ASTROBIOLOGY 2022; 22:1255-1263. [PMID: 35796703 DOI: 10.1089/ast.2021.0070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Before the first humans depart for Mars in the next decade, hundreds of tons of martian water-ice must be harvested to produce propellant for the return vehicle, a process known as in situ resource utilization (ISRU). We describe here an instrument, the Agnostic Life Finder (ALF), that is an inexpensive life-detection add-on to ISRU. ALF exploits a well-supported view that informational genetic biopolymers in life in water must have two structural features: (1) Informational biopolymers must carry a repeating charge; they must be polyelectrolytes. (2) Their building blocks must fit into an aperiodic crystal structure; the building blocks must be size-shape regular. ALF exploits the first structural feature to extract polyelectrolytes from ∼10 cubic meters of mined martian water by applying a voltage gradient perpendicularly to the water's flow. This gradient diverts polyelectrolytes from the flow toward their respective electrodes (polyanions to the anode, polycations to the cathode), where they are captured in cartridges before they encounter the electrodes. There, they can later be released to analyze their building blocks, for example, by mass spectrometry or nanopore. Upstream, martian cells holding martian informational polyelectrolytes are disrupted by ultrasound. To manage the (unknown) conductivity of the water due to the presence of salts, the mined water is preconditioned by electrodialysis using porous membranes. ALF uses only resources and technology that must already be available for ISRU. Thus, life detection is easily and inexpensively integrated into SpaceX or NASA ISRU missions.
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Affiliation(s)
- Jan Špaček
- Firebird Biomolecular Sciences, LLC, Alachua, Florida, USA
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8
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Hoshika S, Shukla MS, Benner SA, Georgiadis MM. Visualizing "Alternative Isoinformational Engineered" DNA in A- and B-Forms at High Resolution. J Am Chem Soc 2022; 144:15603-15611. [PMID: 35969672 DOI: 10.1021/jacs.2c05255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A fundamental property of DNA built from four informational nucleotide units (GCAT) is its ability to adopt different helical forms within the context of the Watson-Crick pair. Well-characterized examples include A-, B-, and Z-DNA. For this study, we created an isoinformational biomimetic polymer, built (like standard DNA) from four informational "letters", but with the building blocks being artificial. This ALternative Isoinformational ENgineered (ALIEN) DNA was hypothesized to support two nucleobase pairs, the P:Z pair matching 2-amino-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one with 6-amino-3-5-nitro-1H-pyridin-2-one and the B:S pair matching 6-amino-4-hydroxy-5-1H-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one. We report two structures of ALIEN DNA duplexes at 1.2 Å resolution and a third at 1.65 Å. All of these are built from a single self-complementary sequence (5'-CTSZZPBSBSZPPBAG) that includes 12 consecutive ALIEN nucleotides. We characterized the helical, nucleobase pair, and dinucleotide step parameters of ALIEN DNA in these structures. In addition to showing that ALIEN pairs retain basic Watson-Crick pairing geometry, two of the ALIEN DNA structures are characterized as A-form DNA and one as B-form DNA. We identified parameters that map differences effecting the transition between the two helical forms; these same parameters distinguish helical forms of isoinformational natural DNA. Collectively, our analyses suggest that ALIEN DNA retains essential structural features of natural DNA, not only its information density and Watson-Crick pairing but also its ability to adopt two canonical forms.
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Madhura S Shukla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Steven A Benner
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
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9
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Smith HH, Hyde AS, Simkus DN, Libby E, Maurer SE, Graham HV, Kempes CP, Sherwood Lollar B, Chou L, Ellington AD, Fricke GM, Girguis PR, Grefenstette NM, Pozarycki CI, House CH, Johnson SS. The Grayness of the Origin of Life. Life (Basel) 2021; 11:498. [PMID: 34072344 PMCID: PMC8226951 DOI: 10.3390/life11060498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/05/2022] Open
Abstract
In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.
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Affiliation(s)
- Hillary H. Smith
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew S. Hyde
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Danielle N. Simkus
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | - Eric Libby
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
- Icelab, Umeå University, 90187 Umeå, Sweden
| | - Sarah E. Maurer
- Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT 06050, USA;
| | - Heather V. Graham
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | | | | | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - G. Matthew Fricke
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87108, USA;
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Natalie M. Grefenstette
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Chad I. Pozarycki
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Christopher H. House
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Science, Technology and International Affairs Program, Georgetown University, Washington, DC 20057, USA
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10
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Bains W, Petkowski JJ, Zhan Z, Seager S. Evaluating Alternatives to Water as Solvents for Life: The Example of Sulfuric Acid. Life (Basel) 2021; 11:400. [PMID: 33925658 PMCID: PMC8145300 DOI: 10.3390/life11050400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 12/18/2022] Open
Abstract
The chemistry of life requires a solvent, which for life on Earth is water. Several alternative solvents have been suggested, but there is little quantitative analysis of their suitability as solvents for life. To support a novel (non-terrestrial) biochemistry, a solvent must be able to form a stable solution of a diverse set of small molecules and polymers, but must not dissolve all molecules. Here, we analyze the potential of concentrated sulfuric acid (CSA) as a solvent for biochemistry. As CSA is a highly effective solvent but a reactive substance, we focused our analysis on the stability of chemicals in sulfuric acid, using a model built from a database of kinetics of reaction of molecules with CSA. We consider the sulfuric acid clouds of Venus as a test case for this approach. The large majority of terrestrial biochemicals have half-lives of less than a second at any altitude in Venus's clouds, but three sets of human-synthesized chemicals are more stable, with average half-lives of days to weeks at the conditions around 60 km altitude on Venus. We show that sufficient chemical structural and functional diversity may be available among those stable chemicals for life that uses concentrated sulfuric acid as a solvent to be plausible. However, analysis of meteoritic chemicals and possible abiotic synthetic paths suggests that postulated paths to the origin of life on Earth are unlikely to operate in CSA. We conclude that, contrary to expectation, sulfuric acid is an interesting candidate solvent for life, but further work is needed to identify a plausible route for life to originate in it.
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Affiliation(s)
- William Bains
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
- School of Physics & Astronomy, Cardiff University, 4 The Parade, Cardiff CF24 3AA, UK
| | - Janusz Jurand Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
| | - Zhuchang Zhan
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Fong KD, Self J, McCloskey BD, Persson KA. Ion Correlations and Their Impact on Transport in Polymer-Based Electrolytes. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02545] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kara D. Fong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Julian Self
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Bryan D. McCloskey
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kristin A. Persson
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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12
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:molecules25153483. [PMID: 32751873 PMCID: PMC7435384 DOI: 10.3390/molecules25153483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.
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13
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Lutz JF. 100th Anniversary of Macromolecular Science Viewpoint: Toward Artificial Life-Supporting Macromolecules. ACS Macro Lett 2020; 9:185-189. [PMID: 35638671 DOI: 10.1021/acsmacrolett.9b00938] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Terrestrial Life is based on polymers. In all known living organisms, DNA stores genetic information, mutates, self-replicates, and guides the synthesis of messenger molecules. Although the function of nucleic acids is well-understood, the development of artificial macromolecular mimics remains very limited. Laboratory-synthesized nucleic acids still support Life, and some nucleic acids analogues exhibit biological functions. Yet, after hundred years of polymer science, no other type of Life-supporting macromolecule (i.e., non-nucleic acids) has ever been reported. In this context, the aim of the present viewpoint is to discuss important challenges that shall be addressed by polymer chemists to achieve artificial Life. Similarly to DNA, an artificial Life-supporting macromolecule shall store information, transfer information, and mutate. Many tools, such as sequence-defined polymer synthesis, polymer modification, supramolecular polymer chemistry, and dynamic chemistry, are already available to chemists to attain these properties. However, the design of artificial Life-supporting macromolecules is hindered by two main factors. First, the chemical search space is enormous, and it is difficult to predict promising structures, even with the help of combinatorial and chemoinformatic tools. Second, rational design is probably a limited approach to achieve macromolecules that shall be involved in nonequilibrium metabolic systems. Hence, a synergic combination of classical polymer chemistry with the more recent field of systems chemistry is probably the key toward the emergence of artificial Life-supporting macromolecules.
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Affiliation(s)
- Jean-François Lutz
- Université de Strasbourg, CNRS - UPR 22, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, France
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14
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15
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Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Nat Chem 2019; 11:533-542. [PMID: 31011171 DOI: 10.1038/s41557-019-0255-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/15/2019] [Indexed: 12/24/2022]
Abstract
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. This polyelectrolyte structure decouples information content (base sequence) from bulk properties, such as solubility, and has been proposed as a defining trait of all informational polymers. However, this conjecture has not been tested experimentally. Here, we describe the encoded synthesis of a genetic polymer with an uncharged backbone chemistry: alkyl phosphonate nucleic acids (phNAs) in which the canonical, negatively charged phosphodiester is replaced by an uncharged P-alkyl phosphonodiester backbone. Using synthetic chemistry and polymerase engineering, we describe the enzymatic, DNA-templated synthesis of P-methyl and P-ethyl phNAs, and the directed evolution of specific streptavidin-binding phNA aptamer ligands directly from random-sequence mixed P-methyl/P-ethyl phNA repertoires. Our results establish an example of the DNA-templated enzymatic synthesis and evolution of an uncharged genetic polymer and provide a foundational methodology for their exploration as a source of novel functional molecules.
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Affiliation(s)
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin T Porebski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sew Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexandra Vaisman
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Roger Woodgate
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
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16
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Pal C, Velusamy A, Sunkari YK, Chakraborty TK. Studies on sugar puckering and glycosidic stabilities of 3'-amino-5'-carboxymethyl-3',5'-dideoxy nucleoside mimics. Org Biomol Chem 2019; 16:6735-6740. [PMID: 30187064 DOI: 10.1039/c8ob01788c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of nucleoside amino acid monomers and dimers has been carried out to evaluate and characterize the impact of the neutral amide backbone on key attributes like puckering of the sugar rings and glycosidic bond strengths of these analogs. The conformational analysis suggests that amide-linked nucleotides have a high predilection towards N-type conformers. The glycosidic bond strength was found to be slightly weaker compared to ribonucleosides under acidic conditions at high temperatures. The results will be helpful to explore in future the development of fully amide-linked oligonucleotides for therapeutic purposes.
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Affiliation(s)
- Chandan Pal
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560 012, India.
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17
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Swain J, Iadevaia G, Hunter CA. H-Bonded Duplexes based on a Phenylacetylene Backbone. J Am Chem Soc 2018; 140:11526-11536. [PMID: 30179469 PMCID: PMC6148443 DOI: 10.1021/jacs.8b08087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 11/30/2022]
Abstract
Complementary phenylacetylene oligomers equipped with phenol and phosphine oxide recognition sites form stable multiply H-bonded duplexes in toluene solution. Oligomers were prepared by Sonogashira coupling of diiodobenzene and bis-acetylene building blocks in the presence of monoacetylene chain terminators. The product mixtures were separated by reverse phase preparative high-pressure liquid chromatography to give a series of pure oligomers up to seven recognition units in length. Duplex formation between length complementary homo-oligomers was demonstrated by 31P NMR denaturation experiments using dimethyl sulfoxide as a competing H-bond acceptor. The denaturation experiments were used to determine the association constants for duplex formation, which increase by nearly 2 orders of magnitude for every phenol-phosphine oxide base-pair added. These experiments show that the phenylacetylene backbone supports formation of extended duplexes with multiple cooperative intermolecular H-bonding interactions, and together with previous studies on the mixed sequence phenylacetylene 2-mer, suggest that this supramolecular architecture is a promising candidate for the development of synthetic information molecules that parallel the properties of nucleic acids.
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Affiliation(s)
- Jonathan
A. Swain
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Karalkar NB, Benner SA. The challenge of synthetic biology. Synthetic Darwinism and the aperiodic crystal structure. Curr Opin Chem Biol 2018; 46:188-195. [PMID: 30098527 DOI: 10.1016/j.cbpa.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/07/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022]
Abstract
'Grand Challenges' offer ways to discover flaws in existing theory without first needing to guess what those flaws are. Our grand challenge here is to reproduce the Darwinism of terran biology, but on molecular platforms different from standard DNA. Access to Darwinism distinguishes the living from the non-living state. However, theory suggests that any biopolymer able to support Darwinism must (a) be able to form Schrödinger's `aperiodic crystal', where different molecular components pack into a single crystal lattice, and (b) have a polyelectrolyte backbone. In 1953, the descriptive biology of Watson and Crick suggested DNA met Schrödinger's criertion, forming a linear crystal with geometrically similar building blocks supported on a polyelectrolye backbone. At the center of genetics were nucleobase pairs that fit into that crystal lattice by having both size complementarity and hydrogen bonding complementarity to enforce a constant geometry. This review covers experiments that show that by adhering to these two structural rules, the aperiodic crystal structure is maintained in DNA having 6 (or more) components. Further, this molecular system is shown to support Darwinism. Together with a deeper understanding of the role played in crystal formation by the poly-charged backbone and the intervening scaffolding, these results define how we might search for Darwinism, and therefore life, on Mars, Europa, Enceladus, and other watery lagoons in our Solar System.
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Affiliation(s)
- Nilesh B Karalkar
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, United States; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, United States.
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19
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Iadevaia G, Núñez-Villanueva D, Stross AE, Hunter CA. Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers. Org Biomol Chem 2018; 16:4183-4190. [PMID: 29790563 PMCID: PMC5989393 DOI: 10.1039/c8ob00819a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/30/2018] [Indexed: 01/06/2023]
Abstract
Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Diego Núñez-Villanueva
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Alexander E. Stross
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
| | - Christopher A. Hunter
- Department of Chemistry
, University of Cambridge
,
Lensfield Road
, Cambridge CB21EW
, UK
.
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20
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Meng M, Ducho C. Oligonucleotide analogues with cationic backbone linkages. Beilstein J Org Chem 2018; 14:1293-1308. [PMID: 29977397 PMCID: PMC6009206 DOI: 10.3762/bjoc.14.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/26/2018] [Indexed: 12/28/2022] Open
Abstract
Their unique ability to selectively bind specific nucleic acid sequences makes oligonucleotides promising bioactive agents. However, modifications of the nucleic acid structure are an essential prerequisite for their application in vivo or even in cellulo. The oligoanionic backbone structure of oligonucleotides mainly hampers their ability to penetrate biological barriers such as cellular membranes. Hence, particular attention has been given to structural modifications of oligonucleotides which reduce their overall number of negative charges. One such approach is the site-specific replacement of the negatively charged phosphate diester linkage with alternative structural motifs which are positively charged at physiological pH, thus resulting in zwitterionic or even oligocationic backbone structures. This review provides a general overview of this concept and summarizes research on four according artificial backbone linkages: aminoalkylated phosphoramidates (and related systems), guanidinium groups, S-methylthiourea motifs, and nucleosyl amino acid (NAA)-derived modifications. The synthesis and properties of the corresponding oligonucleotide analogues are described.
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Affiliation(s)
- Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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21
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Appukutti N, Serpell CJ. High definition polyphosphoesters: between nucleic acids and plastics. Polym Chem 2018. [DOI: 10.1039/c8py00251g] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nucleic acids and synthetic polyphosphoester materials have been distinct fields – this review shows how these areas now comprise a continuum.
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22
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Hazen RM. Chance, necessity and the origins of life: a physical sciences perspective. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160353. [PMID: 29133451 PMCID: PMC5686409 DOI: 10.1098/rsta.2016.0353] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as 'frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Robert M Hazen
- Carnegie Institution for Science, Geophysical Laboratory, 5251 Broad Branch Road NW, Washington, DC 20015, USA
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23
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Stross A, Iadevaia G, Núñez-Villanueva D, Hunter CA. Sequence-Selective Formation of Synthetic H-Bonded Duplexes. J Am Chem Soc 2017; 139:12655-12663. [PMID: 28857551 PMCID: PMC5627343 DOI: 10.1021/jacs.7b06619] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 11/30/2022]
Abstract
Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.
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Affiliation(s)
- Alexander
E. Stross
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Giulia Iadevaia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Diego Núñez-Villanueva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christopher A. Hunter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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24
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Benner SA. Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons. ASTROBIOLOGY 2017; 17:840-851. [PMID: 28665680 PMCID: PMC5610385 DOI: 10.1089/ast.2016.1611] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a "polyelectrolyte." Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block "alphabet." This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus-Life detection-Europa-Icy moon-Biosignatures-Polyelectrolyte theory of the gene. Astrobiology 17, 840-851.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution , Alachua, Florida
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25
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Porco CC. A Community Grows around the Geysering World of Enceladus. ASTROBIOLOGY 2017; 17:815-819. [PMID: 28742370 PMCID: PMC5610423 DOI: 10.1089/ast.2017.1711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The discovery by NASA's Cassini mission at Saturn in 2005 of a large plume of material erupting from the south polar terrain of Enceladus, sourced within a subsurface ocean of salty liquid water laced with organic compounds, has brought together scientists from a diverse range of disciplines over the last decade to evaluate this small moon's potential for extraterrestrial life. The collection of papers published today in Astrobiology, as the mission draws to a close, is the outcome of our most recent meeting at UC Berkeley in June 2016. Key Words: Enceladus-Enceladus Focus Group-Ocean world-Search for biosignatures. Astrobiology 17, 815-819.
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Affiliation(s)
- Carolyn C Porco
- University of California , Berkeley, California
- Space Science Institute , Boulder, Colorado
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26
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Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids. Life (Basel) 2017; 7:life7030035. [PMID: 29061955 PMCID: PMC5617960 DOI: 10.3390/life7030035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/10/2017] [Accepted: 08/19/2017] [Indexed: 01/09/2023] Open
Abstract
The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (β-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (β-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution.
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Núñez-Villanueva D, Hunter CA. Homochiral oligomers with highly flexible backbones form stable H-bonded duplexes. Chem Sci 2017; 8:206-213. [PMID: 28451167 PMCID: PMC5308278 DOI: 10.1039/c6sc02995g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/24/2022] Open
Abstract
Two homochiral building blocks featuring a protected thiol, an alkene and a H-bond recognition unit (phenol or phosphine oxide) have been prepared. Iterative photochemical thiol-ene coupling reactions were used to synthesize oligomers containing 1-4 phosphine oxide and 1-4 phenol recognition sites. Length-complementary H-bond donor and H-bond acceptor oligomers were found to form stable duplexes in toluene. NMR titrations and thermal denaturation experiments show that the association constant and the enthalpy of duplex formation increase significantly for every additional H-bonding unit added to the chain. There is an order of magnitude increase in stability for each additional H-bonding interaction at room temperature indicating that all of the H-bonding sites are fully bound to their complements in the duplexes. The backbone of the thiol-ene duplexes is a highly flexible alkane chain, but this conformational flexibility does not have a negative impact on binding affinity. The average effective molarity for the intramolecular H-bonding interactions that zip up the duplexes is 18 mM. This value is somewhat higher than the EM of 14 mM found for a related family of duplexes, which have the same recognition units but a more rigid backbone prepared using reductive amination chemistry. The flexible thiol-ene AAAA·DDDD duplex is an order of magnitude more stable than the rigid reductive amination AAAA·DDDD duplex. The backbone of the thiol-ene system retains much of its conformational flexibility in the duplex, and these results show that highly flexible molecules can make very stable complexes, provided there is no significant restriction of degrees of freedom on complexation.
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Affiliation(s)
- Diego Núñez-Villanueva
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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Vyborna Y, Altunbas S, Vybornyi M, Häner R. Morphological diversity of supramolecular polymers of DNA-containing oligopyrenes – formation of chiroptically active nanosheets. Chem Commun (Camb) 2017; 53:12128-12131. [DOI: 10.1039/c7cc07511a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Supramolecular polymerization of chimeric DNA-pyrene oligomers leads to 1D and 2D objects depending on the length of the DNA. A single guanosine induces supramolecular chirality in the self-assembled nanosheets.
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Affiliation(s)
- Y. Vyborna
- Department Chemistry and Biochemistry
- University of Bern
- Bern
- Switzerland
| | - S. Altunbas
- Department Chemistry and Biochemistry
- University of Bern
- Bern
- Switzerland
| | - M. Vybornyi
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - R. Häner
- Department Chemistry and Biochemistry
- University of Bern
- Bern
- Switzerland
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Benner SA. Unusual Hydrogen Bonding Patterns and the Role of the Backbone in Nucleic Acid Information Transfer. ACS CENTRAL SCIENCE 2016; 2:882-884. [PMID: 28058276 PMCID: PMC5200930 DOI: 10.1021/acscentsci.6b00344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW, Matsuura M, Fajardo D, Moussatche P. Alternative Watson-Crick Synthetic Genetic Systems. Cold Spring Harb Perspect Biol 2016; 8:a023770. [PMID: 27663774 PMCID: PMC5088529 DOI: 10.1101/cshperspect.a023770] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.
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Affiliation(s)
- Steven A Benner
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Nilesh B Karalkar
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Shuichi Hoshika
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Roberto Laos
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Ryan W Shaw
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Mariko Matsuura
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Diego Fajardo
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Patricia Moussatche
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
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Iadevaia G, Stross AE, Neumann A, Hunter CA. Mix and match backbones for the formation of H-bonded duplexes. Chem Sci 2016; 7:1760-1767. [PMID: 28936325 PMCID: PMC5592378 DOI: 10.1039/c5sc04467g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/18/2015] [Indexed: 11/21/2022] Open
Abstract
The formation of well-defined supramolecular assemblies involves competition between intermolecular and intramolecular interactions, which is quantified by effective molarity. Formation of a duplex between two oligomers equipped with recognition sites displayed along a non-interacting backbone requires that once one intermolecular interaction has been formed, all subsequent interactions take place in an intramolecular sense. The efficiency of this process is governed by the geometric complementarity and conformational flexibility of the backbone linking the recognition sites. Here we report a series of phosphine oxide H-bond acceptor AA 2-mers and phenol H-bond donor DD 2-mers, where the two recognition sites are connected by isomeric backbone modules that vary in geometry and flexibility. All AA and DD combinations form stable AA·DD duplexes, where two cooperative H-bonds lead to an increase in stability of an order of magnitude compared with the corresponding A·D complexes that can only form one H-bond. For all six possible backbone combinations, the effective molarity for duplex formation is approximately constant (7-20 mM). Thus strict complementarity and high degrees of preorganisation are not required for efficient supramolecular assembly. Provided there is some flexibility, quite different backbone modules can be used interchangeably to construct stable H-bonded duplexes.
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Affiliation(s)
- Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Anja Neumann
- Department of Chemistry , University of Sheffield , Sheffield S3 7HF , UK
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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“Post Modern Medicine” would be “calculable and energy-based medicine”: A hypothesis paper. JOURNAL OF MEDICAL HYPOTHESES AND IDEAS 2015. [DOI: 10.1016/j.jmhi.2015.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Stross AE, Iadevaia G, Hunter CA. Cooperative duplex formation by synthetic H-bonding oligomers. Chem Sci 2015; 7:94-101. [PMID: 29861969 PMCID: PMC5950798 DOI: 10.1039/c5sc03414k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/15/2015] [Indexed: 01/12/2023] Open
Abstract
Flexible phenol-phosphine oxide oligomers show promise as a new class of synthetic information molecule.
A series of flexible oligomers equipped with phenol H-bond donors and phosphine oxide H-bond acceptors have been synthesised using reductive amination chemistry. H-bonding interactions between complementary oligomers leads to the formation of double-stranded complexes which were characterised using NMR titrations and thermal denaturation experiments. The stability of the duplex increases by one order of magnitude for every H-bonding group added to the chain. Similarly, the enthalpy change for duplex assembly and the melting temperature for duplex denaturation both increase with increasing chain length. These observations indicate that H-bond formation along the oligomers is cooperative despite the flexible backbone, and the effective molarity for intramolecular H-bond formation (14 mM) is sufficient to propagate the formation of longer duplexes using this approach. The product K EM, which is used to quantify chelate cooperativity is 5, which means that each H-bond is more than 80% populated in the assembled duplex. The modular design of these oligomers represents a general strategy for the design of synthetic information molecules that could potentially encode and replicate chemical information in the same way as nucleic acids.
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Affiliation(s)
- Alexander E Stross
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Giulia Iadevaia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK .
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Schmidtgall B, Spork AP, Wachowius F, Höbartner C, Ducho C. Synthesis and properties of DNA oligonucleotides with a zwitterionic backbone structure. Chem Commun (Camb) 2015; 50:13742-5. [PMID: 25251903 DOI: 10.1039/c4cc06371f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The nucleosyl amino acid (NAA)-modification of oligonucleotides is introduced, which enables the preparation of oligonucleotides with zwitterionic backbone structures. It is demonstrated that partially zwitterionic NAA-modified DNA oligonucleotides are capable of duplex formation with native polyanionic counterstrands and show retained sensitivity towards base-pairing mismatches.
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Affiliation(s)
- Boris Schmidtgall
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33 098 Paderborn, Germany
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Schmidtgall B, Höbartner C, Ducho C. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks. Beilstein J Org Chem 2015; 11:50-60. [PMID: 25670992 PMCID: PMC4311628 DOI: 10.3762/bjoc.11.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022] Open
Abstract
Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.
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Affiliation(s)
- Boris Schmidtgall
- Department of Chemistry, University of Paderborn, Warburger Str. 100, 33 098 Paderborn, Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66 123 Saarbrücken, Germany
| | - Claudia Höbartner
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37 077 Göttingen, Germany
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37 077 Göttingen, Germany
| | - Christian Ducho
- Department of Chemistry, University of Paderborn, Warburger Str. 100, 33 098 Paderborn, Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66 123 Saarbrücken, Germany
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Isobe H, Fujino T. Triazole-linked analogues of DNA and RNA ((TL)DNA and (TL)RNA): synthesis and functions. CHEM REC 2014; 14:41-51. [PMID: 24734308 DOI: 10.1002/tcr.201300023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Click chemistry has provided us with access to DNA and RNA analogues with non-natural triazole internucleoside linkages. The bond periodicity of the oligonucleotides was designed to enforce duplex formation with natural congeners, and the non-cleavable linkages protect the oligomers against nuclease digestion. This account reviews the progress of the triazole-linked analogues over the past five years. Reinforced by their synthetic robustness, these analogues may find various utilities as tools for exploratory research.
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Winiger CB, Langenegger SM, Khorev O, Häner R. Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity. Beilstein J Org Chem 2014; 10:1589-95. [PMID: 25161715 PMCID: PMC4142898 DOI: 10.3762/bjoc.10.164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/17/2014] [Indexed: 12/20/2022] Open
Abstract
Aromatic π-π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA-polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene-PDI interactions that were found to directly influence duplex stability. As the pyrene-PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene-PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π-π stacking interactions.
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Affiliation(s)
- Christian B Winiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Oleg Khorev
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Basílio Janke EM, Weisz K. A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR. Z PHYS CHEM 2013. [DOI: 10.1524/zpch.2013.0382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.
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Neveu M, Kim HJ, Benner SA. The "strong" RNA world hypothesis: fifty years old. ASTROBIOLOGY 2013; 13:391-403. [PMID: 23551238 DOI: 10.1089/ast.2012.0868] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This year marks the 50(th) anniversary of a proposal by Alex Rich that RNA, as a single biopolymer acting in two capacities, might have supported both genetics and catalysis at the origin of life. We review here both published and previously unreported experimental data that provide new perspectives on this old proposal. The new data include evidence that, in the presence of borate, small amounts of carbohydrates can fix large amounts of formaldehyde that are expected in an environment rich in carbon dioxide. Further, we consider other species, including arsenate, arsenite, phosphite, and germanate, that might replace phosphate as linkers in genetic biopolymers. While linkages involving these oxyanions are judged to be too unstable to support genetics on Earth, we consider the possibility that they might do so in colder semi-aqueous environments more exotic than those found on Earth, where cosolvents such as ammonia might prevent freezing at temperatures well below 273 K. These include the ammonia-water environments that are possibly present at low temperatures beneath the surface of Titan, Saturn's largest moon.
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Affiliation(s)
- Marc Neveu
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, USA
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Abstract
The key to the origins of life is the replication of information. Linear polymers such as nucleic acids that both carry information and can be replicated are currently what we consider to be the basis of living systems. However, these two properties are not necessarily coupled. The ability to mutate in a discrete or quantized way, without frequent reversion, may be an additional requirement for Darwinian evolution, in which case the notion that Darwinian evolution defines life may be less of a tautology than previously thought. In this Account, we examine a variety of in vitro systems of increasing complexity, from simple chemical replicators up to complex systems based on in vitro transcription and translation. Comparing and contrasting these systems provides an interesting window onto the molecular origins of life. For nucleic acids, the story likely begins with simple chemical replication, perhaps of the form A + B → T, in which T serves as a template for the joining of A and B. Molecular variants capable of faster replication would come to dominate a population, and the development of cycles in which templates could foster one another's replication would have led to increasingly complex replicators and from thence to the initial genomes. The initial genomes may have been propagated by RNA replicases, ribozymes capable of joining oligonucleotides and eventually polymerizing mononucleotide substrates. As ribozymes were added to the genome to fill gaps in the chemistry necessary for replication, the backbone of a putative RNA world would have emerged. It is likely that such replicators would have been plagued by molecular parasites, which would have been passively replicated by the RNA world machinery without contributing to it. These molecular parasites would have been a major driver for the development of compartmentalization/cellularization, as more robust compartments could have outcompeted parasite-ridden compartments. The eventual outsourcing of metabolic functions (including the replication of nucleic acids) to more competent protein enzymes would complete the journey from an abiotic world to the molecular biology we see today.
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Affiliation(s)
- Adam J. Meyer
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jared W. Ellefson
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
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Cleaves HJ, Michalkova Scott A, Hill FC, Leszczynski J, Sahai N, Hazen R. Mineral-organic interfacial processes: potential roles in the origins of life. Chem Soc Rev 2012; 41:5502-25. [PMID: 22743683 DOI: 10.1039/c2cs35112a] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.
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Affiliation(s)
- H James Cleaves
- Blue Marble Space Institute of Science, Washington, DC 20016, USA
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Benner SA, Kim HJ, Yang Z. Setting the stage: the history, chemistry, and geobiology behind RNA. Cold Spring Harb Perspect Biol 2012; 4:a003541. [PMID: 20880988 DOI: 10.1101/cshperspect.a003541] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth. Further, a definition-theory for life is needed to develop hypotheses relating to the "RNA First" model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; (c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, USA.
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Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity. Proc Natl Acad Sci U S A 2011; 108:13492-7. [PMID: 21825162 DOI: 10.1073/pnas.1107113108] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Multiple lines of evidence support the hypothesis that the early evolution of life was dominated by RNA, which can both transfer information from generation to generation through replication directed by base-pairing, and carry out biochemical activities by folding into functional structures. To understand how life emerged from prebiotic chemistry we must therefore explain the steps that led to the emergence of the RNA world, and in particular, the synthesis of RNA. The generation of pools of highly pure ribonucleotides on the early Earth seems unlikely, but the presence of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone heterogeneity. We suggest that homogeneous monomers might not have been necessary if populations of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible, function would have to be maintained despite the repeated scrambling of backbone chemistry from generation to generation. We have tested this possibility in a simplified model system, by using a T7 RNA polymerase variant capable of transcribing nucleic acids that contain an approximately 11 mixture of deoxy- and ribonucleotides. We readily isolated nucleotide-binding aptamers by utilizing an in vitro selection process that shuffles the order of deoxy- and ribonucleotides in each round. We describe two such RNA/DNA mosaic nucleic acid aptamers that specifically bind ATP and GTP, respectively. We conclude that nonheritable variations in nucleic acid backbone structure may not have posed an insurmountable barrier to the emergence of functionality in early nucleic acids.
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Abstract
Any definition is intricately connected to a theory that gives it meaning. Accordingly, this article discusses various definitions of life held in the astrobiology community by considering their connected "theories of life." These include certain "list" definitions and a popular definition that holds that life is a "self-sustaining chemical system capable of Darwinian evolution." We then act as "anthropologists," studying what scientists do to determine which definition-theories of life they constructively hold as they design missions to seek non-terran life. We also look at how constructive beliefs about biosignatures change as observational data accumulate. And we consider how a definition centered on Darwinian evolution might itself be forced to change as supra-Darwinian species emerge, including in our descendents, and consider the chances of our encountering supra-Darwinian species in our exploration of the Cosmos. Last, we ask what chemical structures might support Darwinian evolution universally; these structures might be universal biosignatures.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology, Gainesville, Florida32601, USA.
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Benner SA, Yang Z, Chen F. Synthetic Biology, Tinkering Biology, and Artificial Biology. What are We Learning? CR CHIM 2010; 14:372-387. [PMID: 29983697 DOI: 10.1016/j.crci.2010.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
While chemical theory cannot yet support an engineering vision that allows molecules, DNA sequences, and proteins to be interchangeable parts in artificial constructs without "tinkering", progress can be made in synthetic biology by pursuing challenges at the limits of existing theory. These force scientists across uncharted terrain where they must address unscripted problems where, if theory is inadequate, failure results. Thus, synthesis drives discovery and paradigm change in ways that analysis cannot. Further, if failures are analyzed, new theories emerge. Here, we illustrate this by synthesizing an artificial genetic system capable of Darwinian evolution, a feature theorized to be universal to life.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology
| | - Fei Chen
- Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology
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Xiao Z, Weisz K. Base-base recognition of nonionic dinucleotide analogues in an apolar environment studied by low-temperature NMR spectroscopy. J Am Chem Soc 2010; 132:3862-9. [PMID: 20180555 DOI: 10.1021/ja910220s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Two self-complementary dinucleotide analogues T(Si)A and A(Si)T with a nonionic diisopropylsilyl-modified backbone were synthesized, and their association in a nonaqueous aprotic environment was studied by NMR spectroscopy. Using a CDClF(2)/CDF(3) solvent mixture, measurements at temperatures as low as 113 K allowed the observation and structural characterization of individual complexes in the slow exchange regime. The A(Si)T analogue associates to exclusively form a dinucleotide antiparallel duplex with regular Watson-Crick base pairing, but both A and T nucleosides exhibit a predominant C3'-endo sugar pucker reminiscent of an A-type conformation. In contrast to A(Si)T, the T(Si)A dinucleotide is found to exhibit significant variability and flexibility. Thus, different secondary structures with weaker hydrogen bonds for all T(Si)A structures are observed at low temperatures. Although a B-like Watson-Crick antiparallel dinucleotide duplex with a preferred C2'-endo sugar pucker largely predominates at temperatures above 153 K, two additional species, namely a dinucleotide Hoogsteen duplex with a syn glycosidic torsion angle of the adenosine nucleoside and a presumably intramolecularly folded structure, are increasingly populated upon further cooling. By adding typical DNA intercalators like anthracene or benz[c]acridine derivatives to the A(Si)T dinucleotide duplex in the aprotic solvent environment, no binding of the polycyclic aromatic molecules can be detected even at lower temperatures. Obviously, van der Waals and stacking interactions are insufficient to compensate for the other unfavorable contributions to the overall free energy of binding, and only in the presence of additional hydrophobic effects in an aqueous environment does binding occur.
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Affiliation(s)
- Zhou Xiao
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution, Gainesville, FL 32604, USA.
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