Chance and necessity in biochemistry: implications for the search for extraterrestrial biomarkers in Earth-like environments

Solid-State Single-Molecule Sensing with the Electronic Life-Detection Instrument for Enceladus/Europa (ELIE)

Growing evidence of the potential habitability of Ocean Worlds across our solar system is motivating the advancement of technologies capable of detecting life as we know it-sharing a common ancestry or physicochemical origin with life on Earth-or don't know it, representing a distinct emergence of life different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of-principle in a laboratory environment, we demonstrate the single-molecule detection of the amino acid L-proline at a 10 μM concentration in a compact system. Based on ELIE's solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecule's highest energy-occupied molecular orbital and lowest energy-unoccupied molecular orbital) as a novel metric to assess amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived α-amino acid abundance distributions to reduce the false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in a plume, surface, or subsurface of ice moons such as Enceladus or Europa. One-Sentence Summary: A solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we don't know it.

Toward Detecting Biosignatures of DNA, Lipids, and Metabolic Intermediates from Bacteria in Ice Grains Emitted by Enceladus and Europa

The reliable identification of biosignatures is key to the search for life elsewhere. On ocean worlds like Enceladus or Europa, this can be achieved by impact ionization mass spectrometers, such as the SUrface Dust Analyzer (SUDA) on board NASA's upcoming Europa Clipper mission. During spacecraft flybys, these instruments can sample ice grains formed from subsurface water and emitted by these moons. Previous laboratory analog experiments have demonstrated that SUDA-type instruments could identify amino acids, fatty acids, and peptides in ice grains and discriminate between their abiotic and biotic origins. Here, we report experiments simulating impact ionization mass spectra of ice grains containing DNA, lipids, and metabolic intermediates extracted from two bacterial cultures: Escherichia coli and Sphingopyxis alaskensis. Salty Enceladan or Europan ocean waters were simulated using matrices with different NaCl concentrations. Characteristic mass spectral signals, such as DNA nucleobases, are clearly identifiable at part-per-million-level concentrations. Mass spectra of all substances exhibit unambiguous biogenic patterns, which in some cases show significant differences between the two bacterial species. Sensitivity to the biosignatures decreases with increasing matrix salinity. The experimental parameters indicate that future impact ionization mass spectrometers will be most sensitive to the investigated biosignatures for ice grain encounter speeds of 4-6 km/s.

Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores

Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.

Lipid biomarkers: molecular tools for illuminating the history of microbial life

Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.

Carbon-Based Materials for Articular Tissue Engineering: From Innovative Scaffolding Materials toward Engineered Living Carbon

Carbon materials constitute a growing family of high-performance materials immersed in ongoing scientific technological revolutions. Their biochemical properties are interesting for a wide set of healthcare applications and their biomechanical performance, which can be modulated to mimic most human tissues, make them remarkable candidates for tissue repair and regeneration, especially for articular problems and osteochondral defects involving diverse tissues with very different morphologies and properties. However, more systematic approaches to the engineering design of carbon-based cell niches and scaffolds are needed and relevant challenges should still be overcome through extensive and collaborative research. In consequence, this study presents a comprehensive description of carbon materials and an explanation of their benefits for regenerative medicine, focusing on their rising impact in the area of osteochondral and articular repair and regeneration. Once the state-of-the-art is illustrated, innovative design and fabrication strategies for artificially recreating the cellular microenvironment within complex articular structures are discussed. Together with these modern design and fabrication approaches, current challenges, and research trends for reaching patients and creating social and economic impacts are examined. In a closing perspective, the engineering of living carbon materials is also presented for the first time and the related fundamental breakthroughs ahead are clarified.

Life on Mars: Independent Genesis or Common Ancestor?

The possibility of biological transfer between planetary bodies is seldom factored into life detection strategies, although the actuality of such an event would have profound implications for how we interpret potential biosignatures found on other worlds. This article addresses the possibility of life on Mars in the context of a biological transfer and an independent genesis of life. The phylogenetic tree of life on Earth is used as a blueprint to interpret evidence of life and as a guideline to determine the likelihood that potential biosignatures could be expressed by martian organisms. Several transfer scenarios are considered, depending on the timing of transfer with respect to the evolution of life on Earth. The implications of each transfer scenario and an independent genesis of life on the biochemical nature of the resulting martian organisms are discussed. The analysis highlights how conceding the possibility of a biological transfer has practical implications for how we search for evidence of life, both in terms of the quality of potential biosignatures and the likelihood that certain biosignatures might be expressed. It is concluded that a degree of uncertainty on the origin of martian organisms might be unavoidable, particularly in the absence of a biochemical context.

Understanding Hypervelocity Sampling of Biosignatures in Space Missions

The atomic-scale fragmentation processes involved in molecules undergoing hypervelocity impacts (HVIs; defined as >3 km/s) are challenging to investigate via experiments and still not well understood. This is particularly relevant for the consistency of biosignals from small-molecular-weight neutral organic molecules obtained during solar system robotic missions sampling atmospheres and plumes at hypervelocities. Experimental measurements to replicate HVI effects on neutral molecules are challenging, both in terms of accelerating uncharged species and isolating the multiple transition states over very rapid timescales (<1 ps). Nonequilibrium first-principles-based simulations extend the range of what is possible with experiments. We report on high-fidelity simulations of the fragmentation of small organic biosignature molecules over the range v = 1-12 km/s, and demonstrate that the fragmentation fraction is a sensitive function of velocity, impact angle, molecular structure, impact surface material, and the presence of surrounding ice shells. Furthermore, we generate interpretable fragmentation pathways and spectra for velocity values above the fragmentation thresholds and reveal how organic molecules encased in ice grains, as would likely be the case for those in "ocean worlds," are preserved at even higher velocities than bare molecules. Our results place ideal spacecraft encounter velocities between 3 and 5 km/s for bare amino and fatty acids and within 4-6 km/s for the same species encased in ice grains and predict the onset of organic fragmentation in ice grains at >5 km/s, both consistent with recent experiments exploring HVI effects using impact-induced ionization and analysis via mass spectrometry and from the analysis of Enceladus organics in Cassini Data. From nanometer-sized ice Ih clusters, we establish that HVI energy is dissipated by ice casings through thermal resistance to the impact shock wave and that an upper fragmentation velocity limit exists at which ultimately any organic contents will be cleaved by the surrounding ice-this provides a fundamental path to characterize micrometer-sized ice grains. Altogether, these results provide quantifiable insights to bracket future instrument design and mission parameters.

Discriminating Abiotic and Biotic Fingerprints of Amino Acids and Fatty Acids in Ice Grains Relevant to Ocean Worlds

Identifying and distinguishing between abiotic and biotic signatures of organic molecules such as amino acids and fatty acids is key to the search for life on extraterrestrial ocean worlds. Impact ionization mass spectrometers can potentially achieve this by sampling water ice grains formed from ocean water and ejected by moons such as Enceladus and Europa, thereby exploring the habitability of their subsurface oceans in spacecraft flybys. Here, we extend previous high-sensitivity laser-based analog experiments of biomolecules in pure water to investigate the mass spectra of amino acids and fatty acids at simulated abiotic and biotic relative abundances. To account for the complex background matrix expected to emerge from a salty Enceladean ocean that has been in extensive chemical exchange with a carbonaceous rocky core, other organic and inorganic constituents are added to the biosignature mixtures. We find that both amino acids and fatty acids produce sodiated molecular peaks in salty solutions. Under the soft ionization conditions expected for low-velocity (2-6 km/s) encounters of an orbiting spacecraft with ice grains, the unfragmented molecular spectral signatures of amino acids and fatty acids accurately reflect the original relative abundances of the parent molecules within the source solution, enabling characteristic abiotic and biotic relative abundance patterns to be identified. No critical interferences with other abiotic organic compounds were observed. Detection limits of the investigated biosignatures under Enceladus-like conditions are salinity dependent (decreasing sensitivity with increasing salinity), at the μM or nM level. The survivability and ionization efficiency of large organic molecules during impact ionization appear to be significantly improved when they are protected by a frozen water matrix. We infer from our experimental results that encounter velocities of 4-6 km/s are most appropriate for impact ionization mass spectrometers to detect and discriminate between abiotic and biotic signatures.

Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater

Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.

Analog Experiments for the Identification of Trace Biosignatures in Ice Grains from Extraterrestrial Ocean Worlds

Reliable identification of biosignatures, such as amino acids, fatty acids, and peptides, on extraterrestrial ocean worlds is a key prerequisite for space missions that search for life or its emergence on these worlds. One promising approach is the use of high-performance in situ impact ionization mass spectrometers to sample water ice grains emerging from ocean-bearing moons such as Europa or Enceladus. A predecessor of such detectors, the Cosmic Dust Analyzer on board the Cassini spacecraft, has proven to be very successful in analyzing inorganic and organic ocean constituents and with that characterizing the habitability of Enceladus ocean. However, biosignatures have not been definitively identified in extraterrestrial ocean environments so far. Here, we investigate with an analog experiment the spectral appearance of amino acids, fatty acids, and peptides in water ice grains, together with their detection limits, as applicable to spaceborne mass spectrometers. We employ a laboratory-based laser induced liquid beam ion desorption technique, proven to simulate accurately the impact ionization mass spectra of water ice grains over a wide range of impact speeds. The investigated organics produce characteristic mass spectra, with molecular peaks as well as clearly identifiable, distinctive fragments. We find the detection limits of these key biosignatures to be at the μM or nM level, depending on the molecular species and instrument polarity, and infer that impact ionization mass spectrometers are most sensitive to the molecular peaks of these biosignatures at encounter velocities of 4-6 km/s.

Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans

The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans. To interpret these data and to help configure instruments for future missions, controlled laboratory experiments and simulations are needed. This review aims to bring together studies and experimental designs from various scientific fields currently investigating the icy moons, including planetary sciences, chemistry, (micro-)biology, geology, glaciology, etc. This chapter provides an overview of successful in situ, in silico, and in vitro experiments, which explore different regions of interest on icy moons, i.e. a potential plume, surface, icy shell, water and brines, hydrothermal vents, and the rocky core.

Membrane Lipid Composition and Amino Acid Excretion Patterns of Methanothermococcus okinawensis Grown in the Presence of Inhibitors Detected in the Enceladian Plume

Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn's icy moon Enceladus. However, little is known about the environmental conditions shaping the synthesis of lipids and amino acids. Here, we present the lipid production and amino acid excretion patterns of the methanogenic archaeon Methanothermococcus okinawensis after exposing it to different multivariate concentrations of the inhibitors ammonium, formaldehyde, and methanol present in the Enceladian plume. M. okinawensis shows different patterns of lipid and amino acids excretion, depending on the amount of these inhibitors in the growth medium. While methanol did not show a significant impact on growth, lipid or amino acid production rates, ammonium and formaldehyde strongly affected these parameters. These findings are important for understanding the eco-physiology of methanogens on Earth and have implications for the use of biomarkers as possible signs of extraterrestrial life for future space missions in the Solar System.

Long-term thermal stability of fluorescent dye used for chiral amino acid analysis on future spaceflight missions

Future spaceflight missions focused on life detection will carry with them new, state-of-the-art instrumentation capable of highly selective and sensitive organic analysis. CE-LIF is an ideal candidate for such a mission due to its high separation efficiency and low LODs. One perceived risk of utilizing this technique on a future mission is the stability of the chemical reagents in the spaceflight environment. Here, we present an investigation of the thermal stability of the fluorescent dye (5-carboxyfluorescein succinimidyl ester) used for amino acid analysis. The dye was stored at 4, 25, and 60°C for 1 month, 6 months, 1 year, and 2 years. When stored at 4°C for 2 years, 25°C for 6 months, or 60°C for 1 month there was no effect on CE-LIF assay performance due to dye degradation. Beyond these time points, while the dye degradation begins to interfere with the analysis, it is still possible to perform the analysis and achieve the majority of amino acid biosignature science goals described in the science definition team report for the potential Europa Lander mission. This work indicates that thermal control of the dye at ≤4°C will be needed during transit on future spaceflight missions to maintain dye stability.

Effects of Gamma and Electron Radiation on the Structural Integrity of Organic Molecules and Macromolecular Biomarkers Measured by Microarray Immunoassays and Their Astrobiological Implications

High-energy ionizing radiation in the form of solar energetic particles and galactic cosmic rays is pervasive on the surface of planetary bodies with thin atmospheres or in space facilities for humans, and it may seriously affect the chemistry and the structure of organic and biological material. We used fluorescent microarray immunoassays to assess how different doses of electron and gamma radiations affect the stability of target compounds such as biological polymers and small molecules (haptens) conjugated to large proteins. The radiation effect was monitored by measuring the loss in the immunoidentification of the target due to an impaired ability of the antibodies for binding their corresponding irradiated and damaged epitopes (the part of the target molecule to which antibodies bind). Exposure to electron radiation alone was more damaging at low doses (1 kGy) than exposure to gamma radiation alone, but this effect was reversed at the highest radiation dose (500 kGy). Differences in the dose-effect immunoidentification patterns suggested that the amount (dose) and not the type of radiation was the main factor for the cumulative damage on the majority of the assayed molecules. Molecules irradiated with both types of radiation showed a response similar to that of the individual treatments at increasing radiation doses, although the pattern obtained with electrons only was the most similar. The calculated radiolysis constant did not show a unique pattern; it rather suggested a different behavior perhaps associated with the unique structure of each molecule. Although not strictly comparable with extraterrestrial conditions because the irradiations were performed under air and at room temperature, our results may contribute to understanding the effects of ionizing radiation on complex molecules and the search for biomarkers through bioaffinity-based systems in planetary exploration.

Functional Properties of Amino Acid Side Chains as Biomarkers of Extraterrestrial Life

The present study proposes to search our solar system (Mars, Enceladus, Europa) for patterns of organic molecules that are universally associated with biological functions and structures. The functions are primarily catalytic because life could only have originated within volume/space-constrained compartments containing chemical reactions catalyzed by certain polymers. The proposed molecular structures are specific groups in the side chains of amino acids with the highest catalytic propensities related to life on Earth, that is, those that most frequently participate as key catalytic groups in the active sites of enzymes such as imidazole, thiol, guanidinium, amide, and carboxyl. Alternatively, these or other catalytic groups can be searched for on non-amino-acid organic molecules, which can be tested for certain hydrolytic catalytic activities. The first scenario assumes that life may have originated in a similar manner as the terrestrial set of α-amino acids, while the second scenario does not set such a requirement. From the catalytic propensity perspective proposed in the first scenario, life must have invented amino acids with high catalytic propensity (His, Cys, Arg) in order to overcome, and be complemented by, the low catalytic propensity of the initially available abiogenic amino acids. The abiogenic and the metabolically invented amino acids with the lowest catalytic propensity can also serve as markers of extraterrestrial life when searching for patterns on the basis of the following functional propensities related to protein secondary/quaternary structure: (1) amino acids that are able to form α-helical intramembrane peptide domains, which can serve as primitive transporters in protocell membrane bilayers and catalysts of simple biochemical reactions; (2) amino acids that tend to accumulate in extremophile proteins of Earth and possibly extraterrestrial life. The catalytic/structural functional propensity approach offers a new perspective in the search for extraterrestrial life and could help unify previous amino acid-based approaches.

Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario

The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration-Life detection-Microbial mat-Life detector chip-Thermogravimetry-Raman spectroscopy-NIR-DRIFTS. Astrobiology 17, 984-996.

Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons

To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a "polyelectrolyte." Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block "alphabet." This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus-Life detection-Europa-Icy moon-Biosignatures-Polyelectrolyte theory of the gene. Astrobiology 17, 840-851.

Alien Mindscapes-A Perspective on the Search for Extraterrestrial Intelligence

Advances in planetary and space sciences, astrobiology, and life and cognitive sciences, combined with developments in communication theory, bioneural computing, machine learning, and big data analysis, create new opportunities to explore the probabilistic nature of alien life. Brought together in a multidisciplinary approach, they have the potential to support an integrated and expanded Search for Extraterrestrial Intelligence (SETI (1) ), a search that includes looking for life as we do not know it. This approach will augment the odds of detecting a signal by broadening our understanding of the evolutionary and systemic components in the search for extraterrestrial intelligence (ETI), provide more targets for radio and optical SETI, and identify new ways of decoding and coding messages using universal markers.

KEY WORDS

SETI-Astrobiology-Coevolution of Earth and life-Planetary habitability and biosignatures. Astrobiology 16, 661-676.

227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

Extraordinarily adaptive properties of the genetically encoded amino acids

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.