Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells

Abstract

Primordial cells presumably combined RNAs, which functioned as catalysts and carriers of genetic information, with an encapsulating membrane of aggregated amphiphilic molecules. Major questions regarding this hypothesis include how the four bases and the sugar in RNA were selected from a mixture of prebiotic compounds and colocalized with such membranes, and how the membranes were stabilized against flocculation in salt water. To address these questions, we explored the possibility that aggregates of decanoic acid, a prebiotic amphiphile, interact with the bases and sugar found in RNA. We found that these bases, as well as some but not all related bases, bind to decanoic acid aggregates. Moreover, both the bases and ribose inhibit flocculation of decanoic acid by salt. The extent of inhibition by the bases correlates with the extent of their binding, and ribose inhibits to a greater extent than three similar sugars. Finally, the stabilizing effects of a base and ribose are additive. Thus, aggregates of a prebiotic amphiphile bind certain heterocyclic bases and sugars, including those found in RNA, and this binding stabilizes the aggregates against salt. These mutually reinforcing mechanisms might have driven the emergence of protocells. RNA is a polymer of units containing the sugar ribose covalently bound to one of four nucleobases; amphiphiles are molecules that possess both a hydrophobic and a hydrophilic moiety and therefore can aggregate into membranes in water. We know that two of the four units of RNA can be synthesized under simulated prebiotic conditions (2), that simple amphiphiles such as fatty acids spontaneously aggregate into vesicles in an aqueous environment (3), and that such vesicles can encapsulate nucleic acid and its building blocks (4, 5). Fundamental questions remain, however, regarding how the bases and sugar in RNA were selected from a heterogeneous mixture of prebiotic organic compounds, concentrated sufficiently to react, and colocalized with vesicles. It also is unclear how the first membranes were stabilized in seawater, given that fatty acids precipitate at high salt concentrations (6).Previous lines of research suggest possible answers to these questions. Prebiotic chemical processes might have preferentially generated at least two of the four nucleotides (consisting of a base bound to ribose and phosphate) from simple organic precursors (2). These building blocks, if appropriately activated, then might have polymerized on mineral surfaces (7), which also stimulate fatty acid vesicle formation (8). Finally, the incorporation of alcohols and glycerol monoesters in fatty acid membranes might have increased their stability in seawater (4, 9-11).We hypothesize a simpler, more integrated scenario that complements these mechanisms. In this scenario, aggregates of amphiphiles preceded RNA and facilitated its synthesis by binding and concentrating the bases and sugar of which it is composed. The observation that the assembly of amphiphilic aggregates proceeds spontaneously, whereas the syn...

Feeling the hidden mechanical forces in lipid bilayer is an original sense

“…Venter and coworkers' Mycoplasma laboratorium experiment (92) or Michael Crichton's Jurassic Park fiction both require placing remodeled or renewed DNAs into a preexisting cell. To completely create life in vitro, synthetic RNAs need to be wrapped inside a man-made bilayer vesicle, as being attempted in the Szostak laboratory (93,94) and elsewhere (95). Mother Nature took her time with available material.…”

Selection of Prebiotic Molecules in Amphiphilic Environments

“…Recently, it was shown that a possible prebiotic amphiphile (decanoic acid) undergoes distinct binding interactions with nucleobases and proteins [30,31]. So, at this stage, they may serve as containments for initial metabolic steps and, most prominently, as an ensemble of encapsulated environments for the replication of RNA molecules.…”

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

“…As for the other heterogeneous media, the lipid matrices could also have played some significant, additional roles in the emergence of compartmentalized precellular systems or protocells (the nucleic acid products can be encapsulated in the reforming vesicles during rehydration) [75,113] or even in the selection of nucleobases from the “prebiotic soup” [114]. …”