1
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Sawant AA, Tripathi S, Galande S, Rajamani S. A Prebiotic Genetic Nucleotide as an Early Darwinian Ancestor for Pre-RNA Evolution. ACS OMEGA 2024; 9:18072-18082. [PMID: 38680342 PMCID: PMC11044211 DOI: 10.1021/acsomega.3c09949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Prebiotic genetic nucleotides (PGNs) often outcompete canonical alphabets in the formation of nucleotides and subsequent RNA oligomerization under early Earth conditions. This indicates that the early genetic code might have been dominated by pre-RNA that contained PGNs for information transfer and catalysis. Despite this, deciphering pre-RNAs' capacity to acquire function and delineating their evolutionary transition to a canonical RNA World has remained under-researched in the origins of life (OoL) field. We report the synthesis of a prebiotically relevant nucleotide (BaTP) containing the noncanonical nucleobase barbituric acid. We demonstrate the first instance of its enzymatic incorporation into an RNA, using a T7 RNA polymerase. BaTP's incorporation into baby spinach aptamer allowed it to retain its overall secondary structure and function. Finally, we also demonstrate faithful transfer of information from the pre-RNA-containing BaTP to DNA, using a high-fidelity RNA-dependent DNA polymerase, alluding to how selection pressures and complexities could have ensued during the molecular evolution of the early genetic code.
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Affiliation(s)
- Anupam A. Sawant
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Sneha Tripathi
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Sanjeev Galande
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
- Center
of Excellence in Epigenetics, Department of Life Sciences, School
of Natural Sciences, Shiv Nadar Institution
of Eminence, Gautam Buddha
Nagar, Uttar Pradesh 201314, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
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2
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Crespo-Hernández CE. Special issue on nucleic acid photophysics. Photochem Photobiol 2024; 100:257-261. [PMID: 38501585 DOI: 10.1111/php.13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/20/2024]
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3
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Roche TP, Fialho DM, Menor-Salván C, Krishnamurthy R, Schuster GB, Hud NV. A Plausible Prebiotic Path to Nucleosides: Ribosides and Related Aldosides Generated from Ribulose, Fructose, and Similar Abiotic Precursors. Chemistry 2023; 29:e202203036. [PMID: 36261321 DOI: 10.1002/chem.202203036] [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: 09/29/2022] [Indexed: 12/12/2022]
Abstract
The prebiotic origins of ribose, nucleosides, and eventually RNA are enduring questions whose answers are central to the RNA world hypothesis. The abiotic synthesis of sugars was first demonstrated over a century ago, but no known prebiotic reaction produces ribose (an aldose sugar) selectively and in good yield. In contrast, ribulose, and fructose (ketose sugars) and other monosaccharides are formed in high yield by several robust abiotic reactions. It is reported here that ketose sugars - both ketopentoses and ketohexoes - serve as precursors for the formation of ribosides and other aldosides, as demonstrated by glycoside-forming reactions involving barbituric acid, a plausibly prebiotic nucleobase. Moreover, a one-pot reaction of glyceraldehyde and barbituric acid was discovered which under mild conditions, and without special minerals or other catalysts, results in the formation of glycosides. These results reveal that an exclusive or high-yielding generation of free ribose was not required for its incorporation into processes that provided the foundations for life.
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Affiliation(s)
- Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Cesar Menor-Salván
- Departmento de Biología de Sistemas/IQAR, Universidad de Alcalá, Madrid, 28806, Spain
| | | | - Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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4
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Ortín-Fernández J, Caldero-Rodríguez NE, Crespo-Hernández CE, Martínez-Fernández L, Corral I. Photophysical Characterization of Isoguanine in a Prebiotic-Like Environment. Chemistry 2023; 29:e202203580. [PMID: 36693799 DOI: 10.1002/chem.202203580] [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: 11/17/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
It is intriguing how a mixture of organic molecules survived the prebiotic UV fluxes and evolved into the actual genetic building blocks. Scientists are trying to shed light on this issue by synthesizing nucleic acid monomers and their analogues under prebiotic Era-like conditions and by exploring their excited state dynamics. To further add to this important body of knowledge, this study discloses new insights into the photophysical properties of protonated isoguanine, an isomorph of guanine, using steady-state and femtosecond broadband transient absorption spectroscopies, and quantum mechanical calculations. Protonated isoguanine decays in ultrafast time scales following 292 nm excitation, consistently with the barrierless paths connecting the bright S1 (ππ*) state with different internal conversion funnels. Complementary calculations for neutral isoguanine predict similar photophysical properties. These results demonstrate that protonated isoguanine can be considered photostable in contrast to protonated guanine, which exhibits 40-fold longer excited state lifetimes.
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Affiliation(s)
- Javier Ortín-Fernández
- Departamento de Química, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | | | | | - Lara Martínez-Fernández
- Departamento de Química, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - Inés Corral
- Departamento de Química, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
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5
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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6
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Vos E, Hoehn SJ, Krul SE, Crespo-Hernández CE, González-Vázquez J, Corral I. Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State. J Phys Chem Lett 2022; 13:2000-2006. [PMID: 35191712 PMCID: PMC8900130 DOI: 10.1021/acs.jpclett.2c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S1(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.
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Affiliation(s)
- Eva Vos
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Sean J. Hoehn
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Sarah E. Krul
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E. Crespo-Hernández
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jesús González-Vázquez
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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7
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On the Photostability of Cyanuric Acid and Its Candidature as a Prebiotic Nucleobase. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041184. [PMID: 35208973 PMCID: PMC8875432 DOI: 10.3390/molecules27041184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 11/28/2022]
Abstract
Cyanuric acid is a triazine derivative that has been identified from reactions performed under prebiotic conditions and has been proposed as a prospective precursor of ancestral RNA. For cyanuric acid to have played a key role during the prebiotic era, it would have needed to survive the harsh electromagnetic radiation conditions reaching the Earth’s surface during prebiotic times (≥200 nm). Therefore, the photostability of cyanuric acid would have been crucial for its accumulation during the prebiotic era. To evaluate the putative photostability of cyanuric acid in water, in this contribution, we employed density functional theory (DFT) and its time-dependent variant (TD-DFT) including implicit and explicit solvent effects. The calculations predict that cyanuric acid has an absorption maximum at ca. 160 nm (7.73 eV), with the lowest-energy absorption band extending to ca. 200 nm in an aqueous solution and exhibiting negligible absorption at longer wavelengths. Excitation of cyanuric acid at 160 nm or longer wavelengths leads to the population of S5,6 singlet states, which have ππ* character and large oscillator strengths (0.8). The population reaching the S5,6 states is expected to internally convert to the S1,2 states in an ultrafast time scale. The S1,2 states, which have nπ* character, are predicted to access a conical intersection with the ground state in a nearly barrierless fashion (ca. ≤ 0.13 eV), thus efficiently returning the population to the ground state. Furthermore, based on calculated spin–orbit coupling elements of ca. 6 to 8 cm−1, the calculations predict that intersystem crossing to the triplet manifold should play a minor role in the electronic relaxation of cyanuric acid. We have also calculated the vertical ionization energy of cyanuric acid at 8.2 eV, which predicts that direct one-photon ionization of cyanuric acid should occur at ca. 150 nm. Collectively, the quantum-chemical calculations predict that cyanuric acid would have been highly photostable under the solar radiation conditions reaching the Earth’s surface during the prebiotic era in an aqueous solution. Of relevance to the chemical origin of life and RNA-first theories, these observations lend support to the idea that cyanuric acid could have accumulated in large quantities during the prebiotic era and thus strengthens its candidature as a relevant prebiotic nucleobase.
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8
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Romeo-Gella F, Arpa EM, Corral I. A molecular insight into the photophysics of barbituric acid, a candidate for canonical nucleobases' ancestor. Phys Chem Chem Phys 2022; 24:1405-1414. [PMID: 34982082 DOI: 10.1039/d1cp04987a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This work investigates the photophysics of barbituric acid at different pH conditions using ab initio methods. Our calculations ascribe the most intense bands at ca. 260 nm at neutral pH and 210 nm at acidic pH conditions in the absorption spectra of this chromophore to the lowest lying ππ* transitions. Consistently with the ultrashort excited state lifetimes experimentally registered, the potential energy landscapes of both the neutral and deprotonated forms of barbituric acid combined with the interpretation of their transient absorption spectra suggest the deactivation of these systems along the singlet manifold. Compared to uracil, its closest natural nucleobase, barbituric acid presents a red shifted absorption spectrum, due to the lowering by more than 0.5 eV of the lowest-energy ππ* excited state, and a much more complex topography of the S1 potential energy surface, with several energetically accessible local minima. This fact, however, does not affect the excited state lifetimes, which for barbituric acid were experimentally registered in the sub-ps time scale.
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Affiliation(s)
- Fernando Romeo-Gella
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Enrique M Arpa
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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9
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Camiruaga A, Usabiaga I, Calabrese C, Lamas I, Basterretxea FJ, Fernández JA. Exploring the Influence of Intermolecular Interactions in Prebiotic Chemistry Using Laser Spectroscopy and Calculations. Chemistry 2021; 28:e202103636. [PMID: 34854511 PMCID: PMC9299682 DOI: 10.1002/chem.202103636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/09/2022]
Abstract
One of the most fascinating questions in chemistry is why nature chose CGAT as the alphabet of life. Very likely, such selection was the result of multiple factors and a long period of refinement. Here, we explore how the intermolecular interactions influenced such process, by characterizing the formation of dimers between adenine, theobromine and 4-aminopyrimidine. Using a combination of mass-resolved excitation spectroscopy and DFT calculations, we determined the structure of adenine-theobromine and 4-aminopyrimidine-theobromine dimers. The binding energy of these dimers is very close to the canonical adenine-thymine nucleobases. Likewise, the dimers are able to adopt Watson-Crick conformations. These findings seem to indicate that there were many options available to build the first versions of the informational polymers, which also had to compete with other molecules, such as 4-aminopyrimidine, which does not have a valid attaching point for a saccharide. For some reason, nature did not select the most strongly-bonded partners or if it did, such proto-bases were later replaced by the nowadays canonical CGAT.
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Affiliation(s)
- Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Camilla Calabrese
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain.,Instituto Biofisika (UPV/EHU-CSIC), University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, Leioa, 48940, Spain
| | - Iker Lamas
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Francisco J Basterretxea
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
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10
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Kaur S, Grover P, Wetmore SD, Sharma P. Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View. J Chem Inf Model 2021; 61:4321-4330. [PMID: 34491053 DOI: 10.1021/acs.jcim.1c00276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous explanation. Recent studies have suggested that noncanonical bases such as barbituric acid (BA), melamine (MM), cyanuric acid (CA), and 2,4,6-triaminopyrimidine (TAP) may have undergone molecular selection within the "prebiotic soup" to spontaneously form supramolecular assemblies, which then covalently assembled into an RNA-like polymer (preRNA). However, information on the role of intrinsic interactions of these candidate heterocycles in their molecular selection as the components of preRNA, and the subsequent transition from preRNA to RNA, is currently missing in the literature. To fill this gap in our knowledge on the origin and evolution of primitive genetics, the present work employs density functional theory (B3LYP-D3) to evaluate and compare the stacking propensities of dimers containing prebiotic noncanonical (BA, MM, CA, and TAP) and/or canonical RNA bases (A, C, G, and U). Our detailed analysis of the variation in stacking strength with respect to four characteristic geometrical parameters between the monomers [i.e., the vertical distance, the angle of rotation, and (two) displacements in the x and y directions] reveals that stacking between nonidentical bases is preferred over identical bases for both prebiotic-prebiotic and canonical-canonical dimers. This not only underscores the similarity between the fundamental chemical properties of preRNA and RNA constituents but also supports the likelihood of the evolution of modern (RNA) genetics from primitive (preRNA) genetics. Furthermore, greater average stacking stabilization of canonical dimers than that of dimers containing one canonical and one preRNA nucleobase (by ∼5 kJ mol-1) or dimers solely containing preRNA nucleobases (by ∼12 kJ mol-1) indicates that enhanced stacking is an important factor that may have spurred the evolution of preRNA to an intermediate informational polymer to RNA. More importantly, our study identifies the central roles of CA, BA, and TAP in stacking stabilization within the preRNA and of BA in stacking interactions within the intermediate polymers and suggests that these heterocycles may have played distinct roles in various stages during the evolution from preRNA to RNA. Overall, our results highlight the significance of stacking interactions in the selection of nucleobase components of preRNA.
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Payal Grover
- Department of Chemistry, Dayanand Anglo-Vedic (DAV) College, Sector 10, Chandigarh 16011, India
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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11
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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12
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Alenaizan A, Borca CH, Karunakaran SC, Kendall AK, Stubbs G, Schuster GB, Sherrill CD, Hud NV. X-ray Fiber Diffraction and Computational Analyses of Stacked Hexads in Supramolecular Polymers: Insight into Self-Assembly in Water by Prospective Prebiotic Nucleobases. J Am Chem Soc 2021; 143:6079-6094. [DOI: 10.1021/jacs.0c12010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Carlos H. Borca
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
| | - Amy K. Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0765, United States
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
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13
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The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems (Origin of Life). Acta Biotheor 2021; 69:67-78. [PMID: 32783083 DOI: 10.1007/s10441-020-09388-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation of quasi-random small peptides, some of them capable to bind this ribozyme structure back and starting to form an initial layer that would produce the larger subunit of the ribosome by accretion. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to the emergence of new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field.
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14
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Rankine CD. Ultrafast excited-state dynamics of promising nucleobase ancestor 2,4,6-triaminopyrimidine. Phys Chem Chem Phys 2021; 23:4007-4017. [PMID: 33554987 DOI: 10.1039/d0cp05609j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultrafast excited-state dynamics of 2,4,6-triaminopyrimidine - thought to be a promising candidate for a proto-RNA nucleobase - have been investigated via static multireference quantum-chemical calculations and mixed-quantum-classical/trajectory surface-hopping dynamics with a focus on the lowest-lying electronic states of the singlet manifold and with a view towards understanding the UV(C)/UV(B) photostability of the molecule. Ultrafast internal conversion channels have been identified that connect the lowest-lying ππ* electronically-excited state of 2,4,6-triaminopyrimidine with the ground electronic state, and non-radiative decay has been observed to take place on the picosecond timescale via a ππ* out-of-plane NH2 ("oop-NH2") minimum-energy crossing point. The short excited-state lifetime is competitive with the excited-state lifetimes of the canonical pyrimidine nucleobases, affirming the promise of 2,4,6-triaminopyrimidine as an ancestor. Evidence for energy-dependent excited-state dynamics is presented, and the open question of intersystem crossing is discussed speculatively.
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Affiliation(s)
- Conor D Rankine
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
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15
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Anderson BA, Fauché K, Karunakaran SC, Yerabolu JR, Hud NV, Krishnamurthy R. The Unexpected Base‐Pairing Behavior of Cyanuric Acid in RNA and Ribose versus Cyanuric Acid Induced Helicene Assembly of Nucleic Acids: Implications for the Pre‐RNA Paradigm. Chemistry 2021; 27:4033-4042. [DOI: 10.1002/chem.202004397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/08/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Brooke A. Anderson
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Kévin Fauché
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Jayasudhan R. Yerabolu
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology 901 Atlantic Drive Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
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16
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Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
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17
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Sandford SA, Nuevo M, Bera PP, Lee TJ. Prebiotic Astrochemistry and the Formation of Molecules of Astrobiological Interest in Interstellar Clouds and Protostellar Disks. Chem Rev 2020; 120:4616-4659. [DOI: 10.1021/acs.chemrev.9b00560] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Scott A. Sandford
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
| | - Michel Nuevo
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Partha P. Bera
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Timothy J. Lee
- NASA Ames Research Center, MS 245-3, Moffett Field, California 94035, United States
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18
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Stolar T, Lukin S, Etter M, Rajić Linarić M, Užarević K, Meštrović E, Halasz I. DNA-specific selectivity in pairing of model nucleobases in the solid state. Chem Commun (Camb) 2020; 56:13524-13527. [DOI: 10.1039/d0cc03491f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state may serve as the reaction medium for selective recognition between model nucleobases.
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Affiliation(s)
| | | | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY)
- 22607 Hamburg
- Germany
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19
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Mariscal C, Barahona A, Aubert-Kato N, Aydinoglu AU, Bartlett S, Cárdenas ML, Chandru K, Cleland C, Cocanougher BT, Comfort N, Cornish-Bowden A, Deacon T, Froese T, Giovannelli D, Hernlund J, Hut P, Kimura J, Maurel MC, Merino N, Moreno A, Nakagawa M, Peretó J, Virgo N, Witkowski O, James Cleaves H. Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report. ORIGINS LIFE EVOL B 2019; 49:111-145. [PMID: 31399826 DOI: 10.1007/s11084-019-09580-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/12/2019] [Indexed: 12/11/2022]
Abstract
In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the "bottom up" approach) and (4) how to infer the nature of the last universal common ancestor (the "top down" approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a" circularity" approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.
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Affiliation(s)
- Carlos Mariscal
- Department of Philosophy, Ecology, Evolution, and Conservation Biology (EECB) Program, and Integrative Neuroscience Program, University of Nevada, Reno (UNR), Reno, Nevada, USA
| | - Ana Barahona
- Department of Evolutionary Biology, School of Sciences, UNAM, 04510, CDMX, Coyoacán, Mexico
| | - Nathanael Aubert-Kato
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Department of Information Sciences, Ochanomizu University, Bunkyoku, Otsuka, 2-1-1, Tokyo, 112-0012, Japan
| | - Arsev Umur Aydinoglu
- Blue Marble Space Institute of Science, Washington, DC, 20011, USA
- Science and Technology Policies Department, Middle East Technical University (METU), 06800, Ankara, Turkey
| | - Stuart Bartlett
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | | | - Kuhan Chandru
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Space Science Centre (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, 43600, UKM Bangi, Selangor, Malaysia
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague, 6, Dejvice, Czech Republic
| | - Carol Cleland
- Department of Philosophy, University of Colorado, Boulder, Colorado, USA
| | - Benjamin T Cocanougher
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Nathaniel Comfort
- Department of the History of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Terrence Deacon
- Department of Anthropology & Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - Tom Froese
- Institute for Applied Mathematics and Systems Research (IIMAS), National Autonomous University of Mexico (UNAM), 04510, Mexico City, Mexico
- Centre for the Sciences of Complexity (C3), National Autonomous University of Mexico (UNAM), 04510, Mexico City, Mexico
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Institute for Advanced Study, Princeton, NJ, 08540, USA
- Department of Marine and Coastal Science, Rutgers University, 71 Dudley Rd, New Brunswick, NJ, 08901, USA
- YHouse, Inc., NY, 10159, New York, USA
- Department of Biology, University of Naples "Federico II", Via Cinthia, 80156, Naples, Italy
| | - John Hernlund
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
| | - Piet Hut
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Institute for Advanced Study, Princeton, NJ, 08540, USA
| | - Jun Kimura
- Department of Earth and Space Science, Osaka University, Machikaneyama-Chou 1-1, Toyonaka City, Osaka, 560-0043, Japan
| | | | - Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Department of Earth Sciences, University of Southern California, California, Los Angeles, 90089, USA
| | - Alvaro Moreno
- Department of Logic and Philosophy of Science, IAS-Research Centre for Life, Mind and Society, University of the Basque Country, Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain
| | - Mayuko Nakagawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
| | - Juli Peretó
- Department of Biochemistry and Molecular Biology, University of Valéncia and Institute for Integrative Systems Biology I2SysBio (University of Valéncia-CSIC), València, Spain
| | - Nathaniel Virgo
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- European Centre for Living Technology, Venice, Italy
| | - Olaf Witkowski
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
- Institute for Advanced Study, Princeton, NJ, 08540, USA
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan.
- Blue Marble Space Institute of Science, Washington, DC, 20011, USA.
- Institute for Advanced Study, Princeton, NJ, 08540, USA.
- European Centre for Living Technology, Venice, Italy.
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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20
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Cruikshank DP, Materese CK, Pendleton YJ, Boston PJ, Grundy WM, Schmitt B, Lisse CM, Runyon KD, Keane JT, Beyer RA, Summers ME, Scipioni F, Stern SA, Dalle Ore CM, Olkin CB, Young LA, Ennico K, Weaver HA, Bray VJ. Prebiotic Chemistry of Pluto. ASTROBIOLOGY 2019; 19:831-848. [PMID: 30907634 DOI: 10.1089/ast.2018.1927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present the case for the presence of complex organic molecules, such as amino acids and nucleobases, formed by abiotic processes on the surface and in near-subsurface regions of Pluto. Pluto's surface is tinted with a range of non-ice substances with colors ranging from light yellow to red to dark brown; the colors match those of laboratory organic residues called tholins. Tholins are broadly characterized as complex, macromolecular organic solids consisting of a network of aromatic structures connected by aliphatic bridging units (e.g., Imanaka et al., 2004; Materese et al., 2014, 2015). The synthesis of tholins in planetary atmospheres and in surface ices has been explored in numerous laboratory experiments, and both gas- and solid-phase varieties are found on Pluto. A third variety of tholins, exposed at a site of tectonic surface fracturing called Virgil Fossae, appears to have come from a reservoir in the subsurface. Eruptions of tholin-laden liquid H2O from a subsurface aqueous repository appear to have covered portions of Virgil Fossae and its surroundings with a uniquely colored deposit (D.P. Cruikshank, personal communication) that is geographically correlated with an exposure of H2O ice that includes spectroscopically detected NH3 (C.M. Dalle Ore, personal communication). The subsurface organic material could have been derived from presolar or solar nebula processes, or might have formed in situ. Photolysis and radiolysis of a mixture of ices relevant to Pluto's surface composition (N2, CH4, CO) have produced strongly colored, complex organics with a significant aromatic content having a high degree of nitrogen substitution similar to the aromatic heterocycles pyrimidine and purine (Materese et al., 2014, 2015; Cruikshank et al., 2016). Experiments with pyrimidines and purines frozen in H2O-NH3 ice resulted in the formation of numerous nucleobases, including the biologically relevant guanine, cytosine, adenine, uracil, and thymine (Materese et al., 2017). The red material associated with the H2O ice may contain nucleobases resulting from energetic processing on Pluto's surface or in the interior. Some other Kuiper Belt objects also exhibit red colors similar to those found on Pluto and may therefore carry similar inventories of complex organic materials. The widespread and ubiquitous nature of similarly complex organic materials observed in a variety of astronomical settings drives the need for additional laboratory and modeling efforts to explain the origin and evolution of organic molecules. Pluto observations reveal complex organics on a small body that remains close to its place of origin in the outermost regions of the Solar System.
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Affiliation(s)
- D P Cruikshank
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - C K Materese
- 2Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Y J Pendleton
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - P J Boston
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - W M Grundy
- 3Lowell Observatory, Flagstaff, Arizona, USA
| | - B Schmitt
- 4Université Grenoble Alpes, CNRS, IPAG, Grenoble, France
| | - C M Lisse
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - K D Runyon
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - J T Keane
- 6California Institute of Technology, Pasadena, California, USA
| | - R A Beyer
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - M E Summers
- 7Department of Physics and Astronomy, George Mason University, Fairfax, Virginia, USA
| | - F Scipioni
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - S A Stern
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - C M Dalle Ore
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - C B Olkin
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - L A Young
- 8Southwest Research Institute, Boulder, Colorado, USA
| | - K Ennico
- 1NASA Ames Research Center, Moffett Field, California, USA
| | - H A Weaver
- 5Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - V J Bray
- 9Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
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21
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Kaur S, Sharma P, Wetmore SD. Can Cyanuric Acid and 2,4,6-Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations. Chemphyschem 2019; 20:1425-1436. [PMID: 30997731 DOI: 10.1002/cphc.201900237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/09/2019] [Indexed: 01/05/2023]
Abstract
As a step toward assessing their fitness as pre-RNA nucleobases, we employ DFT and MD simulations to analyze the noncovalent interactions of cyanuric acid (CA) and 2,4,6-triaminopyrimidine (TAP), and the structural properties of the associated ribonucleosides (rNs) and oligonucleotides. Our calculations reveal that the TAP : CA pair has a comparable hydrogen-bond strength to the canonical A : U pair. This strengthens the candidature of CA and TAP as prebiotic nucleobases. Further, the stacking between two canonical nucleobases is stronger than those between TAP or CA and a canonical base, as well as those between two TAP and/or CA, which indicates that enhanced stacking may have served as a driving force for the evolution from prebiotic to canonical nucleobases. Similarities in the DFT-derived anti/syn rotational barriers and MD-derived (anti) glycosidic conformation of the CA and TAP rNs and canonical rNs further substantiate their candidature as pre-RNA components. Greater deglycosylation barriers (as obtained by DFT calculations) for TAP rNs compared to canonical rNs suggest TAP rNs indicate higher resistance to environmental factors, while lower barriers indicate that CA rNs were likely more suitable for less-challenging locations. Finally, the tight packing in narrow CA:TAP-containing helices suggests that the prebiotic polymers were shielded from water, which would aid their evolution into self-replicating systems. Our calculations thus support proposals that CA and TAP can act as nucleobases of pre-RNA.
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Alberta, T1K 3M4, Canada
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22
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Karunakaran SC, Cafferty BJ, Weigert‐Muñoz A, Schuster GB, Hud NV. Spontaneous Symmetry Breaking in the Formation of Supramolecular Polymers: Implications for the Origin of Biological Homochirality. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Suneesh C. Karunakaran
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Brian J. Cafferty
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Angela Weigert‐Muñoz
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
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23
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Karunakaran SC, Cafferty BJ, Weigert‐Muñoz A, Schuster GB, Hud NV. Spontaneous Symmetry Breaking in the Formation of Supramolecular Polymers: Implications for the Origin of Biological Homochirality. Angew Chem Int Ed Engl 2019; 58:1453-1457. [DOI: 10.1002/anie.201812808] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Suneesh C. Karunakaran
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Brian J. Cafferty
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Angela Weigert‐Muñoz
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology USA
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24
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Kaur S, Sharma P. Radical pathways for the formation of non-canonical nucleobases in prebiotic environments. RSC Adv 2019; 9:36530-36538. [PMID: 35539032 PMCID: PMC9075218 DOI: 10.1039/c9ra08001e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 11/21/2022] Open
Abstract
Due to the inability of canonical nucleobases (adenine, uracil, guanine and cytosine) to spontaneously form ribonucleosides and base pairs in free form in solution, RNA is believed to be preceded by a primitive information polymer (preRNA). The preRNA is proposed to contain non-canonical, heterocyclic bases that possess the above-mentioned capabilities. An extensive search for such candidate heterocycles has recently revealed that barbituric acid (BA), melamine (MM) and 2,4,6-triaminopyrimidine (TAP) have the capability to spontaneously form ribonucleosides and supramolecular assemblies that are held by Watson–Crick type hydrogen-bonded base pairs involving BA, MM, TAP and cyanuric acid (CA) heterocycles. However, despite this evidence, the prebiotic formation pathways of these heterocycles have not been fully explored. Further, for these heterocycles to interact and assemble into informational polymers under prebiotic conditions, it is expected that they should have formed in the proximity of each other. In this context, the present work employs density functional theory to propose the associated radical based formation pathways starting from cyanamide. Our pathways suggest that cyanamide, its derivatives (malonic acid and urea) and malononitrile can form BA, MM, CA and TAP in the presence of ammonia and hydroxyl radicals. In addition to originating from a common precursor, similarities in the highest reaction barriers (13 to 20 kcal mol−1) obtained for these pathways suggest that these heterocycles may likely form under similar conditions. Specifically, these pathways are relevant to high energy events such as meteoritic impact during the late heavy bombardment period on the early earth, which would have created conditions where radicals might have formed in reasonable concentrations. Overall, the present study emphasizes the importance of cyanamide in prebiotic heterocycle formation. The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.![]()
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
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25
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Gate G, Szabla R, Haggmark MR, Šponer J, Sobolewski AL, de Vries MS. Photodynamics of alternative DNA base isoguanine. Phys Chem Chem Phys 2019; 21:13474-13485. [DOI: 10.1039/c9cp01622h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Michael R. Haggmark
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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26
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Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity. Proc Natl Acad Sci U S A 2018; 115:E7658-E7664. [PMID: 29967169 PMCID: PMC6099888 DOI: 10.1073/pnas.1721369115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The columnar liquid crystal phases reported here are physical associations of the smallest molecular species to self-assemble into the duplex base-paired stacked columnar double-helical structures of nucleic acids. These assemblies of monomers can provide starting states capable of partitioning appropriate molecules from solution with a high degree of selectivity, acting as pathways for the prebiotic appearance of molecular selection, self-assembly, and, ultimately, of the sequence-directed assembly of polymers. We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson–Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.
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27
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Mungi CV, Singh SK, Chugh J, Rajamani S. Synthesis of barbituric acid containing nucleotides and their implications for the origin of primitive informational polymers. Phys Chem Chem Phys 2018; 18:20144-52. [PMID: 27153469 DOI: 10.1039/c6cp00686h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Given that all processes in modern biology are encoded and orchestrated by polymers, the origin of informational molecules had to be a crucial and significant step in the origin of life on Earth. An important molecule in this context is RNA that is thought to have allowed the transition from chemistry to biology. However, the RNA molecule is comprised of intramolecular bonds which are prone to hydrolysis, especially so under the harsh conditions of the early Earth. Furthermore, the formation of nucleotides with extant bases and their subsequent polymerization have both been problematic, to say the least. Alternate heterocycles, in contrast, have resulted in nucleosides in higher yields, suggesting a viable and prebiotically relevant solution to the longstanding "nucleoside problem". In the present study, we have synthesized a nucleotide using ribose 5'-monophosphate (rMP) and barbituric acid (BA), as the base analog, using dry-heating conditions that are thought to be prevalent in several regimes of the early Earth. Polymerization of the resultant monomers, i.e. BA-nucleotides, was also observed when dehydration-rehydration cycles were carried out at low pH and high temperature. The resulting RNA-like oligomers have intact bases unlike in reactions that were carried out with canonical nucleotides, which resulted in abasic sites under acidic conditions due to cleavage of the N-glycosidic linkages. Furthermore, the incorporation of BA directly into preformed sugar-phosphate backbones was also observed when rMP oligomers were subjected to heating with BA. The results from our aforementioned experiments provide preliminary evidence that BA could have been a putative precursor of modern nucleobases, which could have been incorporated into primitive informational polymers that predated the molecules of an RNA world. Moreover, they also highlight that the prebiotic soup, which would have been replete with alternate heterocycles, could have allowed the sampling of other such heterocycles, which would have had a selective advantage under pertinent selection pressures. Importantly, these kinds of processes have implications for shaping the prebiotic landscape that allowed for the emergence of primitive informational polymers of the pre-RNA world(s), prior to the emergence of a putative RNA world.
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Affiliation(s)
- Chaitanya V Mungi
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Sachin Kumar Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Jeetender Chugh
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India. and Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India.
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28
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Szabla R, Góra RW, Šponer J. Ultrafast excited-state dynamics of isocytosine. Phys Chem Chem Phys 2018; 18:20208-18. [PMID: 27346684 DOI: 10.1039/c6cp01391k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alternative nucleobase isocytosine has long been considered as a plausible component of hypothetical primordial informational polymers. To examine this hypothesis we investigated the excited-state dynamics of the two most abundant forms of isocytosine in the gas phase (keto and enol). Our surface-hopping nonadiabatic molecular dynamics simulations employing the algebraic diagrammatic construction to the second order [ADC(2)] method for the electronic structure calculations suggest that both tautomers undergo efficient radiationless deactivation to the electronic ground state with time constants which amount to τketo = 182 fs and τenol = 533 fs. The dominant photorelaxation pathways correspond to ring-puckering (ππ* surface) and C[double bond, length as m-dash]O stretching/N-H tilting (nπ* surface) for the enol and keto forms respectively. Based on these findings, we infer that isocytosine is a relatively photostable compound in the gas phase and in these terms resembles biologically relevant nucleobases. The estimated S1 [radiolysis arrow - arrow with voltage kink] T1 intersystem crossing rate constant of 8.02 × 10(10) s(-1) suggests that triplet states might also play an important role in the overall excited-state dynamics of the keto tautomer. The reliability of ADC(2)-based surface-hopping molecular dynamics simulations was tested against multireference quantum-chemical calculations and the potential limitations of the employed ADC(2) approach are briefly discussed.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. and CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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29
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Li C, Cafferty BJ, Karunakaran SC, Schuster GB, Hud NV. Formation of supramolecular assemblies and liquid crystals by purine nucleobases and cyanuric acid in water: implications for the possible origins of RNA. Phys Chem Chem Phys 2018; 18:20091-6. [PMID: 27253677 DOI: 10.1039/c6cp03047e] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The free nucleobases and mononucleotides of RNA do not form Watson-Crick base pairs in water, a fact that presents several challenges for the prebiotic synthesis of RNA. 2,6-Diaminopurine and adenosine-5'-monophosphate (AMP) are shown to form supramolecular assemblies with cyanuric acid in water. These assemblies and their propensity to form liquid crystals suggest a possible means by which non-covalent structures might have originally selected the shape of the Watson-Crick base pairs.
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Affiliation(s)
- C Li
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA. and State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - B J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - S C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - G B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - N V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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30
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Xiao Y, Zhang J, Lang M. Melamine driven supramolecular self-assembly of nucleobase derivatives in water. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.28954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yan Xiao
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Jiaxiao Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Meidong Lang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering; East China University of Science and Technology; Shanghai 200237 China
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31
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Karunakaran SC, Cafferty BJ, Peláez-Fernández M, Neselu K, Schmidt-Krey I, Fernandez-Nieves A, Schuster GB, Hud NV. Exquisite regulation of supramolecular equilibrium polymers in water: chain stoppers control length, polydispersity and viscoelasticity. Polym Chem 2018. [DOI: 10.1039/c8py01146j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Positively charged molecules with planar surfaces control the length of supramolecular polymers formed by 2,4,6-triaminopyrimidine and a modified cyanuric acid.
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Affiliation(s)
| | - Brian J. Cafferty
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | | | - Kasahun Neselu
- School of Biological Sciences
- Georgia Institute of Technology
- Atlanta
- USA
| | | | | | - Gary B. Schuster
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Nicholas V. Hud
- Department of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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32
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Fialho DM, Clarke KC, Moore MK, Schuster GB, Krishnamurthy R, Hud NV. Glycosylation of a model proto-RNA nucleobase with non-ribose sugars: implications for the prebiotic synthesis of nucleosides. Org Biomol Chem 2018; 16:1263-1271. [DOI: 10.1039/c7ob03017g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of the earliest nucleosides is an important, but unresolved, element of the origins of life that may have been facilitated by heterocycle reactivity and self-assembly.
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Affiliation(s)
- David M. Fialho
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA 30033
- NSF-NASA Center for Chemical Evolution
| | - Kimberly C. Clarke
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA 30033
- NSF-NASA Center for Chemical Evolution
| | - Megan K. Moore
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA 30033
- NSF-NASA Center for Chemical Evolution
| | - Gary B. Schuster
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA 30033
- NSF-NASA Center for Chemical Evolution
| | | | - Nicholas V. Hud
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA 30033
- NSF-NASA Center for Chemical Evolution
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33
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Abstract
The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.
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Affiliation(s)
- Samuel Boldissar
- Department of Chemistry and Biochemistry University of California Santa Barbara
- USA
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34
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Tupper AS, Shi K, Higgs PG. The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture. Life (Basel) 2017; 7:life7040041. [PMID: 29088116 PMCID: PMC5745554 DOI: 10.3390/life7040041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 01/11/2023] Open
Abstract
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3'-5' bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture. We show that template-directed replication can lead to the emergence of all the uniform properties of RNA by the same mechanism. We study a computational model in which nucleotides react via polymerization, hydrolysis, and template-directed ligation. Uniform strands act as templates for ligation of shorter oligomers of the same type, whereas mixed strands do not act as templates. The three uniform properties emerge naturally when the ligation rate is high. If there is an exact symmetry, as with the chase of chirality, the uniform property arises via a symmetry-breaking phase transition. If there is no exact symmetry, as with monomer selection and backbone regioselectivity, the uniform property emerges gradually as the rate of template-directed ligation is increased.
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Affiliation(s)
- Andrew S Tupper
- Origins Institute and Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON L8S 4L8, Canada.
| | - Kevin Shi
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Paul G Higgs
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada.
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35
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Berenbeim JA, Boldissar S, Siouri FM, Gate G, Haggmark MR, Aboulache B, Cohen T, de Vries MS. Excited-State Dynamics of Isocytosine: A Hybrid Case of Canonical Nucleobase Photodynamics. J Phys Chem Lett 2017; 8:5184-5189. [PMID: 28985073 DOI: 10.1021/acs.jpclett.7b02032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present resonant two-photon ionization (R2PI) spectra of isocytosine (isoC) and pump-probe results on two of its tautomers. IsoC is one of a handful of alternative bases that have been proposed in scenarios of prebiotic chemistry. It is structurally similar to both cytosine (C) and guanine (G). We compare the excited-state dynamics with the Watson-Crick (WC) C and G tautomeric forms. These results suggest that the excited-state dynamics of WC form of G may primarily depend on the heterocyclic substructure of the pyrimidine moiety, which is chemically identical to isoC. For WC isoC we find a single excited-state decay with a rate of ∼1010 s-1, while the enol form has multiple decay rates, the fastest of which is 7 times slower than for WC isoC. The excited-state dynamics of isoC exhibits striking similarities with that of G, more so than with the photodynamics of C.
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Affiliation(s)
- Jacob A Berenbeim
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Faady M Siouri
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Gregory Gate
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Michael R Haggmark
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Briana Aboulache
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Trevor Cohen
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
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36
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Kim EK, Martin V, Krishnamurthy R. Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA. Chemistry 2017; 23:12668-12675. [PMID: 28708927 DOI: 10.1002/chem.201702912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 02/05/2023]
Abstract
The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors.
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Affiliation(s)
- Eun-Kyong Kim
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Vincent Martin
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
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37
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Materese CK, Nuevo M, Sandford SA. The Formation of Nucleobases from the Ultraviolet Photoirradiation of Purine in Simple Astrophysical Ice Analogues. ASTROBIOLOGY 2017; 17:761-770. [PMID: 28723229 PMCID: PMC5808537 DOI: 10.1089/ast.2016.1613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nucleobases are the informational subunits of RNA and DNA and are essential to all known forms of life. The nucleobases can be divided into two groups of molecules: the pyrimidine-based compounds that include uracil, cytosine, and thymine, and the purine-based compounds that include adenine and guanine. Previous work in our laboratory has demonstrated that uracil, cytosine, thymine, and other nonbiological, less common nucleobases can form abiotically from the UV photoirradiation of pyrimidine in simple astrophysical ice analogues containing combinations of H2O, NH3, and CH4. In this work, we focused on the UV photoirradiation of purine mixed with combinations of H2O and NH3 ices to determine whether or not the full complement of biological nucleobases can be formed abiotically under astrophysical conditions. Room-temperature analyses of the resulting photoproducts resulted in the detection of adenine, guanine, and numerous other functionalized purine derivatives. Key Words: Pyrimidine-Nucleobases-Interstellar; Ices-Cometary; Ices-Molecular processes-Prebiotic chemistry. Astrobiology 17, 761-770.
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Affiliation(s)
- Christopher K. Materese
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
- Bay Area Environmental Research Institute, 625 2 St., Suite 209, Petaluma, CA 94952, USA
| | - Michel Nuevo
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
- Bay Area Environmental Research Institute, 625 2 St., Suite 209, Petaluma, CA 94952, USA
| | - Scott A. Sandford
- NASA Ames Research Center, Space Science and Astrobiology Division, MS 245-6, Moffett Field, CA 94035, USA
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38
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Kaur S, Sharma P, Wetmore SD. Structural and electronic properties of barbituric acid and melamine-containing ribonucleosides as plausible components of prebiotic RNA: implications for prebiotic self-assembly. Phys Chem Chem Phys 2017; 19:30762-30771. [DOI: 10.1039/c7cp06123d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT calculations are employed to assess the fitness of barbituric acid and melamine to act as components of prebiotic RNA.
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Affiliation(s)
- Sarabjeet Kaur
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry
- University of Lethbridge
- Canada
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39
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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40
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Albrecht L, Wilson KA, Wetmore SD. Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4. Molecules 2016; 21:molecules21070822. [PMID: 27347908 PMCID: PMC6273265 DOI: 10.3390/molecules21070822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 11/25/2022] Open
Abstract
Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1’–C1’ base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases.
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Affiliation(s)
- Laura Albrecht
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
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41
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Spontaneous formation and base pairing of plausible prebiotic nucleotides in water. Nat Commun 2016; 7:11328. [PMID: 27108699 PMCID: PMC4848480 DOI: 10.1038/ncomms11328] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 03/16/2016] [Indexed: 12/03/2022] Open
Abstract
The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. One of the questions for prebiotic chemistry is the formation of complementary base pairing systems. Here, the authors show that plausible two prebiotic heterocycles can form glycosidic bonds with ribose in water and that these spontaneously base-pair in aqueous solution.
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42
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Brister MM, Pollum M, Crespo-Hernández CE. Photochemical etiology of promising ancestors of the RNA nucleobases. Phys Chem Chem Phys 2016; 18:20097-103. [DOI: 10.1039/c6cp00639f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Barbituric acid and 2,4,6-triaminopyrimidine dissipate ultraviolet radiation efficiently as heat to the environment, thus supporting their feasibility as prebiotic ancestors to the RNA nucleobases.
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Affiliation(s)
- M. M. Brister
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
| | - M. Pollum
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
| | - C. E. Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- Cleveland
- USA
| |
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