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Kufner CL, Crucilla S, Ding D, Stadlbauer P, Šponer J, Szostak JW, Sasselov DD, Szabla R. Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chem Sci 2024; 15:2158-2166. [PMID: 38332835 PMCID: PMC10848779 DOI: 10.1039/d3sc04971j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/27/2023] [Indexed: 02/10/2024] Open
Abstract
Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A-˙G+˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.
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Affiliation(s)
- Corinna L Kufner
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Sarah Crucilla
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
- Department of Earth and Planetary Sciences, Harvard University Cambridge Massachusetts 02138 USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital Boston Massachusetts 02114 USA
- Department of Chemistry and Chemical Biology, Harvard University Cambridge Massachusetts 02138 USA
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jack W Szostak
- Howard Hughes Medical Institute, The University of Chicago Chicago IL 60637 USA
- Department of Chemistry, The University of Chicago Chicago Illinois 60637 USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Rafał Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 Wrocław 50-370 Poland
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2
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Jiang CZ, Rimmer PB, Lozano GG, Tosca NJ, Kufner CL, Sasselov DD, Thompson SJ. Iron-sulfur chemistry can explain the ultraviolet absorber in the clouds of Venus. Sci Adv 2024; 10:eadg8826. [PMID: 38170780 PMCID: PMC10776003 DOI: 10.1126/sciadv.adg8826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
The clouds of Venus are believed to be composed of sulfuric acid (H2SO4) and minor constituents including iron-bearing compounds, and their respective concentrations vary with height in the thick Venusian atmosphere. This study experimentally investigates possible iron-bearing mineral phases that are stable under the unique conditions within Venusian clouds. Our results demonstrate that ferric iron can react with sulfuric acid to form two mineral phases: rhomboclase [(H5O2)Fe(SO4)2·3H2O] and acid ferric sulfate [(H3O)Fe(SO4)2]. A combination of these two mineral phases and dissolved Fe3+ in varying concentrations of sulfuric acid are shown to be good candidates for explaining the 200- to 300-nm and 300- to 500-nm features of the reported unknown UV absorber. We, therefore, hypothesize a rich and largely unexplored heterogeneous chemistry in the cloud droplets of Venus that has a large effect on the optical properties of the clouds and the behavior of trace gas species throughout Venus's atmosphere.
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Affiliation(s)
- Clancy Zhijian Jiang
- Department of Earth Sciences, University of Cambridge, Downing St., Cambridge CB2 3EQ, UK
| | - Paul B. Rimmer
- Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Gabriella G. Lozano
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA
| | - Nicholas J. Tosca
- Department of Earth Sciences, University of Cambridge, Downing St., Cambridge CB2 3EQ, UK
| | - Corinna L. Kufner
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA
| | - Dimitar D. Sasselov
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA
| | - Samantha J. Thompson
- Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
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3
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Crucilla SJ, Ding D, Lozano GG, Szostak JW, Sasselov DD, Kufner CL. UV-driven self-repair of cyclobutane pyrimidine dimers in RNA. Chem Commun (Camb) 2023; 59:13603-13606. [PMID: 37899697 DOI: 10.1039/d3cc04013e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Nucleic acids can be damaged by ultraviolet (UV) irradiation, forming structural photolesions such as cyclobutane-pyrimidine-dimers (CPD). In modern organisms, sophisticated enzymes repair CPD lesions in DNA, but to our knowledge, no RNA-specific enzymes exist for CPD repair. Here, we show for the first time that RNA can protect itself from photolesions by an intrinsic UV-induced self-repair mechanism. This mechanism, prior to this study, has exclusively been observed in DNA and is based on charge transfer from CPD-adjacent bases. In a comparative study, we determined the quantum yields of the self-repair of the CPD-containing RNA sequence, GAU = U to GAUU (0.23%), and DNA sequence, d(GAT = T) to d(GATT) (0.44%), upon 285 nm irradiation via UV/Vis spectroscopy and HPLC analysis. After several hours of irradiation, a maximum conversion yield of ∼16% for GAU = U and ∼33% for d(GAT = T) was reached. We examined the dynamics of the intermediate charge transfer (CT) state responsible for the self-repair with ultrafast UV pump - IR probe spectroscopy. In the dinucleotides GA and d(GA), we found comparable quantum yields of the CT state of ∼50% and lifetimes on the order of several hundred picoseconds. Charge transfer in RNA strands might lead to reactions currently not considered in RNA photochemistry and may help understanding RNA damage formation and repair in modern organisms and viruses. On the UV-rich surface of the early Earth, these self-stabilizing mechanisms likely affected the selection of the earliest nucleotide sequences from which the first organisms may have developed.
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Affiliation(s)
- Sarah J Crucilla
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gabriella G Lozano
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Dimitar D Sasselov
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
| | - Corinna L Kufner
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
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4
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Ozturk SF, Bhowmick DK, Kapon Y, Sang Y, Kumar A, Paltiel Y, Naaman R, Sasselov DD. Chirality-induced avalanche magnetization of magnetite by an RNA precursor. Nat Commun 2023; 14:6351. [PMID: 37816811 PMCID: PMC10564924 DOI: 10.1038/s41467-023-42130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023] Open
Abstract
Homochirality is a hallmark of life on Earth. To achieve and maintain homochirality within a prebiotic network, the presence of an environmental factor acting as a chiral agent and providing a persistent chiral bias to prebiotic chemistry is highly advantageous. Magnetized surfaces are prebiotically plausible chiral agents due to the chiral-induced spin selectivity (CISS) effect, and they were utilized to attain homochiral ribose-aminooxazoline (RAO), an RNA precursor. However, natural magnetic minerals are typically weakly magnetized, necessitating mechanisms to enhance their magnetization for their use as effective chiral agents. Here, we report the magnetization of magnetic surfaces by crystallizing enantiopure RAO, whereby chiral molecules induce a uniform surface magnetization due to the CISS effect, which spreads across the magnetic surface akin to an avalanche. Chirality-induced avalanche magnetization enables a feedback between chiral molecules and magnetic surfaces, which can amplify a weak magnetization and allow for highly efficient spin-selective processes on magnetic minerals.
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Affiliation(s)
- S Furkan Ozturk
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
| | - Deb Kumar Bhowmick
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot, 76100, Israel
| | - Yael Kapon
- Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yutao Sang
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot, 76100, Israel
| | - Anil Kumar
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot, 76100, Israel
| | - Yossi Paltiel
- Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute, Rehovot, 76100, Israel
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5
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Ozturk SF, Sasselov DD, Sutherland JD. The central dogma of biological homochirality: How does chiral information propagate in a prebiotic network? J Chem Phys 2023; 159:061102. [PMID: 37551802 PMCID: PMC7615580 DOI: 10.1063/5.0156527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/05/2023] [Indexed: 08/09/2023] Open
Abstract
Biological systems are homochiral, raising the question of how a racemic mixture of prebiotically synthesized biomolecules could attain a homochiral state at the network level. Based on our recent results, we aim to address a related question of how chiral information might have flowed in a prebiotic network. Utilizing the crystallization properties of the central ribonucleic acid (RNA) precursor known as ribose-aminooxazoline (RAO), we showed that its homochiral crystals can be obtained from its fully racemic solution on a magnetic mineral surface due to the chiral-induced spin selectivity (CISS) effect [Ozturk et al., arXiv:2303.01394 (2023)]. Moreover, we uncovered a mechanism facilitated by the CISS effect through which chiral molecules, such as RAO, can uniformly magnetize such surfaces in a variety of planetary environments in a persistent manner [Ozturk et al., arXiv:2304.09095 (2023)]. All this is very tantalizing because recent experiments with tRNA analogs demonstrate high stereoselectivity in the attachment of L-amino acids to D-ribonucleotides, enabling the transfer of homochirality from RNA to peptides [Wu et al., J. Am. Chem. Soc. 143, 11836 (2021)]. Therefore, the biological homochirality problem may be reduced to ensuring that a single common RNA precursor (e.g., RAO) can be made homochiral. The emergence of homochirality at RAO then allows for the chiral information to propagate through RNA, then to peptides, and ultimately through enantioselective catalysis to metabolites. This directionality of the chiral information flow parallels that of the central dogma of molecular biology-the unidirectional transfer of genetic information from nucleic acids to proteins [F. H. Crick, in Symposia of the Society for Experimental Biology, Number XII: The Biological Replication of Macromolecules, edited by F. K. Sanders (Cambridge University Press, Cambridge, 1958), pp. 138-163; and F. Crick, Nature 227, 561 (1970)].
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Affiliation(s)
- S. Furkan Ozturk
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Dimitar D. Sasselov
- Department of Astronomy, Harvard University, Cambridge, Massachusetts 02138, USA
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6
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Ozturk SF, Liu Z, Sutherland JD, Sasselov DD. Origin of biological homochirality by crystallization of an RNA precursor on a magnetic surface. Sci Adv 2023; 9:eadg8274. [PMID: 37285423 PMCID: PMC10246896 DOI: 10.1126/sciadv.adg8274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
Homochirality is a signature of life on Earth, yet its origins remain an unsolved puzzle. Achieving homochirality is essential for a high-yielding prebiotic network capable of producing functional polymers like RNA and peptides on a persistent basis. Because of the chiral-induced spin selectivity effect, which established a strong coupling between electron spin and molecular chirality, magnetic surfaces can act as chiral agents and be templates for the enantioselective crystallization of chiral molecules. Here, we studied the spin-selective crystallization of racemic ribo-aminooxazoline (RAO), an RNA precursor, on magnetite (Fe3O4) surfaces, achieving an unprecedented enantiomeric excess (ee) of about 60%. Following the initial enrichment, we then obtained homochiral (100% ee) crystals of RAO after a subsequent crystallization. Our results demonstrate a prebiotically plausible way of achieving system-level homochirality from completely racemic starting materials, in a shallow-lake environment on early Earth where sedimentary magnetite deposits are expected to be common.
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Affiliation(s)
- S. Furkan Ozturk
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - John D. Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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7
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Kufner CL, Bucher DB, Sasselov DD. The Photophysics of Nucleic Acids: Consequences for the Emergence of Life. ChemSystemsChem 2022. [DOI: 10.1002/syst.202200019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Dominik Benjamin Bucher
- Technical University of Munich: Technische Universitat Munchen Department of Chemistry Lichtenbergstr. 4 85748 Munich GERMANY
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8
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Abstract
Ultraviolet (UV) light plays a key role in surficial theories of the origin of life, and numerous studies have focused on constraining the atmospheric transmission of UV radiation on early Earth. However, the UV transmission of the natural waters in which origins-of-life chemistry (prebiotic chemistry) is postulated to have occurred is poorly constrained. In this work, we combine laboratory and literature-derived absorption spectra of potential aqueous-phase prebiotic UV absorbers with literature estimates of their concentrations on early Earth to constrain the prebiotic UV environment in marine and terrestrial natural waters, and we consider the implications for prebiotic chemistry. We find that prebiotic freshwaters were largely transparent in the UV, contrary to assumptions in some models of prebiotic chemistry. Some waters, such as high-salinity waters like carbonate lakes, may be deficient in shortwave (≤220 nm) UV flux. More dramatically, ferrous waters can be strongly UV-shielded, particularly if the Fe2+ forms highly UV-absorbent species such as FeCN64-. Such waters may be compelling venues for UV-averse origin-of-life scenarios but are unfavorable for some UV-dependent prebiotic chemistries. UV light can trigger photochemistry even if attenuated through photochemical transformations of the absorber (e.g., eaq- production from halide irradiation), which may have both constructive and destructive effects for prebiotic syntheses. Prebiotic chemistries that invoke waters that contain such absorbers must self-consistently account for the chemical effects of these transformations. The speciation and abundance of Fe2+ in natural waters on early Earth is a major uncertainty and should be prioritized for further investigation, as it played a major role in UV transmission in prebiotic natural waters.
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Affiliation(s)
- Sukrit Ranjan
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Physics and Astronomy, Center for Interdisciplinary Exploration and Research in Astrophysics, Northwestern University, Evanston, Illinois, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Address correspondence to: Sukrit Ranjan, Department of Physics and Astronomy, Center for Interdisciplinary Exploration and Research in Astrophysics, Northwestern University, 1800 Sherman Avenue, 6th Floor, Evanston, IL 60601, USA
| | - Corinna L. Kufner
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
| | | | - Zoe R. Todd
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Azra Haseki
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard College, Cambridge, Massachusetts, USA
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9
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Liu Z, Wu LF, Kufner CL, Sasselov DD, Fischer WW, Sutherland JD. Prebiotic photoredox synthesis from carbon dioxide and sulfite. Nat Chem 2021; 13:1126-1132. [PMID: 34635812 PMCID: PMC7611910 DOI: 10.1038/s41557-021-00789-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.
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Affiliation(s)
- Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Corinna L Kufner
- Harvard-Smithsonian Center for Astrophysics, Massachusetts, MA, USA
| | | | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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10
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Janicki M, Kufner CL, Todd ZR, Kim SC, O’Flaherty DK, Szostak JW, Šponer J, Góra RW, Sasselov DD, Szabla R. Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides. J Phys Chem Lett 2021; 12:6707-6713. [PMID: 34260253 PMCID: PMC9634911 DOI: 10.1021/acs.jpclett.1c01384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose. Our transient absorption spectroscopy experiments demonstrate that thiocytosine exhibits 5 times longer excited-state lifetime and different excited-state absorption features than thiocytidine. On the basis of accurate quantum chemical simulations, we assign these differences to the dominant population of a shorter-lived triplet nπ* state in the nucleoside and longer-lived triplet ππ* states in the nucleobase. This explains the distinctive photoanomerziation of thiocytidine and indicates that the nucleoside will be a less efficient phototherapeutic agent with regard to singlet oxygen generation.
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Affiliation(s)
- Mikołaj
J. Janicki
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Corinna L. Kufner
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Zoe R. Todd
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Seohyun C. Kim
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jiří Šponer
- Institute
of Biophysics, Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacky
University Olomouc, Slechtitelu
241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Robert W. Góra
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Dimitar D. Sasselov
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Rafał Szabla
- EaStCHEM,
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
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11
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Todd ZR, Szostak JW, Sasselov DD. Shielding from UV Photodamage: Implications for Surficial Origins of Life Chemistry on the Early Earth. ACS Earth Space Chem 2021; 5:239-246. [PMID: 36317066 PMCID: PMC9616438 DOI: 10.1021/acsearthspacechem.0c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UV light has been invoked as a source of energy for driving prebiotic chemistry, but such high energy photons are also known to cause damage to biomolecules and their precursors. One potential mechanism for increasing the lifetime of UV-photounstable molecules is to invoke a protection or shielding mechanism. UV shielding could either occur by the molecule in question itself (self-shielding) or by the presence of other UV-absorbing molecules. We investigate and illustrate these two shielding mechanisms as means of increasing the lifetime of 2-aminooxazole (AO), a prebiotic precursor molecule moderately susceptible to UV photodamage, with an expected half-life of 7 h on the surface of the early Earth. AO can be protected by being present in high concentrations, such that it self-shields. AO can similarly be protected by the presence of UV-absorbing nucleosides; the degree of protection depends on the concentration and identity of the nucleoside. The purine nucleosides (A, G, and I) confer more protection than the pyrimidines (C and U). We find that 0.1 mM purine ribonucleosides affords AO about the same protection as 1 mM AO self-shielding, corresponding to a lifetime enhancement of 2-3×. This suggests that only a modest yield of nucleosides can potentially allow for protection of UV photounstable molecules, and therefore this could be a plausible mechanism for protecting sensitive molecules while prebiotic synthesis is occurring simultaneously. Our findings suggest that both synthetic and degradative reactions can proceed at the same time, given various degrees of shielding.
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Affiliation(s)
- Zoe R. Todd
- Center
for Astrophysics Harvard and Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Dimitar D. Sasselov
- Center
for Astrophysics Harvard and Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
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12
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Todd ZR, Fahrenbach AC, Ranjan S, Magnani CJ, Szostak JW, Sasselov DD. Ultraviolet-Driven Deamination of Cytidine Ribonucleotides Under Planetary Conditions. Astrobiology 2020; 20:878-888. [PMID: 32267736 PMCID: PMC9634989 DOI: 10.1089/ast.2019.2182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A previously proposed synthesis of pyrimidine ribonucleotides makes use of ultraviolet (UV) light to convert β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate, while simultaneously selectively degrading synthetic byproducts. Past studies of the photochemical reactions of pyrimidines have employed mercury arc lamps, characterized by narrowband emission centered at 254 nm, which is not representative of the UV environment of the early Earth. To further assess this process under more realistic circumstances, we investigated the wavelength dependence of the UV-driven conversion of β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate. We used constraints provided by planetary environments to assess the implications for pyrimidine nucleotides on the early Earth. We found that the wavelengths of light (255-285 nm) that most efficiently drive the deamination of β-d-ribocytidine-2',3'-cyclic phosphate to β-d-ribouridine-2',3'-cyclic phosphate are accessible on planetary surfaces such as those of the Hadean-Archaean Earth for CO2-N2-dominated atmospheres. However, continued irradiation could eventually lead to low levels of ribocytidine in a low-temperature, highly irradiated environment, if production rates are slow.
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Affiliation(s)
- Zoe R. Todd
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
- Address correspondence to: Zoe R. Todd, Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, 60 Garden Street Mail-Stop 10, Cambridge, MA 02138
| | | | - Sukrit Ranjan
- SCOL Postdoctoral Fellow, Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher J. Magnani
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Dimitar D. Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts
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Sasselov DD, Grotzinger JP, Sutherland JD. The origin of life as a planetary phenomenon. Sci Adv 2020; 6:eaax3419. [PMID: 32076638 PMCID: PMC7002131 DOI: 10.1126/sciadv.aax3419] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/22/2019] [Indexed: 05/03/2023]
Abstract
We advocate an integrative approach between laboratory experiments in prebiotic chemistry and geologic, geochemical, and astrophysical observations to help assemble a robust chemical pathway to life that can be reproduced in the laboratory. The cyanosulfidic chemistry scenario described here was developed by such an integrative iterative process. We discuss how it maps onto evolving planetary surface environments on early Earth and Mars and the value of comparative planetary evolution. The results indicate that Mars can offer direct evidence for geochemical conditions similar to prebiotic Earth, whose early record has been erased. The Jezero crater is now the chosen landing site for NASA's Mars 2020 rover, making this an extraordinary opportunity for a breakthrough in understanding life's origins.
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Affiliation(s)
- Dimitar D. Sasselov
- Department of Astronomy, Harvard University, 60 Garden St., Cambridge, MA 02138, USA
- Corresponding author.
| | - John P. Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - John D. Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge CB2 0QH, UK
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14
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Zeng L, Jacobsen SB, Sasselov DD, Petaev MI, Vanderburg A, Lopez-Morales M, Perez-Mercader J, Mattsson TR, Li G, Heising MZ, Bonomo AS, Damasso M, Berger TA, Cao H, Levi A, Wordsworth RD. Growth model interpretation of planet size distribution. Proc Natl Acad Sci U S A 2019; 116:9723-9728. [PMID: 31036661 PMCID: PMC6525489 DOI: 10.1073/pnas.1812905116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The radii and orbital periods of 4,000+ confirmed/candidate exoplanets have been precisely measured by the Kepler mission. The radii show a bimodal distribution, with two peaks corresponding to smaller planets (likely rocky) and larger intermediate-size planets, respectively. While only the masses of the planets orbiting the brightest stars can be determined by ground-based spectroscopic observations, these observations allow calculation of their average densities placing constraints on the bulk compositions and internal structures. However, an important question about the composition of planets ranging from 2 to 4 Earth radii (R⊕) still remains. They may either have a rocky core enveloped in a H2-He gaseous envelope (gas dwarfs) or contain a significant amount of multicomponent, H2O-dominated ices/fluids (water worlds). Planets in the mass range of 10-15 M⊕, if half-ice and half-rock by mass, have radii of 2.5 R⊕, which exactly match the second peak of the exoplanet radius bimodal distribution. Any planet in the 2- to 4-R⊕ range requires a gas envelope of at most a few mass percentage points, regardless of the core composition. To resolve the ambiguity of internal compositions, we use a growth model and conduct Monte Carlo simulations to demonstrate that many intermediate-size planets are "water worlds."
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Affiliation(s)
- Li Zeng
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138;
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Stein B Jacobsen
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | - Dimitar D Sasselov
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Michail I Petaev
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Andrew Vanderburg
- Department of Astronomy, The University of Texas at Austin, Austin, TX 78712
| | - Mercedes Lopez-Morales
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Juan Perez-Mercader
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | - Thomas R Mattsson
- High Energy Density Physics Theory Department, Sandia National Laboratories, Albuquerque, NM 87185
| | - Gongjie Li
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30313
| | - Matthew Z Heising
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Aldo S Bonomo
- Istituto Nazionale di Astrofisica-Osservatorio Astrofisico di Torino, 10025 Pino Torinese, Italy
| | - Mario Damasso
- Istituto Nazionale di Astrofisica-Osservatorio Astrofisico di Torino, 10025 Pino Torinese, Italy
| | - Travis A Berger
- Institute for Astronomy, University of Hawaii, Honolulu, HI 96822
| | - Hao Cao
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
| | - Amit Levi
- Center for Astrophysics | Harvard & Smithsonian, Department of Astronomy, Harvard University, MA 02138
| | - Robin D Wordsworth
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138
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Todd ZR, Szabla R, Szostak JW, Sasselov DD. UV photostability of three 2-aminoazoles with key roles in prebiotic chemistry on the early earth. Chem Commun (Camb) 2019; 55:10388-10391. [PMID: 31380533 DOI: 10.1039/c9cc05265h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Three related molecules in the 2-aminoazole family are potentially important for prebiotic chemistry: 2-aminooxazole, 2-aminoimidazole, and 2-aminothiazole, which can provide critical functions as an intermediate in nucleotide synthesis, a nucleotide activating agent, and a selective agent, respectively. Here, we examine the wavelength-dependent photodegradation of these three molecules under mid-range UV light (210-290 nm). We then assess the implications of the observed degradation rates for the proposed prebiotic roles of these compounds. We find that all three 2-aminoazoles degrade under UV light, with half lives ranging from ≈7-100 hours under a solar-like spectrum. 2-Aminooxazole is the least photostable, while 2-aminoimidazole is the most photostable. The relative photostabilities are consistent with the order in which these molecules would be used prebiotically: AO is used first to build nucleotides and AI is used last to activate them.
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Affiliation(s)
- Zoe R Todd
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA.
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16
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Ranjan S, Todd ZR, Sutherland JD, Sasselov DD. Sulfidic Anion Concentrations on Early Earth for Surficial Origins-of-Life Chemistry. Astrobiology 2018; 18:1023-1040. [PMID: 29627997 PMCID: PMC6225604 DOI: 10.1089/ast.2017.1770] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
A key challenge in origin-of-life studies is understanding the environmental conditions on early Earth under which abiogenesis occurred. While some constraints do exist (e.g., zircon evidence for surface liquid water), relatively few constraints exist on the abundances of trace chemical species, which are relevant to assessing the plausibility and guiding the development of postulated prebiotic chemical pathways which depend on these species. In this work, we combine literature photochemistry models with simple equilibrium chemistry calculations to place constraints on the plausible range of concentrations of sulfidic anions (HS-, HSO3-, SO32-) available in surficial aquatic reservoirs on early Earth due to outgassing of SO2 and H2S and their dissolution into small shallow surface water reservoirs like lakes. We find that this mechanism could have supplied prebiotically relevant levels of SO2-derived anions, but not H2S-derived anions. Radiative transfer modeling suggests UV light would have remained abundant on the planet surface for all but the largest volcanic explosions. We apply our results to the case study of the proposed prebiotic reaction network of Patel et al. ( 2015 ) and discuss the implications for improving its prebiotic plausibility. In general, epochs of moderately high volcanism could have been especially conducive to cyanosulfidic prebiotic chemistry. Our work can be similarly applied to assess and improve the prebiotic plausibility of other postulated surficial prebiotic chemistries that are sensitive to sulfidic anions, and our methods adapted to study other atmospherically derived trace species.
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Affiliation(s)
- Sukrit Ranjan
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
- MIT Department of Earth, Atmospheric, and Planetary Sciences, Cambridge, Massachusetts, USA
| | - Zoe R. Todd
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA
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17
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Xu J, Ritson DJ, Ranjan S, Todd ZR, Sasselov DD, Sutherland JD. Photochemical reductive homologation of hydrogen cyanide using sulfite and ferrocyanide. Chem Commun (Camb) 2018; 54:5566-5569. [PMID: 29761807 PMCID: PMC5972737 DOI: 10.1039/c8cc01499j] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Photoredox cycling during UV irradiation of ferrocyanide ([FeII(CN)6]4-) in the presence of stoichiometric sulfite (SO32-) is shown to be an extremely effective way to drive the reductive homologation of hydrogen cyanide (HCN) to simple sugars and precursors of hydroxy acids and amino acids.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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18
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Todd ZR, Fahrenbach AC, Magnani CJ, Ranjan S, Björkbom A, Szostak JW, Sasselov DD. Solvated-electron production using cyanocuprates is compatible with the UV-environment on a Hadean–Archaean Earth. Chem Commun (Camb) 2018; 54:1121-1124. [PMID: 29334083 PMCID: PMC9631354 DOI: 10.1039/c7cc07748c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV-driven photoredox processing of cyanocuprates can generate simple sugars necessary for prebiotic synthesis. We investigate the wavelength dependence of this process from 215 to 295 nm and generally observe faster rates at shorter wavelengths. The most efficient wavelengths are accessible to a range of potential prebiotic atmospheres, supporting the potential role of cyanocuprate photochemistry in prebiotic synthesis on the early Earth. Simple sugars necessary for the synthesis of prebiotic molecules can be generated from UV-driven cyanocuprate photoprocessing under conditions consistent with those expected on the surface of the early Earth.![]()
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Affiliation(s)
- Zoe R. Todd
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Albert C. Fahrenbach
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Christopher J. Magnani
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Sukrit Ranjan
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
| | - Anders Björkbom
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Jack W. Szostak
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- 185 Cambridge Street
- Boston
| | - Dimitar D. Sasselov
- Department of Astronomy
- Harvard-Smithsonian Center for Astrophysics
- 60 Garden Street
- Cambridge
- USA
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19
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Ranjan S, Wordsworth R, Sasselov DD. Atmospheric Constraints on the Surface UV Environment of Mars at 3.9 Ga Relevant to Prebiotic Chemistry. Astrobiology 2017; 17:687-708. [PMID: 28537771 DOI: 10.1089/ast.2016.1596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent findings suggest that Mars may have been a clement environment for the emergence of life and may even have compared favorably to Earth in this regard. These findings have revived interest in the hypothesis that prebiotically important molecules or even nascent life may have formed on Mars and been transferred to Earth. UV light plays a key role in prebiotic chemistry. Characterizing the early martian surface UV environment is key to understanding how Mars compares to Earth as a venue for prebiotic chemistry. Here, we present two-stream, multilayer calculations of the UV surface radiance on Mars at 3.9 Ga to constrain the surface UV environment as a function of atmospheric state. We explore a wide range of atmospheric pressures, temperatures, and compositions that correspond to the diversity of martian atmospheric states consistent with available constraints. We include the effects of clouds and dust. We calculate dose rates to quantify the effect of different atmospheric states on UV-sensitive prebiotic chemistry. We find that, for normative clear-sky CO2-H2O atmospheres, the UV environment on young Mars is comparable to young Earth. This similarity is robust to moderate cloud cover; thick clouds (τcloud ≥ 100) are required to significantly affect the martian UV environment, because cloud absorption is degenerate with atmospheric CO2. On the other hand, absorption from SO2, H2S, and dust is nondegenerate with CO2, meaning that, if these constituents build up to significant levels, surface UV fluence can be suppressed. These absorbers have spectrally variable absorption, meaning that their presence affects prebiotic pathways in different ways. In particular, high SO2 environments may admit UV fluence that favors pathways conducive to abiogenesis over pathways unfavorable to it. However, better measurements of the spectral quantum yields of these pathways are required to evaluate this hypothesis definitively. Key Words: Radiative transfer-Origin of life-Mars-UV radiation-Prebiotic chemistry. Astrobiology 17, 687-708.
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Affiliation(s)
- Sukrit Ranjan
- 1 Harvard-Smithsonian Center for Astrophysics , Cambridge, Massachusetts
| | - Robin Wordsworth
- 2 Harvard Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts
- 3 Department of Earth and Planetary Sciences, Harvard University , Cambridge, Massachusetts
| | - Dimitar D Sasselov
- 1 Harvard-Smithsonian Center for Astrophysics , Cambridge, Massachusetts
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20
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Bonfio C, Valer L, Scintilla S, Shah S, Evans DJ, Jin L, Szostak JW, Sasselov DD, Sutherland JD, Mansy SS. UV-light-driven prebiotic synthesis of iron-sulfur clusters. Nat Chem 2017; 9:1229-1234. [PMID: 29168482 DOI: 10.1038/nchem.2817] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/01/2017] [Indexed: 12/17/2022]
Abstract
Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine-containing peptides and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur-cluster-dependent metabolism.
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Affiliation(s)
- Claudia Bonfio
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Luca Valer
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | | | - Sachin Shah
- Chemistry, School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK
| | - David J Evans
- Chemistry, School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK
| | - Lin Jin
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, Massachusetts 02138, USA
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Sheref S Mansy
- CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
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21
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Abstract
The UV environment is a key boundary condition to abiogenesis. However, considerable uncertainty exists as to planetary conditions and hence surface UV at abiogenesis. Here, we present two-stream multilayer clear-sky calculations of the UV surface radiance on Earth at 3.9 Ga to constrain the UV surface fluence as a function of albedo, solar zenith angle (SZA), and atmospheric composition. Variation in albedo and latitude (through SZA) can affect maximum photoreaction rates by a factor of >10.4; for the same atmosphere, photoreactions can proceed an order of magnitude faster at the equator of a snowball Earth than at the poles of a warmer world. Hence, surface conditions are important considerations when computing prebiotic UV fluences. For climatically reasonable levels of CO2, fluence shortward of 189 nm is screened out, meaning that prebiotic chemistry is robustly shielded from variations in UV fluence due to solar flares or variability. Strong shielding from CO2 also means that the UV surface fluence is insensitive to plausible levels of CH4, O2, and O3. At scattering wavelengths, UV fluence drops off comparatively slowly with increasing CO2 levels. However, if SO2 and/or H2S can build up to the ≥1-100 ppm level as hypothesized by some workers, then they can dramatically suppress surface fluence and hence prebiotic photoprocesses. H2O is a robust UV shield for λ < 198 nm. This means that regardless of the levels of other atmospheric gases, fluence ≲198 nm is only available for cold, dry atmospheres, meaning sources with emission ≲198 (e.g., ArF excimer lasers) can only be used in simulations of cold environments with low abundance of volcanogenic gases. On the other hand, fluence at 254 nm is unshielded by H2O and is available across a broad range of [Formula: see text], meaning that mercury lamps are suitable for initial studies regardless of the uncertainty in primordial H2O and CO2 levels. Key Words: Radiative transfer-Origin of life-Planetary environments-UV radiation-Prebiotic chemistry. Astrobiology 17, 169-204.
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Affiliation(s)
- Sukrit Ranjan
- Harvard-Smithsonian Center for Astrophysics , Cambridge, Massachusetts
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22
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Abstract
Ultraviolet radiation is common to most planetary environments and could play a key role in the chemistry of molecules relevant to abiogenesis (prebiotic chemistry). In this work, we explore the impact of UV light on prebiotic chemistry that might occur in liquid water on the surface of a planet with an atmosphere. We consider effects including atmospheric absorption, attenuation by water, and stellar variability to constrain the UV input as a function of wavelength. We conclude that the UV environment would be characterized by broadband input, and wavelengths below 204 nm and 168 nm would be shielded out by atmospheric CO2 and water, respectively. We compare this broadband prebiotic UV input to the narrowband UV sources (e.g., mercury lamps) often used in laboratory studies of prebiotic chemistry and explore the implications for the conclusions drawn from these experiments. We consider as case studies the ribonucleotide synthesis pathway of Powner et al. (2009) and the sugar synthesis pathway of Ritson and Sutherland (2012). Irradiation by narrowband UV light from a mercury lamp formed an integral component of these studies; we quantitatively explore the impact of more realistic UV input on the conclusions that can be drawn from these experiments. Finally, we explore the constraints solar UV input places on the buildup of prebiotically important feedstock gasses like CH4 and HCN. Our results demonstrate the importance of characterizing the wavelength dependence (action spectra) of prebiotic synthesis pathways to determine how pathways derived under laboratory irradiation conditions will function under planetary prebiotic conditions.
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Affiliation(s)
- Sukrit Ranjan
- Harvard-Smithsonian Center for Astrophysics , Cambridge, Massachusetts
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23
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Fressin F, Torres G, Rowe JF, Charbonneau D, Rogers LA, Ballard S, Batalha NM, Borucki WJ, Bryson ST, Buchhave LA, Ciardi DR, Désert JM, Dressing CD, Fabrycky DC, Ford EB, Gautier III TN, Henze CE, Holman MJ, Howard A, Howell SB, Jenkins JM, Koch DG, Latham DW, Lissauer JJ, Marcy GW, Quinn SN, Ragozzine D, Sasselov DD, Seager S, Barclay T, Mullally F, Seader SE, Still M, Twicken JD, Thompson SE, Uddin K. Two Earth-sized planets orbiting Kepler-20. Nature 2011; 482:195-8. [DOI: 10.1038/nature10780] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 12/13/2011] [Indexed: 11/09/2022]
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24
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Holman MJ, Fabrycky DC, Ragozzine D, Ford EB, Steffen JH, Welsh WF, Lissauer JJ, Latham DW, Marcy GW, Walkowicz LM, Batalha NM, Jenkins JM, Rowe JF, Cochran WD, Fressin F, Torres G, Buchhave LA, Sasselov DD, Borucki WJ, Koch DG, Basri G, Brown TM, Caldwell DA, Charbonneau D, Dunham EW, Gautier TN, Geary JC, Gilliland RL, Haas MR, Howell SB, Ciardi DR, Endl M, Fischer D, Fürész G, Hartman JD, Isaacson H, Johnson JA, MacQueen PJ, Moorhead AV, Morehead RC, Orosz JA. Kepler-9: A System of Multiple Planets Transiting a Sun-Like Star, Confirmed by Timing Variations. Science 2010; 330:51-4. [DOI: 10.1126/science.1195778] [Citation(s) in RCA: 311] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Matthew J. Holman
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Daniel C. Fabrycky
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Darin Ragozzine
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Eric B. Ford
- University of Florida, Gainesville, FL 32611, USA
| | - Jason H. Steffen
- Fermilab Center for Particle Astrophysics, Batavia, IL 60510, USA
| | | | - Jack J. Lissauer
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- Stanford University, Stanford, CA 94305, USA
| | - David W. Latham
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | | | | | | | - Jon M. Jenkins
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- SETI Institute, Mountain View, CA 94043, USA
| | - Jason F. Rowe
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Francois Fressin
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Guillermo Torres
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Lars A. Buchhave
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
- Niels Bohr Institute, Copenhagen University, DK-2100 Copenhagen, Denmark
| | - Dimitar D. Sasselov
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | | | - David G. Koch
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Gibor Basri
- University of California, Berkeley, CA 94720, USA
| | - Timothy M. Brown
- Las Cumbres Observatory Global Telescope, Goleta, CA 93117, USA
- University of California, Santa Barbara, CA 93106, USA
| | - Douglas A. Caldwell
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- SETI Institute, Mountain View, CA 94043, USA
| | - David Charbonneau
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | | | - Thomas N. Gautier
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, CA 91109, USA
| | - John C. Geary
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | | | | | - Steve B. Howell
- National Optical Astronomy Observatory, Tucson, AZ 85719, USA
| | - David R. Ciardi
- NASA Exoplanet Science Institute/California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Gábor Fürész
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
| | - Joel D. Hartman
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA
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Jacobsen SB, Ranen MC, Petaev MI, Remo JL, O'Connell RJ, Sasselov DD. Isotopes as clues to the origin and earliest differentiation history of the Earth. Philos Trans A Math Phys Eng Sci 2008; 366:4129-4162. [PMID: 18826920 DOI: 10.1098/rsta.2008.0174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Measurable variations in (182)W/(183)W, (142)Nd/(144)Nd, (129)Xe/(130)Xe and (136)XePu/(130)Xe in the Earth and meteorites provide a record of accretion and formation of the core, early crust and atmosphere. These variations are due to the decay of the now extinct nuclides (182)Hf, (146)Sm, (129)I and (244)Pu. The (l82)Hf-(182)W system is the best accretion and core-formation chronometer, which yields a mean time of Earth's formation of 10Myr, and a total time scale of 30Myr. New laser shock data at conditions comparable with those in the Earth's deep mantle subsequent to the giant Moon-forming impact suggest that metal-silicate equilibration was rapid enough for the Hf-W chronometer to reliably record this time scale. The coupled (146)Sm-(147)Sm chronometer is the best system for determining the initial silicate differentiation (magma ocean crystallization and proto-crust formation), which took place at ca 4.47Ga or perhaps even earlier. The presence of a large (129)Xe excess in the deep Earth is consistent with a very early atmosphere formation (as early as 30Myr); however, the interpretation is complicated by the fact that most of the atmospheric Xe may be from a volatile-rich late veneer.
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Affiliation(s)
- Stein B Jacobsen
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA.
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Konacki M, Torres G, Jha S, Sasselov DD. An extrasolar planet that transits the disk of its parent star. Nature 2003; 421:507-9. [PMID: 12556885 DOI: 10.1038/nature01379] [Citation(s) in RCA: 251] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2002] [Accepted: 12/30/2002] [Indexed: 11/09/2022]
Abstract
Planets orbiting other stars could in principle be found through the periodic dimming of starlight as a planet moves across--or 'transits'--the line of sight between the observer and the star. Depending on the size of the planet relative to the star, the dimming could reach a few per cent of the apparent brightness of the star. Despite many searches, no transiting planet has been discovered in this way; the one known transiting planet--HD209458b--was first discovered using precise measurements of the parent star's radial velocity and only subsequently detected photometrically. Here we report radial velocity measurements of the star OGLE-TR-56, which was previously found to exhibit a 1.2-day transit-like light curve in a survey looking for gravitational microlensing events. The velocity changes that we detect correlate with the light curve, from which we conclude that they are probably induced by an object of around 0.9 Jupiter masses in an orbit only 0.023 au from its star. We estimate the planetary radius to be around 1.3 Jupiter radii and its density to be about 0.5 g x cm(-3). This object is hotter than any known planet (approximately 1,900 K), but is still stable against long-term evaporation or tidal disruption.
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Affiliation(s)
- Maciej Konacki
- Division of Geological & Planetary Sciences 150-21, California Institute of Technology, Pasadena, California 91125, USA.
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