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A Continuous Reaction Network That Produces RNA Precursors

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A Continuous Reaction Network That Produces RNA Precursors A continuous reaction network that produces RNA precursors Ruiqin Yia, Quoc Phuong Tranb, Sarfaraz Alib, Isao Yodac, Zachary R. Adamd,e, H. James Cleaves IIa,e,f, and Albert C. Fahrenbachb,1 aEarth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan; bSchool of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; cCo-60 Radiation Facility, Tokyo Institute of Technology, Tokyo 152-8550, Japan; dDepartment of Planetary Sciences, University of Arizona, Tucson, AZ 85721; eBlue Marble Space Institute of Science, Seattle, WA 98154; and fProgram in Interdisciplinary Studies, Institute for Advanced Study, Princeton, NJ 08540 Edited by Chad A. Mirkin, Northwestern University, Evanston, IL, and approved April 17, 2020 (received for review December 19, 2019) Continuous reaction networks, which do not rely on purification or target molecules must occur in the presence of whatever side timely additions of reagents, serve as models for chemical evolution products also formed as a consequence of the initial conditions. and have been demonstrated for compounds thought to have The basic feedstocks of prebiotic chemistry are thought to be small played important roles for the origins of life such as amino acids, molecules of a limited type, i.e., C1 compounds (22). Thus, the hydroxy acids, and sugars. Step-by-step chemical protocols for ri- reaction network ought to begin with a set of small molecules that bonucleotide synthesis are known, but demonstrating their syn- are likely to have been provided by the environment. The aim of thesis in the context of continuous reaction networks remains a this study is not an attempt to prove a specific geological scenario, major challenge. Herein, compounds proposed to be important for but to assess whether continuous reaction networks are capable of prebiotic RNA synthesis, including glycolaldehyde, cyanamide, producing RNA precursors, and ultimately RNA itself. 2-aminooxazole, and 2-aminoimidazole, are generated from a con- Herein, a continuous reaction network that generates RNA tinuous reaction network, starting from an aqueous mixture of precursors according to the constraints described above is dem- NaCl, NH4Cl, phosphate, and HCN as the only carbon source. No onstrated. This reaction network begins with hydrogen cyanide well-timed addition of any other reagents is required. The reaction (HCN) as the only organic feedstock, along with sodium chloride network is driven by a combination of γ radiolysis and dry-down. γ (NaCl), ammonium chloride (NH4Cl), and inorganic phosphate Radiolysis results in a complex mixture of organics, including the CHEMISTRY (P ). HCN is a common chemical product of an array of high- glycolaldehyde-derived glyceronitrile and cyanamide. This mixture i energy atmospheric processes, for example, UV radiation-driven is then dried down, generating free glycolaldehyde that then reacts photochemistry, fixation by lightning, atmospheric impingement with cyanamide/NH3 to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models of energetic particles, and impact-induced aerodynamic ablation how precursors for generating RNA and other classes of compounds (23, 24). This mixture is then made to react by exposure to ionizing γ may arise spontaneously from a complex mixture that originates gamma ( ) radiation. After dry-down of the resulting mixture, from simple reagents. compounds known to be important for abiotic RNA synthesis, in particular, cyanamide, glycolaldehyde, 2-aminooxazole, and systems chemistry | radiolysis | prebiotic chemistry | RNA world | 2-aminoimidazole are produced. wet–dry cycles 2-Aminooxazole and 2-Aminoimidazole Synthesis in the Context of the RNA World Hypothesis he complex and far-from-equilibrium nature of biochemical One of the most well-studied abiotic syntheses of the pyrimidine reaction networks may have originated from simpler non- T ribonucleotides, employing simple reagents and conditions, was living ones (1, 2), which nevertheless may have contained a large number of interacting organic compounds. A variety of reaction networks capable of generating complex mixtures of molecules Significance hypothesized to be relevant to life’s origins have been demon- strated, particularly for amino acids (3, 4), hydroxy acids (5), and RNA may have been the original polymer to arise spontaneously sugars (6–8). The RNA world hypothesis (9) has led to the in- on the early Earth through natural geochemistry. Although di- ’ vestigation of possible prebiotic synthetic pathways for RNA, in rect physical evidence regarding early Earth s geochemistry is particular the ribonucleoside monophosphates (10–16). Critiques extremely limited, complex chemical reaction networks are (6, 17–20) of these pathways, however, have focused on the fact thought to have played an important role in chemical evolution. that many of the experimental procedures employ step-by-step The present study demonstrates an experimental model reaction chemical protocols or well-timed addition steps, which are sug- network that generates a number of compounds that can lead to RNA synthesis in a single mixture starting from simple organic gested to be implausible in environmental settings. These types of and inorganic feedstocks. Models of this type will help explain procedures have previously been referred to as “discontinuous which conditions are needed to produce RNA in primitive synthesis” models (19), with experimental interventions conducted planetary settings. to minimize the production of complex mixtures in favor of spe- cific targets. Although investigations of stepwise syntheses are Author contributions: R.Y., Z.R.A., H.J.C., and A.C.F. designed research; R.Y., Q.P.T., S.A., crucial for reaction pathway discovery, it is still unclear whether I.Y., and A.C.F. performed research; R.Y., Q.P.T., S.A., and A.C.F. analyzed data; and R.Y., such chemical protocols can be realized in the context of hypo- Z.R.A., H.J.C., and A.C.F. wrote the paper. thetical continuous reaction networks from which early life may The authors declare no competing interest. have emerged. This article is a PNAS Direct Submission. Here, a “continuous reaction network” is defined as one which Published under the PNAS license. is minimally manipulated (21), to most accurately simulate a 1To whom correspondence may be addressed. Email: [email protected]. natural environment, e.g., in which intermediates are not purified, This article contains supporting information online at https://www.pnas.org/lookup/suppl/ side products are not removed, and new reagents other than the doi:10.1073/pnas.1922139117/-/DCSupplemental. initial starting materials are not added. Therefore, the synthesis of First published June 2, 2020. www.pnas.org/cgi/doi/10.1073/pnas.1922139117 PNAS | June 16, 2020 | vol. 117 | no. 24 | 13267–13274 Downloaded by guest on September 28, 2021 e‒ + e‒ + pioneered by Orgel and coworkers (10) and extensively elabo- 2 aq / 2H 2 aq / 2H H O HCN H O HCN rated by Sutherland and coworkers (11, 25). Instead of direct HCN 2 2 condensation of ribose with a pyrimidine, both the D-ribose and NH NH nucleobase components are built up concurrently. This synthesis, 3 1 3 2 sometimes referred to as the Powner–Sutherland pathway, makes use of simple hydroxyaldehydes, namely, glycolaldehyde Scheme 2. The Kiliani–Fischer synthesis of glycolaldehyde, which equili- brates to glyceronitrile given excess HCN. This version of the synthesis makes and D-glyceraldehyde (Scheme 1). The first step is the reaction of ‒ use of solvated electrons (e aq) as the reducing agent. glycolaldehyde with cyanamide in the presence of Pi, which acts as a general-base catalyst, yielding 2-aminooxazole. This compound ′ ′ can serve as an intermediate for both cytidine and uridine 2 ,3 - more details, see ref. 35 and SI Appendix, Schemes). High con- cyclic phosphates. Szostak and coworkers (26) later demonstrated centrations of NaCl favor cyanamide through a pathway that may that when NH4Cl is added to the mixture of glycolaldehyde and involve cyanogen chloride as an intermediate, a compound which cyanamide, 2-aminoimidazole is produced (see refs. 11 and 26 was also observed (Scheme 3). Cyanogen chloride itself is pro- ‒ for discussion of the proposed mechanisms), a structurally posed to form by reaction of CN with radiolytically produced similarcompoundthatservesasaneffectiveleavinggroupin HOCl, although another pathway could involve a Cl-containing the context of nonenzymatic template-directed RNA synthesis radical intermediate. This radiolytic reaction network has the po- (27). 2-Aminooxazole selectively reacts with glyceraldehyde, tential to produce 2-aminooxazole and 2-aminoimidazole starting potentially allowing 2-aminoimidazole to accumulate for later from simple initial conditions in a continuous manner, if glyceroni- use. Although flow chemistry has been employed to synthesize trile can be employed as a source of glycolaldehyde in the synthesis. 2-aminooxazole without purification (28), orderly mixing of re- agents was still required. A reaction network that generates both Results 2-aminooxazole and 2-aminoimidazole from a common carbon Dry-Down Enables 2-Aminooxazole Synthesis. The first step in the source and in a continuous fashion has yet to be demonstrated (29). synthesis of 2-aminooxazole is nucleophilic addition of cyana- mide to the carbonyl of glycolaldehyde (Scheme 4, Top). Excess Radiolysis as a Driving Force cyanide almost completely inhibits the reaction
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