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Abiotic Synthesis of Purine and Pyrimidine Ribonucleosides in Aqueous Microdroplets

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Abiotic Synthesis of Purine and Pyrimidine Ribonucleosides in Aqueous Microdroplets Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets Inho Nama,b, Hong Gil Nama,c,1, and Richard N. Zareb,1 aCenter for Plant Aging Research, Institute for Basic Science, Daegu 42988, Republic of Korea; bDepartment of Chemistry, Stanford University, Stanford, CA 94305; and cDepartment of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea Contributed by Richard N. Zare, November 27, 2017 (sent for review October 24, 2017; reviewed by Bengt J. F. Nordén and Veronica Vaida) Aqueous microdroplets (<1.3 μm in diameter on average) containing In a recent study, we showed a synthetic pathway for the 15 mM D-ribose, 15 mM phosphoric acid, and 5 mM of a nucleobase formation of Rib-1-P using aqueous, high–surface-area micro- (uracil, adenine, cytosine, or hypoxanthine) are electrosprayed from a droplets. This surface or near-surface reaction circumvents the capillary at +5 kV into a mass spectrometer at room temperature and fundamental thermodynamic problem of the condensation re- 2+ 1 atm pressure with 3 mM divalent magnesium ion (Mg )asacat- action (12). It has been suggested that the air–water interface alyst. Mass spectra show the formation of ribonucleosides that com- provides a favorable environment for the prebiotic synthesis of prise a four-letter alphabet of RNA with a yield of 2.5% of uridine (U), biomolecules (12–17). Using the Rib-1-P made in the above 2.5% of adenosine (A), 0.7% of cytidine (C), and 1.7% of inosine (I) during the flight time of ∼50 μs. In the case of uridine, no catalyst is abiotic manner and the salvage pathway shown in Fig. 1, we required. An aqueous solution containing guanine cannot be gener- successfully generated uridine (U) (12), one of the pyrimidine ated under the same conditions given the extreme insolubility of ribonucleosides, in aqueous microdroplets. However, we did not guanine in water. However, inosine can base pair with cytidine and investigate whether this process represents a general abiotic thus substitute for guanosine. Thus, a full set of ribonucleosides pathway for the generation of both purine and pyrimidine ribo- to generate the purine–pyrimidine base pairs A-U and I-C are nucleosides. Here, we show the abiotic generation of the ribo- spontaneously generated in aqueous microdroplets under similar nucleosides adenosine (A), cytidine (C), and inosine (I) by mild conditions. surmounting the thermodynamic barrier for these reactions at or CHEMISTRY near the surface of room-temperature water microdroplets. microdroplet chemistry | origin of life | prebiotic chemistry | purine Guanine is practically insoluble in water, which precludes the ribonucleosides | pyrimidine ribonucleosides generation of aqueous microdroplets containing guanine (18). Nevertheless, inosine (I) can base pair with cytidine (C), and thus ne hypothesis concerning the origin of life postulates an the full base pairs of ribonucleosides can be synthesized and ORNA world that existed on Earth before modern cells arose survive under the same prebiotic conditions. In the micro- + (1). According to this hypothesis, RNA stored genetic in- droplets, a small concentration of divalent magnesium ion (Mg2 ), formation and catalyzed chemical reactions in primitive cells (2, EVOLUTION one of the main elements of Earth’s crust (19), serves to catalyze 3). However, a major missing link has been how to construct the process. Because mists, clouds, and sprays are thought to be from simpler molecules the ribonucleosides, which are the building blocks of RNA (1–3). This challenge seems quite common on early Earth, these findings provide a possible missing daunting because the making of ribonucleosides in a water so- link as to how the RNA world came about. lution from ribose and some suitable nucleobase, such as the purines adenine and guanine, and the pyrimidines uracil and Significance cytosine, is thermodynamically uphill (4, 5). Recently, possible routes for the prebiotic synthesis of purine and pyrimidine ri- Discovery of an improved prebiotic method for the synthesis of bonucleosides were studied by bypassing the biological synthesis ribonucleosides provides support to theories that posit a cen- mechanism (5–8). These routes demand different environments, tral role for RNA in the origin of life. It has been assumed that although it might be more favorable if purine and pyrimidine ribonucleosides arose through an abiotic process in which ri- ribonucleosides could be condensed in the same environment for bose and nucleobases became conjoined, but the direct con- the fabrication of RNA. Moreover, these mechanisms require densation of nucleobases with ribose to give ribonucleosides in complex, sequential reactions with reaction times in the range of bulk solution is thermodynamically uphill. We show a general days, which may make them less relevant for creating a prebiotic synthetic path for ribonucleosides, both purine and pyrimidine chemistry in which RNA could develop. As described below, we bases, using an abiotic salvage pathway in a microdroplet en- + present an alternative route for the synthesis of ribonucleosides vironment with divalent magnesium ion (Mg2 ) as a catalyst. that seems to be sufficiently mild and general that it might have Purine and pyrimidine ribonucleosides are formed simulta- played a role in turning simpler molecules into biomolecules. neously under the same conditions, which suggests a possible In cells, the synthesis of ribonucleosides takes two paths: nu- scenario for the spontaneous production of random ribonu- cleotide metabolism and the salvage pathway (9–11). In nucle- cleosides necessary to generate various types of primitive RNA. otide metabolism, 5-phosphoribosyl-1-pyrophosphate (PRPP) Author contributions: I.N., H.G.N., and R.N.Z. designed research; I.N. performed research; formed from D-ribose-5-phosphate (Rib-5-P) and nucleobases I.N., H.G.N., and R.N.Z. analyzed data; H.G.N. and R.N.Z. directed and supervised the are changed into a ribonucleotide and two phosphates (9). As project; and I.N., H.G.N., and R.N.Z. wrote the paper. part of the salvage pathway, Rib-1-P and a nucleobase are Reviewers: B.J.F.N., Chalmers University of Technology; and V.V., University of Colorado. transformed into a ribonucleoside and a phosphate (9–11), as The authors declare no conflict of interest. illustrated in Fig. 1. The salvage pathway in vivo is a reaction in This open access article is distributed under Creative Commons Attribution-NonCommercial- which ribonucleosides are synthesized from organic intermedi- NoDerivatives License 4.0 (CC BY-NC-ND). ates. Specifically, Rib-1-P is added to a free nucleobase by a 1To whom correspondence may be addressed. Email: [email protected] or zare@stanford. phosphorylase enzyme to form a ribonucleoside. The most im- edu. portant part of both reactions is that a carbon atom at the first This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. position (C1) in ribose links to the nucleobase. 1073/pnas.1718559115/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1718559115 PNAS Early Edition | 1of5 Downloaded by guest on September 25, 2021 120 psi using an electrospray ionization (ESI) source placed in front of a high-resolution mass spectrometer, as shown in Fig. S1 (20). The microdroplets traveled 5 mm at room temperature and atmospheric pressure before the reaction was stopped upon entering the heated inlet of a mass spectrometer (21). Under these conditions, a corresponding reaction time was estimated to be ∼50 μs on the basis of the droplet speed (∼100 m/s) (22, 23). The droplets were positively charged by external application of a po- tential of +5 kV to the ESI source. When a high electric field is applied to droplets, the electric charge makes an electrical force inside the droplets, which generates a droplet explosion into very fine microdroplets (Coulomb explosion) (24). Therefore, the ex- ternal charge mainly affects the size of droplets, and the size of droplets controls the yield of ribonucleosides in aqueous micro- droplets. Here, the sizes of droplets were observed to be, on average, <1.3 μmindiameter(Fig. S2), as determined optically (25). Without application of the external potential, the average diameter of droplets is 12.5 μm, which means the volume of droplets is at least three orders of magnitude larger than that with the external voltage. The significantly smaller surface-to-volume ratio is one of the main reasons that production of ribonucleo- sides was reduced in uncharged microdroplets (Fig. S2). We also Fig. 1. Reaction mechanism for the prebiotic synthesis of ribonucleosides by checked the mass spectra of the products in microdroplets by using + an abiotic salvage pathway using Rib-1-P as the intermediate. the above experimental scheme without Mg2 . We found peaks for the mass of precursors D-ribose, phosphoric acid, and a nucleobase, m z = m/z = Results such as / 136.061 for protonated adenine, 112.050 for protonated cytosine, m/z = 137.046 for protonated hypoxanthine, Generation of Aqueous Microdroplets Containing Precursors. We and m/z = 231.026 for Rib-1-P, as shown in Fig. S3. However, the performed reactions to generate ribonucleosides by the abiotic ribonucleosides adenosine, cytidine, and inosine were not detected salvage pathway in aqueous microdroplets (Fig. 1). The micro- in microdroplets under these conditions. droplets contained 15 mM D-ribose; 15 mM phosphoric acid; and 5 mM adenine, cytosine, or hypoxanthine, which were all in Thermodynamic Considerations Concerning Ribonucleoside Generation deionized water. Studies were carried out in the presence of the in Aqueous Microdroplets. To determine the reaction barrier, we + divalent magnesium ion (3 mM Mg2 ). Microdroplets were present the free energy diagrams for the abiotic salvage pathways generated from bulk solution with a nebulizing gas (dry N2)at of adenosine, cytidine, inosine, and uridine showing the changes of A B C D Fig.
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