Ziwei
Liu
a,
Angelica
Mariani
a,
Longfei
Wu
a,
Dougal
Ritson
a,
Andrea
Folli
b,
Damien
Murphy
b and
John
Sutherland
*a
aMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, UK. E-mail: johns@mrc-lmb.cam.ac.uk
bSchool of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
First published on 25th July 2018
During the transition from prebiotic chemistry to biology, a period of solution-phase, non-enzymatic activation of (oligo)nucleotides must have occurred, and accordingly, a mechanism for phosphate activation must have existed. Herein, we detail results of an investigation into prebiotic phosphate activation chemistry using simple, prebiotically available nitriles whose reactivity is increased by Cu2+ ions. Furthermore, although Cu2+ ions are known to catalyse the hydrolysis of phosphodiester bonds, we found this deleterious activity to be almost completely suppressed by inclusion of amino acids or dipeptides, which may suggest a productive relationship between protein and RNA from the outset.
The early phase of high energy chemistry which must have taken place on primitive Earth, would be expected to generate a significant amount of small, multiple bond-rich molecules.10 If the potential energy locked in these multiple bonds could be harnessed, plentiful sources of prebiotic activating agents could have been available. This was recognized many years ago and was partly why molecules such as cyanate (NCO−), cyanogen ((CN)2) and cyanamide (NH2CN) were investigated as prebiotic activating agents.1 It is noteworthy that a large number of (proto)biomolecules are accessible in prebiotically plausible syntheses using, or producing, these same, small, high energy molecules.10,11 These chemical networks are consistent with a geochemical scenario.10b,11c,12 Given that these molecules are omnipresent in our protometabolic network, we were curious if their re-evaluation, in the context of our developing geochemical model, could provide a means to overcome inherent kinetic barriers and ‘switch on’ their reactivity by nitrile coordination. Thus, our attention turned to Fe2+, Fe3+, Ni2+, Cu2+, Co2+ and Zn2+ ions. Intriguingly, work from the Dronskowski group had shown that a variety of transition metal cations form complexes with cyanamide 1. Being azophilic Cu2+ is expected to associate strongly with cyanamide 1,13 but this is in contrast to oxophilic metal ions such as Mg2+. We began to examine the effect of these ions on reaction of adenosine 3′-phosphate (2, A3′P) with 1.
Next, we investigated whether Cu2+ could catalyse phosphate activation using other prebiotically relevant nitrile-containing molecules (Table 1).11 Acetonitrile 4, 3-aminopropionitrile 5 and glycolonitrile 6 were unsuccessful in promoting Cu(II)-catalysed cyclization of A3′P 2. Cyanate 7 and cyanogen 8 displayed a dual behaviour, producing 3 together with the 2′-adduct which will be discussed later (9, Scheme 1). Intriguingly, cyanogen 8 reacts with A3′P 2 even in the absence of a metal catalyst; however, the relative formation of the cyclised product and the 2′-transfer product is greatly affected by including Cu2+ in the mixture. And the reaction of A3′P with other nitriles in the absence of Cu2+ is insignificant.
Entry | Nitrile | R | Yield of 3 or 2′-transfer adductsa (%) | |||||
---|---|---|---|---|---|---|---|---|
CuCl2 | CuCl2 and Gly | CuCl2 and GlyGly | ||||||
3 | 2′-adduct | 3 | 2′-adduct | 3 | 2′-adduct | |||
a Standard reaction conditions: nitrile (100 mM), 2 (50 mM), CuCl2 (25 mM) and Gly or GlyGly (50 mM) in 90% H2O, 10% D2O at pH 4 (entries 1, 5 and 8) or pH 5.5 (entries 2, 3, 4, 6 and 7), heated at 40 °C for 20 hours. b Inferred from the amount of 3 plus adenosine 2′-phosphate A2′P 12, assuming that when 3 hydrolyses it always gives 2 and 12 in 1.8:1 ratios.17 c Not detected. d Initial pH 5.5. e Initial pH 4. | ||||||||
1 | 1 | 84 | n.d.c | 85d | n.d. | 80 | n.d. | |
2 | 4 | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | |
3 | 5 | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | |
4 | 6 | 5 | n.d. | 2 | n.d. | n.d. | n.d. | |
5 | 7 | 24 | 15 | 21 | 8 | 23 | 5.4 | |
6 | 8 | 53 | 6 | 50 | 4 | 97e | 3 | |
7 | 10 | 75 | n.d. | 60 | n.d. | 5 | n.d. | |
8 | 11 | 35 | n.d. | 22 | n.d. | 34 | n.d. |
Scheme 1 Mechanism of cyclisation vs. transfer in the cyanate- or cyanogen-mediated activation of 2 and 1H NMR spectra of the mixtures. (a) 1H NMR spectrum after 20 h following incubation of 2 (50 mM), CuCl2 (25 mM) and cyanate 7 (100 mM) at pH 4, 40 °C, showing the formation of 3 and 9a; (b) 1H NMR spectrum after 1 h following incubation of 2 (12.5 mM), Gly (50 mM) CuCl2 (25 mM) and cyanogen 8 (100 mM) at pH 5.5, RT, showing the formation of 3 and 9b; (c) as (b) but without CuCl2. N.B. conditions are different to Table 1. |
We then turned our attention to aminoacetonitrile 10 and 2-aminopropionitrile 11, the Strecker precursors of glycine and alanine, respectively, previously shown to originate from the same prebiotic pathways that form ribonucleotides, amino acids and phospholipid precursors.11c Interestingly, attack of a nucleoside monophosphate onto an α-aminonitrile would involve the formation of a transient imidoyl phosphate, analogous to the mixed anhydride produced by aminoacylation of nucleotides,14a,15 with the only difference being an imidoyl-13 instead of a carbonyl-14 derivative (Scheme 2). Based on the observation by Moureu and Bongrand16 that cuprous cyanoacetylide undergoes Glaser coupling17 to give dicyanodiacetylene on oxidation, we did not investigate Cu2+-catalysed addition of phosphates to cyanoacetylene as the related Eglinton reaction18 was anticipated.
Scheme 2 Structure of nucleoside 3′-phosphate imidoyl-13 and carbonyl-14 mixed anhydride derivatives. |
Whilst mixed anhydride 14 has been previously been shown to both cyclise and give the 2′-adduct, both α-aminonitriles 10 and 11 triggered cyclisation of 2, but the related 2′-transferred products were not detected. We speculate that the reactivity and/or the geometry of 13 could be altered by the simultaneous coordination of both the imido- and amino-nitrogen atoms to copper, somehow favouring cyclisation and hydrolysis over transfer. In this regard, we performed an experiment in which A5′P, aminoacetonitrile and Cu2+ were incubated in either H216O, H218O or a mixture of H216O/H218O (1:2), and monitored the isotopic composition of the products by mass spectrometry. In the absence of a vicinal hydroxyl group, activation of the 5′-phosphate of A5′P would result in the attack of water either on the activated phosphate or on the imidoyl-carbon of the imidoyl phosphate, producing 18O-labelled A5′P or 18O-labelled glycinamide, respectively (Scheme S1, S2 and Fig. S1†). In our system, glycinamide was the only new labelled product detected (the ratio of unlabelled/18O-labelled glycinamide was equal to the H216O/H218O ratio), thereby suggesting the selective attack of water on the imidoyl-carbon, and possibly a link with the aminoacyl-transfer chemistry described by Schimmel and co-workers on a minihelix.19
Optimization for cyclisation of A3′P 2 to 3 by modifying reaction conditions revealed that moderate to high yields could be obtained under slightly acidic conditions, but, alongside the expected cyclized product, we could detect the formation of adenosine 2′-phosphate (A2′P, 12, Tables 1 and S2†).
Reasoning that the latter derived from hydrolysis of the former as the reaction progressed, we started examining the hydrolysis of 3 under these reaction conditions. As expected, Cu2+ catalysed the opening of the cyclic phosphate both at pH 4 and 5.5, producing 2 and 12 in 1.8:1 ratios.20 We thus wondered if ligands able to coordinate Cu2+ would attenuate the metal's hydrolytic activity. In particular, we focused our attention on prebiotically plausible chelating agents able to form bi- and tri-dentate complexes with copper ions,21 namely glycinamide, as the by-product of the aminoacetonitrile-mediated activation described above, its hydrolysis product glycine (Gly) and the dipeptide glycylglycine (GlyGly). The excellent coordinating properties of these ligands (Table S3†) considerably decreased the degree of cyclic phosphate hydrolysis, probably by competing with 3 for binding to the metal centre. In parallel, we examined urea and ammonium carbonate, the by-products of the cyanamide and cyanate-mediated activation, respectively, but, unsurprisingly, these failed to protect the cyclic phosphate from hydrolysis, presumably as a consequence of less favourable monodentate binding to copper.
Cu2+, as Mg2+, and other divalent metal ions, is also well known for its ability to catalyse RNA degradation,22 which proceeds through attack on the phosphodiester bond by the vicinal 2′-OH group, with formation of shorter 2′,3′-cyclic phosphate-terminated oligonucleotides (or a mixture of 2′- and 3′-monophosphates if the hydrolysis progresses further23). As a model for RNA degradation, we followed the hydrolysis of a 6-carboxyfluorescein (FAM)-labelled 10-mer RNA oligonucleotide incubated with CuCl2, in the presence or in the absence, of different amounts of Gly or GlyGly (60 °C, reactions monitored after 23 and 48 h). Whilst at pH 4, Cu2+ didn't affect the integrity of RNA (compared to buffer levels), at pH 5.2 and 7.0 (whereupon extensive precipitation of Cu(OH)2 occurred) the metal efficiently promoted RNA hydrolysis, with more than 96% and 57% degradation, respectively, after only 23 h. Remarkably, RNA was efficiently protected from Cu2+-catalysed degradation by addition of a small excess of Gly or GlyGly, despite the higher solubility of the metal under these conditions (Table S4 and Fig. S2–S6†). This is reminiscent of the demonstration that citrate protects RNA from Mg2+-catalysed degradation.24
We next tested the effect of these additives on the phosphate activation reaction, incubating 2, cyanamide 1 and Cu2+ with either Gly or GlyGly. Both ligands suppressed the Cu2+-catalysed hydrolysis of the cyclic product, with the net effect of boosting the yield of 3 (Tables S5 and S6†). In the presence of Gly the activation of 2 to give 3 was highly efficient both at pH 4 and 5.5 (85% or 78%, respectively), however, with GlyGly the yields were reduced when the reaction was performed at pH 5.5 (37%). Likewise, the yields were negatively affected when the ligands were in high excess relative to copper. EPR spectroscopy of the Cu2+–GlyGly complex helped to elucidate the reasons for these outcomes. The coordination mode of GlyGly to Cu2+ is highly dependent on the pH of the solution, with the possibility of forming multiple species at equilibrium (over the pH range 4–7), including highly stable metal chelates.21 In agreement with previous literature,25 the EPR spectra of Cu2+–GlyGly mixtures at pH 4 mainly resembled the spectra of the aqua complex Cu(H2O)62+, with smaller contributions from other species, presumably the two GlyGly bidentate complexes (Scheme S3, Fig S7 and Table S7†). Increasing the pH of the solution from 4 to 5.5 led to the almost complete disappearance of Cu(H2O)62+ signal, and the spectra were dominated by the tridentate complex of Cu2+ and GlyGly (Fig. S7 and S8†). From these data, it is clear that as the pH of the mixture increases, the tridentate complex is formed at the expense of the cyanamide-induced activation of 2. Thus, at high ligands concentrations, coordination of Gly and GlyGly to Cu2+ could saturate the metal ion coordination sphere, preventing cyclic phosphate and RNA hydrolysis. However, the competitive binding of 1 to Cu2+ in the presence of these ligands is still possible. The available data do not allow a detailed picture of the mechanism, although we suspect that there are several catalytically active complexes. Further investigation was not made as our interests were with the conversion per se. With the possibility of small alterations in the reaction conditions perturbing yields and product distribution, we explored the cyanamide 1-Cu2+-mediated nucleotide activation over a range of temperatures (Fig. S9†), pHs and concentrations, obtaining the maximum yields of 84% and 90% of 3 (other nucleotides shown in Table S8†) when the reaction was performed with 1 (100 mM), 2 (12.5 mM) and CuCl2 (25 mM) in the presence of Gly (pH 5.5, 50 mM, 40 °C) or GlyGly (pH 4, 12.5 mM, 40 °C), respectively. It was found that multiple equivalents of cyanamide are required for optimum yield, we assume that water competes with phosphate in the attack on metal coordinated cyanamide with the result that multiple equivalents of urea are formed as a by-product.
Footnote |
† Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc02513d |
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