Scanning tunnelling microscopy and molecular modelling of xanthine monolayers self-assembled at the solid-liquid interface: relevance to the origin of life

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS₂in aqueous environment. The ssDNA sequences [T₁₀, G₁₀, A₁₀, C₁₀, U₁₀, (GT)₅, and (AC)₅] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS₂(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS₂surface and facilitate future studies in design of functional DNA/MoS₂structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Self-assembly of N3-substituted xanthines in the solid state and at the solid-liquid interface

The self-assembly of small molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by exploiting the rich programmability of artificial nucleobases undergoing self-assembly through strong H bonds. Here N(3)-functionalized xanthine modules are described, which are capable of self-associating through self-complementary H-bonding patterns to form H-bonded supramolecular ribbons. The self-association of xanthines through directional H bonding between neighboring molecules allows the controlled generation of highly compact 1D supramolecular polymeric ribbons on graphite. These architectures have been characterized by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional theory (DFT) studies and X-ray diffraction.

Biomolecules at interfaces: chiral, naturally

Interfaces are a most important environment in natural and synthetic chemistries for a wide variety of processes, such as catalysis, recognition, separation, and so on. Naturally occurring systems have evolved to one handedness and the study of interfaces where biomolecules are located is a potentially revealing pursuit with regard to understanding the reasons and importance of stereochemistry in these environments. Equally, the spontaneous resolution of achiral and chiral compounds at interfaces could lead to explanations regarding the emergence of single handedness in proteins and sugars. Also, the attachment of biomolecules to surfaces leads to systems capable of stereoselective processes which may be useful for the applications mentioned above. The review covers systems ranging from small biomolecules studied under ultrapure conditions in vacuum to protein adsorption to surfaces in solution, and the techniques that can be used to study them.

Supramolecular ring structures of 7-methylguanine: a computational study of its self-assembly and anion binding

The density functional theory calculations of 7-methylguanine clusters revealed that stable ring assemblies can be formed with or without anions in the center position and hexameric clusters are the most stable and most planar ones. The coordination of anions (Cl⁻, Br⁻, NO₃⁻) stabilizes and thus favors the formation of planar aggregates. We believe that the predicted planar structures stabilized by anions are good models for self-assembly structures formed at solid-liquid or solid-gas interfaces. Comparing the bonding and average H-bond energy to reference ribbon calculations we pointed out the presence of the previously introduced cooperativity effect in circular supramolecular structures of 7-methylguanine.

Homochiral xanthine quintet networks self-assembled on Au(111) surfaces

Xanthine molecule is an intermediate in nucleic acid degradation from the deamination of guanine and is also a compound present in the ancient solar system that is found in high concentrations in extraterrestrial meteorites. The self-assembly of xanthine molecules on inorganic surfaces is therefore of interest for the study of biochemical processes, and it may also be relevant to the fundamental understanding of prebiotic biosynthesis. Using a combination of high-resolution scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, two new homochiral xanthine structures have been found on Au(111) under ultrahigh vacuum conditions. Xanthine molecules are found to be self-assembled into two extended homochiral networks tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Our findings indicate that the deamination of guanine into xanthine leads to a very different base pairing potential and the chemical properties of the base which may be of relevance to the function of the cell and potential development of human diseases. Moreover, the adsorption of xanthine molecules on inorganic surfaces leading to homochiral assemblies may be of interest for the fundamental understanding of the emerged chirality at early stages of life.

With a grain of salt: what halite has to offer to discussions on the origin of life

This experimental study investigated how the dynamics of the crystallization of the evaporite mineral halite could affect the accumulation and preservation of organic macromolecules present in the crystallizing solution. Halite was grown under controlled conditions in the presence of polymer nanoparticles that acted as an analog to protocellular material. Optical microscopy, atomic force microscopy, and laser scanning confocal fluorescence microscopy were used to trace the localization of the nanoparticles during and after growth of halite crystals. The present study revealed that the organic nanoparticles were not regularly incorporated within the halite, but were very concentrated on its surfaces. Their distribution was controlled dominantly by the morphologic surface features of the mineral rather than by specific molecular interactions with an atomic plane of the mineral. This means that the distribution of organic molecules was controlled by surfaces like those of halite's evaporitic growth forms. The experiments with halite also demonstrated that a mineral need not continuously incorporate organic molecules during its crystallization to preserve those molecules: After rejection by (non-incorporation into) the crystallizing halite, the organic nanoparticles increased in concentration in the evaporating brine. They ultimately either adsorbed in rectilinear patterns onto the hopper-enhanced surfaces and along discontinuities within the crystals, or they were encapsulated within fluid inclusions. Of additional importance in origin-of-life considerations is the fact that halite in the natural environment rapidly can change its role from that of a protective repository (in the absence of water) to that of a source of organic particles (as soon as water is present) when the mineral dissolves.

Chirality of living systems: a helping hand from crystals and oligopeptides

Left-right asymmetry is ubiquitous in nature. Recent studies reveal changes in the energy and growth rate of crystal surfaces to which D or L amino acids bind, with the binding itself being dictated by stereochemical matching. Likewise, oligomerization of amino acids appears to be a chiroselective process that enables the propagation of sequences with defined handedness.[[For a definition of chiroselective self-assembly, see: M. Bolli, R. Micura, A. Eschenmoser, Chem. Biol. 1997, 4, 309-320.]] These results, along with related findings on symmetry breaking and further amplification of asymmetry at a supramolecular level, constitute new insights into the origin of homochirality in living species.

Primordial coding of amino acids by adsorbed purine bases

Scanning tunneling microscopy and chromatography experiments exploring the potential templating properties of nucleic acid bases adsorbed to the surface of crystalline graphite, revealed that the interactions of amino acids with the bare crystal surface are significantly modulated by the prior adsorption of adenine and hypoxanthine. These bases are the coding elements of a putative purine-only genetic alphabet and the observed effects are different for each of the bases. Such mapping between bases and amino acids provides a coding mechanism. These observations demonstrate that a simple pre-RNA amino acid discrimination mechanism could have existed on the prebiotic Earth providing critical functionality for the origin of life.

Life before RNA

The hypothesis that life originated and evolved from linear informational molecules capable of facilitating their own catalytic replication is deeply entrenched. However, widespread acceptance of this paradigm seems oblivious to a lack of direct experimental support. Here, we outline the fundamental objections to the de novo appearance of linear, self-replicating polymers and examine an alternative hypothesis of template-directed coding of peptide catalysts by adsorbed purine bases. The bases (which encode biological information in modern nucleic acids) spontaneously self-organize into two-dimensional molecular solids adsorbed to the uncharged surfaces of crystalline minerals; their molecular arrangement is specified by hydrogen bonding rules between adjacent molecules and can possess the aperiodic complexity to encode putative protobiological information. The persistence of such information through self-reproduction, together with the capacity of adsorbed bases to exhibit enantiomorphism and effect amino acid discrimination, would seem to provide the necessary machinery for a primitive genetic coding mechanism.

Origins of life: a route to nanotechnology

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.

Differential adsorption of nucleic acid bases: Relevance to the origin of life

The adsorption of organic molecules onto the surfaces of inorganic solids has long been considered a process relevant to the origin of life. We have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in water on the surface of crystalline graphite. The markedly different adsorption behavior of the bases describes an elutropic series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. We propose that such differential properties were relevant to the prebiotic chemistry of the bases and may have influenced the composition of the primordial genetic architecture.

Self-programmable, self-assembling two-dimensional genetic matter

Putative two-dimensional coding systems can be constructed from aqueous solutions of purine and pyrimidine nucleic acid bases evaporated at moderate temperatures on the surfaces of inorganic solids. The resultant structures are monolayers which are formed spontaneously by molecular self-assembly and they have been observed with molecular resolution by scanning tunnelling microscopy (STM). When formed from solutions of a single base, the monolayers of adenine and uracil have crystalline characteristics and the STM images can be interpreted in terms of the geometrical placement of planar arranged molecules that interact laterally by intermolecular hydrogen bonding. When formed from solutions containing a mixture of adenine and uracil, the monolayers have aperiodic structures. Small crystalline domains within these monolayers can be interpreted in terms of the single phase configurations of the molecules and the remaining aperiodic structures can presumably be interpreted, geometrically, in terms of the 21 theoretically possible adenine-adenine, uracil-uracil and adenine-uracil hydrogen bonding interactions. We propose that combinatorial arrangements of planar arranged purine and pyrimidine bases could provide the necessary complexity to act as a primitive genetic mechanism and may have relevance to the origin of life.