1
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Agmon I. Three Biopolymers and Origin of Life Scenarios. Life (Basel) 2024; 14:277. [PMID: 38398786 PMCID: PMC10890401 DOI: 10.3390/life14020277] [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: 12/28/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to emerge autonomously, sustain, and evolve continuously towards life as we know it. The analysis incorporates current biological knowledge gained from high-resolution structural data and large sequence datasets, together with experimental results concerned with RNA replication and with the activity demonstrated by standalone constructs of the ribosomal Peptidyl Transferase Center region. The scrutiny excludes the DNA-protein combination and assigns negligible likelihood to the existence of an RNA-DNA world, as well as to an RNA world that contained a replicase made of RNA. It points to the precedence of an RNA-protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. This molecular set constitutes a feasible starting point for a continuous evolutionary path, proceeding via natural processes from the inanimate matter towards life as we know it.
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Affiliation(s)
- Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
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2
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Wei D, Wang Y, Song D, Zhang Z, Wang J, Chen JY, Li Z, Yu H. A Nucleic Acid Sequence That is Catalytically Active in Both RNA and TNA Backbones. ACS Synth Biol 2022; 11:3874-3885. [PMID: 36278399 DOI: 10.1021/acssynbio.2c00479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Threose nucleic acid (TNA) is considered a potential RNA progenitor due to its chemical simplicity, base pairing property, and capability of folding into a functional tertiary structure. However, it is unknown whether the functional property can be maintained during transition from TNA to RNA. Here, we use a toggle in vitro selection to identify nucleic acid catalyst sequences that are active in both TNA and RNA backbones. One such nucleic acid enzyme with exchangeable backbone (CAMELEON) catalyzes an RNA cleavage reaction when prepared as TNA (T) and RNA (R). Further biochemical characterization reveals that CAMELEON R and T exhibit different catalytic behaviors such as rate enhancement and magnesium dependence. Structural probing and mutagenesis experiments suggest that they likely fold into distinct tertiary structures. This work demonstrates that the catalytic activity can be preserved during backbone transition from TNA to RNA and provides further experimental support for TNA as an RNA precursor in evolution.
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Affiliation(s)
- Dongying Wei
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Yueyao Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu210023, China
| | - Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Juan Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu210023, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
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3
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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4
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Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication. Genes (Basel) 2021; 12:genes12122023. [PMID: 34946975 PMCID: PMC8701183 DOI: 10.3390/genes12122023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Nirenberg's genetic code chart shows a profound correspondence between codons and amino acids. The aim of this article is to try to explain the primordial formation of the codon degeneracy. It remains a puzzle how informative molecules arose from the supposed prebiotic random sequences. If introducing an initial driving force based on the relative stabilities of triplex base pairs, the prebiotic sequence evolution became innately nonrandom. Thus, the primordial assignment of the 64 codons to the 20 amino acids has been explained in detail according to base substitutions during the coevolution of tRNAs with aaRSs; meanwhile, the classification of aaRSs has also been explained.
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5
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Xu J, Green NJ, Russell DA, Liu Z, Sutherland JD. Prebiotic Photochemical Coproduction of Purine Ribo- and Deoxyribonucleosides. J Am Chem Soc 2021; 143:14482-14486. [PMID: 34469129 PMCID: PMC8607323 DOI: 10.1021/jacs.1c07403] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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The
hypothesis that life on Earth may have started with a heterogeneous
nucleic acid genetic system including both RNA and DNA has attracted
broad interest. The recent finding that two RNA subunits (cytidine,
C, and uridine, U) and two DNA subunits (deoxyadenosine, dA, and deoxyinosine,
dI) can be coproduced in the same reaction network, compatible with
a consistent geological scenario, supports this theory. However, a
prebiotically plausible synthesis of the missing units (purine ribonucleosides
and pyrimidine deoxyribonucleosides) in a unified reaction network
remains elusive. Herein, we disclose a strictly stereoselective and
furanosyl-selective synthesis of purine ribonucleosides (adenosine,
A, and inosine, I) and purine deoxynucleosides (dA and dI), alongside
one another, via a key photochemical reaction of thioanhydroadenosine
with sulfite in alkaline solution (pH 8–10). Mechanistic studies
suggest an unexpected recombination of sulfite and nucleoside alkyl
radicals underpins the formation of the ribo C2′–O bond.
The coproduction of A, I, dA, and dI from a common intermediate, and
under conditions likely to have prevailed in at least some primordial
locales, is suggestive of the potential coexistence of RNA and DNA
building blocks at the dawn of life.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Nicholas J Green
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - David A Russell
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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6
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Rüdisser SH, Goldberg N, Ebert MO, Kovacs H, Gossert AD. Efficient affinity ranking of fluorinated ligands by 19F NMR: CSAR and FastCSAR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:579-594. [PMID: 32556806 DOI: 10.1007/s10858-020-00325-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Fluorine NMR has recently gained high popularity in drug discovery as it allows efficient and sensitive screening of large numbers of ligands. However, the positive hits found in screening must subsequently be ranked according to their affinity in order to prioritize them for follow-up chemistry. Unfortunately, the primary read-out from the screening experiments, namely the increased relaxation rate upon binding, is not proportional to the affinity of the ligand, as it is polluted by effects such as exchange broadening. Here we present the method CSAR (Chemical Shift-anisotropy-based Affinity Ranking) for reliable ranking of fluorinated ligands by NMR, without the need of isotope labeled protein, titrations or setting up a reporter format. Our strategy is to produce relaxation data that is directly proportional to the binding affinity. This is achieved by removing all other contributions to relaxation as follows: (i) exchange effects are efficiently suppressed by using high power spin lock pulses, (ii) dipolar relaxation effects are approximately subtracted by measuring at two different magnetic fields and (iii) differences in chemical shift anisotropy are normalized using calculated values. A similar ranking can be obtained with the simplified approach FastCSAR that relies on a measurement of a single relaxation experiment at high field (preferably > 600 MHz). An affinity ranking obtained in this simple way will enable prioritizing ligands and thus improve the efficiency of fragment-based drug design.
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Affiliation(s)
- Simon H Rüdisser
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Nils Goldberg
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie, ETH Zürich, 8093, Zürich, Switzerland
| | | | - Alvar D Gossert
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland.
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland.
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7
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Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides. Nature 2020; 582:60-66. [PMID: 32494078 DOI: 10.1038/s41586-020-2330-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 11/08/2022]
Abstract
The nature of the first genetic polymer is the subject of major debate1. Although the 'RNA world' theory suggests that RNA was the first replicable information carrier of the prebiotic era-that is, prior to the dawn of life2,3-other evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA4. Such a theory streamlines the eventual 'genetic takeover' of homogeneous DNA from RNA as the principal information-storage molecule, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario. Here we demonstrate a high-yielding, completely stereo-, regio- and furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides: deoxyadenosine and deoxyinosine. Our synthesis uses key intermediates in the prebiotic synthesis of the canonical pyrimidine ribonucleosides (cytidine and uridine), and we show that, once generated, the pyrimidines persist throughout the synthesis of the purine deoxyribonucleosides, leading to a mixture of deoxyadenosine, deoxyinosine, cytidine and uridine. These results support the notion that purine deoxyribonucleosides and pyrimidine ribonucleosides may have coexisted before the emergence of life5.
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8
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Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides. J Am Chem Soc 2020; 142:2317-2326. [PMID: 31913615 PMCID: PMC7577264 DOI: 10.1021/jacs.9b11239] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The abiotic synthesis of ribonucleotides
is thought to have been
an essential step toward the emergence of the RNA world. However,
it is likely that the prebiotic synthesis of ribonucleotides was accompanied
by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides,
and other variations on the canonical nucleotides. In order to understand
how relatively homogeneous RNA could have emerged from such complex
mixtures, we have examined the properties of arabinonucleotides and
2′-deoxyribonucleotides in nonenzymatic template-directed primer
extension reactions. We show that nonenzymatic primer extension with
activated arabinonucleotides is much less efficient than with activated
ribonucleotides, and furthermore that once an arabinonucleotide is
incorporated, continued primer extension is strongly inhibited. As
previously shown, 2′-deoxyribonucleotides are also less efficiently
incorporated in primer extension reactions, but the difference is
more modest. Experiments with mixtures of nucleotides suggest that
the coexistence of ribo- and arabinonucleotides does not impede the
copying of RNA templates. Moreover, chimeric oligoribonucleotides
containing 2′-deoxy- or arabinonucleotides are effective templates
for RNA synthesis. We propose that the initial genetic polymers were
random sequence chimeric oligonucleotides formed by untemplated polymerization,
but that template copying chemistry favored RNA synthesis; multiple
rounds of replication may have led to pools of oligomers composed
mainly of RNA.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Wen Zhang
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Valeria Rondo-Brovetto
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
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9
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Abstract
Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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10
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Bhowmik S, Krishnamurthy R. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nat Chem 2019; 11:1009-1018. [PMID: 31527850 PMCID: PMC6815252 DOI: 10.1038/s41557-019-0322-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/31/2019] [Indexed: 01/01/2023]
Abstract
Hypotheses of the origins of RNA and DNA are generally centred on the prebiotic synthesis of a pristine system (pre-RNA or RNA), which gives rise to its descendent. However, a lack of specificity in the synthesis of genetic polymers would probably result in chimeric sequences; the roles and fate of such sequences are unknown. Here, we show that chimeras, exemplified by mixed threose nucleic acid (TNA)-RNA and RNA-DNA oligonucleotides, preferentially bind to, and act as templates for, homogeneous TNA, RNA and DNA ligands. The chimeric templates can act as a catalyst that mediates the ligation of oligomers to give homogeneous backbone sequences, and the regeneration of the chimeric templates potentiates a scenario for a possible cross-catalytic cycle with amplification. This process provides a proof-of-principle demonstration of a heterogeneity-to-homogeneity scenario and also gives credence to the idea that DNA could appear concurrently with RNA, instead of being its later descendent.
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Affiliation(s)
- Subhendu Bhowmik
- The Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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11
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Banwell EF, Piette BMAG, Taormina A, Heddle JG. Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator. Mol Biol Evol 2019; 35:404-416. [PMID: 29126321 PMCID: PMC5850689 DOI: 10.1093/molbev/msx292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Even the simplest organisms are too complex to have spontaneously arisen fully formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of evolution: the Initial Darwinian Ancestor. Here, we suggest that nucleopeptide reciprocal replicators could have carried out this important role and contend that this is the simplest way to explain extant replication systems in a mathematically consistent way. We propose short nucleic acid templates on which amino-acylated adapters assembled. Spatial localization drives peptide ligation from activated precursors to generate phosphodiester-bond-catalytic peptides. Comprising autocatalytic protein and nucleic acid sequences, this dynamical system links and unifies several previous hypotheses and provides a plausible model for the emergence of DNA and the operational code.
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Affiliation(s)
- Eleanor F Banwell
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - Anne Taormina
- Department for Mathematical Sciences, Durham University, Durham, United Kingdom
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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12
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Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
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Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
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13
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Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA. Proc Natl Acad Sci U S A 2018; 115:13318-13323. [PMID: 30509978 PMCID: PMC6310819 DOI: 10.1073/pnas.1814367115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA world hypothesis assumes the abiotic synthesis of nucleotides, as well as their participation in nonenzymatic RNA replication. Whereas prebiotic syntheses of the canonical purine nucleotides remain inefficient, a prebiotically plausible route to the 8-oxo-purines has been reported. Although these noncanonical purine nucleotides are known to engage in non-Watson–Crick pairing with their canonical purine counterparts, their behavior in nonenzymatic RNA copying has not been evaluated. Our study indicates that none of the 8-oxo-purines behaves as a suitable substrate for nonenzymatic RNA copying. However, inosine turns out to exhibit reasonable rates and fidelities in RNA copying reactions. We propose that inosine could have served as a surrogate for guanosine in the early emergence of life. The emergence of primordial RNA-based life would have required the abiotic synthesis of nucleotides, and their participation in nonenzymatic RNA replication. Although considerable progress has been made toward potentially prebiotic syntheses of the pyrimidine nucleotides (C and U) and their 2-thio variants, efficient routes to the canonical purine nucleotides (A and G) remain elusive. Reported syntheses are low yielding and generate a large number of undesired side products. Recently, a potentially prebiotic pathway to 8-oxo-adenosine and 8-oxo-inosine has been demonstrated, raising the question of the suitability of the 8-oxo-purines as substrates for prebiotic RNA replication. Here we show that the 8-oxo-purine nucleotides are poor substrates for nonenzymatic RNA primer extension, both as activated monomers and when present in the template strand; their presence at the end of a primer also strongly reduces the rate and fidelity of primer extension. To provide a proper comparison with 8-oxo-inosine, we also examined primer extension reactions with inosine, and found that inosine exhibits surprisingly rapid and accurate nonenzymatic RNA copying. We propose that inosine, which can be derived from adenosine by deamination, could have acted as a surrogate for G in the earliest stages of the emergence of life.
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14
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Leamy KA, Yennawar NH, Bevilacqua PC. Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms. Biochemistry 2018; 57:2994-3002. [PMID: 29733204 PMCID: PMC6726375 DOI: 10.1021/acs.biochem.8b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A diverse set of organisms has adapted to live under extreme conditions. The molecular origin of the stability is unclear, however. It is not known whether the adaptation of functional RNAs, which have intricate tertiary structures, arises from strengthening of tertiary or secondary structure. Herein we evaluate effects of sequence changes on the thermostability of tRNAphe using experimental and computational approaches. To separate out effects of secondary and tertiary structure on thermostability, we modify base pairing strength in the acceptor stem, which does not participate in tertiary structure. In dilute solution conditions, strengthening secondary structure leads to non-two-state thermal denaturation curves and has small effects on thermostability, or the temperature at which tertiary structure and function are lost. In contrast, under cellular conditions with crowding and Mg2+-chelated amino acids, where two-state cooperative unfolding is maintained, strengthening secondary structure enhances thermostability. Investigation of stabilities of each tRNA stem across 44 organisms with a range of optimal growing temperatures revealed that organisms that grow in warmer environments have more stable stems. We also used Shannon entropies to identify positions of higher and lower information content, or sequence conservation, in tRNAphe and found that secondary structures have modest information content allowing them to drive thermal adaptation, while tertiary structures have maximal information content hindering them from participating in thermal adaptation. Base-paired regions with no tertiary structure and modest information content thus offer a facile evolutionary route to enhancing the thermostability of functional RNA by the simple molecular rules of base pairing.
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Affiliation(s)
- Kathleen A Leamy
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Neela H Yennawar
- Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Philip C Bevilacqua
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biochemistry and Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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15
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Kumar VA. Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis. Org Biomol Chem 2018; 14:10123-10133. [PMID: 27714238 DOI: 10.1039/c6ob01796g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.
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Affiliation(s)
- Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, 411008, India.
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16
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Ma W. What Does "the RNA World" Mean to "the Origin of Life"? Life (Basel) 2017; 7:life7040049. [PMID: 29186049 PMCID: PMC5745562 DOI: 10.3390/life7040049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/30/2017] [Accepted: 11/24/2017] [Indexed: 12/30/2022] Open
Abstract
Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the “unitary-protocell”, which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level—no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before protocells emerged. The selection pressure that was favoring the exploration of more and more fundamental raw materials resulted in an evolutionary tendency of life to become more and more self-sustained. New functions for the entities to adapt to environments, including those that are involved in the self-sustainment per se, would bring new burdens to the self-sustainment—the advantage of these functions must overweigh the corresponding disadvantage.
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Affiliation(s)
- Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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17
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Giurgiu C, Li L, O’Flaherty DK, Tam CP, Szostak JW. A Mechanistic Explanation for the Regioselectivity of Nonenzymatic RNA Primer Extension. J Am Chem Soc 2017; 139:16741-16747. [PMID: 29112424 PMCID: PMC6326530 DOI: 10.1021/jacs.7b08784] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 11/28/2022]
Abstract
A working model of nonenzymatic RNA primer extension could illuminate how prebiotic chemistry transitioned to biology. All currently known experimental reconstructions of nonenzymatic RNA primer extension yield a mixture of 2'-5' and 3'-5' internucleotide linkages. Although long seen as a major problem, the causes of the poor regioselectivity of the reaction are unknown. We used a combination of different leaving groups, nucleobases, and templating sequences to uncover the factors that yield selective formation of 3'-5' internucleotide linkages. We found that fast and high yielding reactions selectively form 3'-5' linkages. Additionally, in all cases with high 3'-5' regioselectivity, Watson-Crick base pairing between the RNA monomers and the template is observed at the extension site and at the adjacent downstream position. Mismatched base-pairs and other factors that would perturb the geometry of the imidazolium bridged intermediate lower both the rate and regioselectivity of the reaction.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Li Li
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department
of Molecular Biology, and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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18
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Emergence of native peptide sequences in prebiotic replication networks. Nat Commun 2017; 8:434. [PMID: 28874657 PMCID: PMC5585222 DOI: 10.1038/s41467-017-00463-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.The synthesis of biopolymers in living cells is perfected by complex machinery, however this was not the case on early Earth. Here the authors show the role of non-enzymatic replication in the enrichment of certain products within prebiotically relevant mixtures.
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19
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Shen F, Luo Z, Liu H, Wang R, Zhang S, Gan J, Sheng J. Structural insights into RNA duplexes with multiple 2΄-5΄-linkages. Nucleic Acids Res 2017; 45:3537-3546. [PMID: 28034958 PMCID: PMC5389462 DOI: 10.1093/nar/gkw1307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/20/2016] [Indexed: 01/15/2023] Open
Abstract
2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.
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Affiliation(s)
- Fusheng Shen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Zhipu Luo
- Synchrotron Radiation Research Section, MCL National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Shenglong Zhang
- Department of Life Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.,The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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20
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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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21
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Lupas AN, Alva V. Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins. J Struct Biol 2017; 198:74-81. [DOI: 10.1016/j.jsb.2017.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 11/16/2022]
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22
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Krishnamurthy R. Giving Rise to Life: Transition from Prebiotic Chemistry to Protobiology. Acc Chem Res 2017; 50:455-459. [PMID: 28945387 DOI: 10.1021/acs.accounts.6b00470] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The challenge of a chemical approach to the origins of life problem involves comprehending the transition from prebiotic chemistry to protobiology. This endeavor demands demonstrating the metamorphosis of a diverse pool of prebiotic building blocks (heterogeneous heterogeneity) into a conglomerate self-assembling system (homogeneous heterogeneity) capable of evolution.
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Affiliation(s)
- Ramanarayanan Krishnamurthy
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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23
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Gavette JV, Stoop M, Hud NV, Krishnamurthy R. RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse V. Gavette
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Matthias Stoop
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
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24
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Gavette JV, Stoop M, Hud NV, Krishnamurthy R. RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World. Angew Chem Int Ed Engl 2016; 55:13204-13209. [DOI: 10.1002/anie.201607919] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse V. Gavette
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Matthias Stoop
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta GA 30332 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution; Atlanta GA 30332 USA
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25
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Abstract
Understanding how life arose is a fundamental problem of biology. Much progress has been made by adopting a synthetic and mechanistic perspective on originating life. We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated informational and functional roles. There is cause for optimism on this difficult problem: the prebiotic chemical inventory may not have been as nightmarishly complex as previously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of self-replicating RNA; encapsulation in protocells provides evolutionary and biophysical advantages. Nevertheless, major issues remain unsolved, such as the origin of a genetic code. Attention to this field is particularly timely given the accelerating discovery and characterization of exoplanets.
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26
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Introduction to Virus Origins and Their Role in Biological Evolution. VIRUS AS POPULATIONS 2016. [PMCID: PMC7204881 DOI: 10.1016/b978-0-12-800837-9.00001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viruses are extremely abundant and diverse parasites of cells. They might have arisen during an early phase of the evolution of life on Earth dominated by RNA or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate: viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via lateral transfers of genes. These two models bear on considering viruses predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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27
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Ma W, Yu C, Zhang W, Wu S, Feng Y. The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover. BMC Evol Biol 2015; 15:272. [PMID: 26643199 PMCID: PMC4672488 DOI: 10.1186/s12862-015-0548-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is now popularly accepted that there was an "RNA world" in early evolution of life. This idea has a direct consequence that later on there should have been a takeover of genetic material - RNA by DNA. However, since genetic material carries genetic information, the "source code" of all living activities, it is actually reasonable to question the plausibility of such a "revolutionary" transition. Due to our inability to model relevant "primitive living systems" in reality, it is as yet impossible to explore the plausibility and mechanisms of the "genetic takeover" by experiments. RESULTS Here we investigated this issue by computer simulation using a Monte-Carlo method. It shows that an RNA-by-DNA genetic takeover may be triggered by the emergence of a nucleotide reductase ribozyme with a moderate activity in a pure RNA system. The transition is unstable and limited in scale (i.e., cannot spread in the population), but can get strengthened and globalized if certain parameters are changed against RNA (i.e., in favor of DNA). In relation to the subsequent evolution, an advanced system with a larger genome, which uses DNA as genetic material and RNA as functional material, is modeled - the system cannot sustain if the nucleotide reductase ribozyme is "turned off" (thus, DNA cannot be synthesized). Moreover, the advanced system cannot sustain if only DNA's stability, template suitability or replication fidelity (any of the three) is turned down to the level of RNA's. CONCLUSIONS Genetic takeover should be plausible. In the RNA world, such a takeover may have been triggered by the emergence of some ribozyme favoring the formation of deoxynucleotides. The transition may initially have been "weak", but could have been reinforced by environmental changes unfavorable to RNA (such as temperature or pH rise), and would have ultimately become irreversible accompanying the genome's enlargement. Several virtues of DNA (versus RNA) - higher stability against hydrolysis, greater suitability as template and higher fidelity in replication, should have, each in its own way, all been significant for the genetic takeover in evolution. This study enhances our understandings of the relationship between information and material in the living world.
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Affiliation(s)
- Wentao Ma
- College of Life Sciences, Wuhan University, Wuhan, 430072, P.R.China.
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, 430072, P.R.China
| | - Wentao Zhang
- College of Computer Sciences, Wuhan University, Wuhan, 430072, P.R.China
| | - Sanmao Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, P.R.China
| | - Yu Feng
- College of Life Sciences, Wuhan University, Wuhan, 430072, P.R.China
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28
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Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet 2015; 16:567-82. [PMID: 26347030 DOI: 10.1038/nrg3937] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.
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29
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Zhuang Z, Pan R, Zhang Q, Huang H. Molecular recognition of pyrimidine nucleobases by triplex DNA receptors. Bioorg Med Chem Lett 2015; 25:1520-4. [DOI: 10.1016/j.bmcl.2015.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 11/29/2022]
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30
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Xu L, Wang W, Zhang L, Chong J, Huang X, Wang D. Impact of template backbone heterogeneity on RNA polymerase II transcription. Nucleic Acids Res 2015; 43:2232-41. [PMID: 25662224 PMCID: PMC4344504 DOI: 10.1093/nar/gkv059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 02/03/2023] Open
Abstract
Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3'-5' or 2'-5' orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary 'imperfect' DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA.
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Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Wei Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Lu Zhang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jenny Chong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, CA 92093-0625, USA
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32
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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33
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Bernhardt HS, Sandwick RK. Purine biosynthetic intermediate-containing ribose-phosphate polymers as evolutionary precursors to RNA. J Mol Evol 2014; 79:91-104. [PMID: 25179142 DOI: 10.1007/s00239-014-9640-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
Abstract
The RNA world hypothesis proposes that RNA once functioned as the principal genetic material and biological catalyst. However, RNA is a complex molecule made up of phosphate, ribose, and nucleobase moieties, and its evolution is unclear. Yakhnin has proposed a period of prebiotic chemical evolution prior to the advent of replication and Darwinian evolution, in which macromolecules containing polyols joined by phosphodiester linkages underwent spontaneous transesterification reactions with selection for stability. Although he proposes that the nucleobases were obtained during this stage from less stable macromolecules, the ultimate source of the nucleobases is not addressed. We propose that the purine nucleobases arose in situ from simpler precursors attached to a ribose-phosphate backbone, and that the weaker and less specific intra- and interstrand interactions between these precursors were the forerunners to the base pairing and base stacking interactions of the modern RNA nucleobases. Further, in line with Granick's hypothesis of biosynthetic pathways recapitulating evolution, we propose that these simpler precursors were the same or similar to intermediates of the modern de novo purine biosynthetic pathway. We propose that successive nucleobase precursors formed progressively stronger interactions that stabilized the ribose-phosphate polymer, and that the increased stability of the parent polymer drove the selection and further chemical evolution of the purine nucleobases. Such interactions may have included hydrogen bonding between ribose hydroxyls, hydrogen bonding between carbonyl oxygens and protonated amine side groups, the intra- and interstrand coordination of metal cations, and the stacking of imidazole rings. Five of the eleven steps of the modern de novo purine biosynthetic pathway have previously been shown to have alternative nonenzymatic syntheses, while a sixth step has also been proposed to occur nonenzymatically, supporting a prebiotic origin for the pathway.
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Affiliation(s)
- Harold S Bernhardt
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand,
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35
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Ritson DJ, Sutherland JD. Conversion of biosynthetic precursors of RNA to those of DNA by photoredox chemistry. J Mol Evol 2014; 78:245-50. [PMID: 24736972 PMCID: PMC4037592 DOI: 10.1007/s00239-014-9617-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/20/2014] [Indexed: 11/29/2022]
Abstract
Soon after the origin of RNA-based life, depletion of prebiotically synthesised ribonucleotides would have driven the evolution of a biosynthetic pathway to these key building blocks. Ribozyme-catalysed nucleosidation-the key biosynthetic step-requires that ribose and the nucleobases are produced by abiotic chemistry and are relatively stable to the conditions of their synthesis. The most plausible prebiotic synthesis of sugars involves photoreduction of cyanohydrins by hydrogen sulphide in the presence of copper(I) cyanide, and we therefore subjected ribose to these conditions whereupon it was partially converted to 2-deoxyribose. Furthermore, a derivative of uracil is reduced under similar conditions to thymine. Thus, DNA biosynthetic precursors can be formed abiotically from those of RNA allowing for an early evolutionary transition to life based on RNA and DNA.
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Affiliation(s)
- Dougal J Ritson
- MRC-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK,
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Arnaut V, Langecker M, Simmel FC. Nanopore force spectroscopy of aptamer-ligand complexes. Biophys J 2014; 105:1199-207. [PMID: 24010663 DOI: 10.1016/j.bpj.2013.07.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 01/07/2023] Open
Abstract
The stability of aptamer-ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans-cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer-target interactions in this case, the stability of the ligand-free aptamer-containing G-quadruplexes-is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified.
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Affiliation(s)
- Vera Arnaut
- Lehrstuhl für Bioelektronik, Physik Department, Technische Universität München, Garching, Germany
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Li L, Szostak JW. The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids. J Am Chem Soc 2014; 136:2858-65. [PMID: 24499340 PMCID: PMC3982932 DOI: 10.1021/ja412079b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Indexed: 02/07/2023]
Abstract
The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.
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Affiliation(s)
- Li Li
- Howard Hughes
Medical Institute, Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard Hughes
Medical Institute, Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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Structural insights into the effects of 2'-5' linkages on the RNA duplex. Proc Natl Acad Sci U S A 2014; 111:3050-5. [PMID: 24516151 DOI: 10.1073/pnas.1317799111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2'-5' linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.
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Abstract
For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Informatics in the Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA.
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Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity. Nat Chem 2013; 5:390-4. [PMID: 23609089 PMCID: PMC4088963 DOI: 10.1038/nchem.1623] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/12/2013] [Indexed: 11/08/2022]
Abstract
A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand that contains a mixture of 2'-5' and 3'-5' linkages, rather than the selective synthesis of only 3'-5' linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer.
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Bowler FR, Chan CKW, Duffy CD, Gerland B, Islam S, Powner MW, Sutherland JD, Xu J. Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation. Nat Chem 2013; 5:383-9. [PMID: 23609088 DOI: 10.1038/nchem.1626] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/14/2013] [Indexed: 11/09/2022]
Abstract
The recent synthesis of pyrimidine ribonucleoside-2',3'-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3',5'-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2'-hydroxyl group of oligoribonucleotide-3'-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation. The 2'-O-acetyl group at the ligation junction of the product RNA strand can be removed under conditions that leave the internucleotide bonds intact. Remarkably, acetylation of mixed oligomers that possess either 2'- or 3'-terminal phosphates is selective for the 2'-hydroxyl group of the latter. This newly discovered chemistry thus suggests a prebiotic route from ribonucleoside-2',3'-cyclic phosphates to predominantly 3',5'-linked RNA via partially 2'-O-acetylated RNA.
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Affiliation(s)
- Frank R Bowler
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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Attwater J, Tagami S, Kimoto M, Butler K, Kool ET, Wengel J, Herdewijn P, Hirao I, Holliger P. Chemical fidelity of an RNA polymerase ribozyme. Chem Sci 2013. [DOI: 10.1039/c3sc50574j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Engelhart AE, Powner MW, Szostak JW. 7 Imperfect RNA synthesis via model prebiotic reactions and consequences for functional RNAs. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Takeuchi N, Hogeweg P. Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life. Phys Life Rev 2012; 9:219-63. [PMID: 22727399 PMCID: PMC3466355 DOI: 10.1016/j.plrev.2012.06.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 06/04/2012] [Indexed: 11/29/2022]
Abstract
We review computational studies on prebiotic evolution, focusing on informatic processes in RNA-like replicator systems. In particular, we consider the following processes: the maintenance of information by replicators with and without interactions, the acquisition of information by replicators having a complex genotype-phenotype map, the generation of information by replicators having a complex genotype-phenotype-interaction map, and the storage of information by replicators serving as dedicated templates. Focusing on these informatic aspects, we review studies on quasi-species, error threshold, RNA-folding genotype-phenotype map, hypercycle, multilevel selection (including spatial self-organization, classical group selection, and compartmentalization), and the origin of DNA-like replicators. In conclusion, we pose a future question for theoretical studies on the origin of life.
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Affiliation(s)
- Nobuto Takeuchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
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Powner MW, Zheng SL, Szostak JW. Multicomponent assembly of proposed DNA precursors in water. J Am Chem Soc 2012; 134:13889-95. [PMID: 22839703 PMCID: PMC3424849 DOI: 10.1021/ja306176n] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a novel pathway for the prebiotic synthesis of 2'-deoxynucleotides. Consideration of the constitutional chemical relationships between glycolaldehyde and β-mercapto-acetaldehyde, and the corresponding proteinogenic amino acids, serine and cysteine, led us to explore the consequences of the corresponding sulfur substitution for our previously proposed pathways leading to the canonical ribonucleotides. We demonstrate that just as 2-aminooxazole-an important prebiotic ribonucleotide precursor-is readily formed from glycolaldehyde and cyanamide, so is 2-aminothiazole formed from β-mercapto-acetaldehyde and cyanamide in water at neutral pH. Indeed, both the oxazole and the thiazole can be formed together in a one-pot reaction, and can be co-purified by crystallization or sublimation. We then show that 2-aminothiazole can take part in a 3-component carbon-carbon bond-forming reaction in water that leads to the diastereoselective synthesis of masked 2'-thiosugars regiospecifically tethered to purine precursors, which would lead to 2'-deoxynucleotides upon desulfurization. The possibility of an abiotic route to the 2'-deoxynucleotides provides a new perspective on the evolutionary origins of DNA. We also show that 2-aminothiazole is able to sequester, through reversible aminal formation, the important nucleotide precursors glycolaldehyde and glyceraldehyde in a stable, crystalline form.
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Affiliation(s)
- Matthew W Powner
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ, UK.
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