Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers.

Sebastian Himbert,Maikel C Rheinstädter,David W Deamer,Mindy Chapman

doi:10.1038/srep31285

Sebastian Himbert, Maikel C Rheinstädter + Show 2 more

Open Access

https://doi.org/10.1038/srep31285

Copy DOI

Abstract

RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5′-adenosine monophosphate (AMP) and 5′-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone, and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.

Highlights

A testable hypothesis is that an early RNA-based life form may have preceded the appearance of the DNA/ protein code that is universal to life on Earth[5,6]
A typical diffraction pattern is shown in Fig. 2a, using NH4Cl mixed with adenosine monophosphate (AMP)/uridine monophosphate (UMP)
Based on the observation by Toppozini et al.[13] these distances can be modeled by 2-dimensional nucleotide arrangements, where the AMP and UMP molecules take a flat position between the bilayers

Summary

Introduction

A testable hypothesis is that an early RNA-based life form may have preceded the appearance of the DNA/ protein code that is universal to life on Earth[5,6]. A second promoter was reported by Da Silva et al.[14] who achieved even higher yields of polymers when the mononucleotides were mixed with inorganic salts, such as NaCl, KCl and NH4Cl. To address the effect of confinement and anhydrous conditions in the polymerization reaction, we investigated the organization of adenosine (AMP) and uridine monophosphate (UMP) in different environments. Inorganic salts provide confinement under anhydrous conditions because solutes like nucleotides are excluded from salt crystals during drying and become concentrated as thin films on the crystal surfaces (Fig. 1c). Mineral surfaces, such as Montmorillonite clay with their nanoporous structure serve to confine chemically activated nucleotides[15,16] (Fig. 1d). The charged clay surface attracts the nucleotides and the increased local concentration may promote ester bond synthesis between nucleotides during dehydration

Methods

Results

Discussion

Conclusion