Ribonucleotides

Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?

Quantum mechanical calculations are used to explore the thermodynamics of possible prebiotic synthesis of the building blocks of nucleic acids. Different combinations of D-ribofuranose (Ribf) and N-(2-aminoethyl)-glycine (AEG) (trifunctional connectors (TCs)); the nature of the Ribf, its anomeric form, and its ring puckering (conformation); and the nature of the nucleobases (recognition units (RUs)) are considered. The combinatorial explosion of possible nucleosides has been drastically reduced on physicochemical grounds followed by a detailed thermodynamic evaluation of alternative synthetic pathways. The synthesis of nucleosides containing N-(2-aminoethyl)-glycine (AEG) is predicted to be thermodynamically favored suggesting a possible role of AEG as a component of an ancestral proto-RNA that may have preceded today's nucleic acids. A new pathway for the building of free nucleotides (exemplified by 5'-uridine monophosphate (UMP)) and of AEG dipeptides is proposed. This new pathway leads to a spontaneous formation of free UMP assisted by an AEG nucleoside in an aqueous environment. This appears to be a workaround to the "water problem" that prohibits the synthesis of nucleotides in water.

Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate*

A mechanism of nucleoside triphosphorylation would have been critical in an evolving "RNA world" to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. Previous reports have demonstrated that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under prebiotically-relevant conditions, but their reaction rates were unknown and the influence of reaction conditions not well-characterized. Here we established a sensitive assay that allowed for the determination of second-order rate constants for all four rNTPs, ranging from 1.7×10^-6 to 6.5×10^-6  M^-1  s^-1 . The ATP reaction shows a linear dependence on pH and Mg²⁺ , and an enthalpy of activation of 88±4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.

A Step toward Molecular Evolution of RNA: Ribose Binds to Prebiotic Fatty Acid Membranes, and Nucleosides Bind Better than Individual Bases Do

A major challenge in understanding how biological cells arose on the early Earth is explaining how RNA and membranes originally colocalized. We propose that the building blocks of RNA (nucleobases and ribose) bound to self-assembled prebiotic membranes. We have previously demonstrated that the bases bind to membranes composed of a prebiotic fatty acid, but evidence for the binding of sugars has remained a technical challenge. Here, we used pulsed-field gradient NMR spectroscopy to demonstrate that ribose and other sugars bind to membranes of decanoic acid. Moreover, the binding of some bases is strongly enhanced when they are linked to ribose to form a nucleoside or - with the addition of phosphate - a nucleotide. This enhanced binding could have played a role in the molecular evolution leading to the production of RNA.

D-ribose and pathogenesis of Alzheimer's disease

It is estimated that the global prevalence of dementia will rise as high as 24 million and predicted to be double in every 20 years which is attributed to the fact that the ageing population is increasing and so more individuals are at risk of developing neurodegenerative diseases like Alzheimer's. Many scientists favored glycation of proteins such as tau, amyloid beta (Aβ) etc. as one of the important risk factor in Alzheimer's disease (AD). Since, D-ribose shows highest glycation ability among other sugars hence, produces advanced glycation end products (AGEs) rapidly. However, there are several other mechanisms suggested by researchers through which D-ribose may cause cognitive impairments. There is a concern related to diabetic patients since they also suffer from D-ribose metabolism, may be more prone to AD risk. Thus, it is imperative that the pathogenesis and the pathways involved in AD progression are explored in the light of ribosylation and AGEs formation for identifying suitable diagnostics marker for early diagnosis or finding promising therapeutic outcomes.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth

Understanding how life began is one of the most fascinating problems to solve. By approaching this enigma from a chemistry perspective, the goal is to define what series of chemical reactions could lead to the synthesis of nucleotides, amino acids, lipids, and other cellular components from simple feedstocks under prebiotically plausible conditions. It is well established that evolution of life involved RNA which plays central roles in both inheritance and catalysis. In this review, we present historically important and recently published articles aimed at understanding the emergence of RNA nucleosides and nucleotides on the early Earth.

Selective prebiotic conversion of pyrimidine and purine anhydronucleosides into Watson-Crick base-pairing arabino-furanosyl nucleosides in water

Prebiotic nucleotide synthesis is crucial to understanding the origins of life on Earth. There are numerous candidates for life's first nucleic acid, however, currently no prebiotic method to selectively and concurrently synthesise the canonical Watson-Crick base-pairing pyrimidine (C, U) and purine (A, G) nucleosides exists for any genetic polymer. Here, we demonstrate the divergent prebiotic synthesis of arabinonucleic acid (ANA) nucleosides. The complete set of canonical nucleosides is delivered from one reaction sequence, with regiospecific glycosidation and complete furanosyl selectivity. We observe photochemical 8-mercaptopurine reduction is efficient for the canonical purines (A, G), but not the non-canonical purine inosine (I). Our results demonstrate that synthesis of ANA may have been facile under conditions that comply with plausible geochemical environments on early Earth and, given that ANA is capable of encoding RNA/DNA compatible information and evolving to yield catalytic ANA-zymes, ANA may have played a critical role during the origins of life.

Subsumed complexity: abiogenesis as a by-product of complex energy transduction

The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry called subsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state. There is evidence for an emergent level of complexity that is overlooked in most conceptualizations of abiogenesis that arises from populations of compounds formed from atomic energy input. We posit that different forms of energy input can exhibit different degrees of dissipation complexity within an identical chemical medium. By extension, the maximum capacity for organic chemical complexification across molecular and macromolecular scales subsumes, rather than emerges from, the underlying complexity of energy transduction processes that drive their production and modification.This article is part of the themed issue 'Reconceptualizing the origins of life'.

A theoretical insight into the formation mechanisms of C/N-ribonucleosides with pyrimidine and ribose

The detailed formation mechanisms of C-ribonucleoside and N-ribonucleoside via the reaction of 2,4,6-triaminopyrimidine (TAP) with (d)-ribose in aqueous solution were explored using density functional theory (DFT). The calculations indicate that five isomers (α,β-furanose, α,β-pyranose and open-chain aldehyde) of (d)-ribose can exist in equilibrium in aqueous solution. In contrast to cyclic isomers, an open-chain aldehyde is most feasible to react with TAP. In general, the formation pathways of C-nucleoside and N-nucleoside proceed in three steps including nucleophilic addition, dehydration and cyclization. The calculated apparent activation energies are 28.8 kcal mol^-1 and 29.2 kcal mol^-1, respectively. It suggests that both C- and N-nucleoside can be formed in aqueous solution, which is in good agreement with the experimental results. The water molecule plays an important "H-bridge" role by the hydrogen atom relay. Finally, a model structure of nucleobase, which will be beneficial for the C-C glycosidic bond formation, is proposed.

Origin of Life and the Phosphate Transfer Catalyst

In this paper, we revisit several issues relevant to origin-of-life research and propose a Phosphate Transfer Catalyst hypothesis that furthers our understanding of some of the key events in prebiotic chemical evolution. In the Phosphate Transfer Catalyst hypothesis, we assume the existence of hypothetical metallopeptides with phosphate transfer activity that use abundant polyphosphates as both substrates and energy sources. Nonspecific catalysis by this phosphate transfer catalyst would provide a variety of different products such as phosphoryl amino acids, nucleosides, polyphosphate nucleotides, nucleic acids, and aminoacylated nucleic acids. Moreover, being an autocatalytic set and metabolic driver at the same time, it could possibly replicate itself and produce a collective system of two polymerases; a nucleic acid able to catalyze peptide bond formation and a peptide able to polymerize nucleic acids. The genetic code starts at first as a system that reduces the energy barrier by bringing substrates (2'/3' aminoacyl-nucleotides) together, an ancestral form of the catalysis performed by modern ribosomes. Key Words: Origin of life-Prebiotic chemistry-Catalysis-Nucleic acids. Astrobiology 17, 277-285.

A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells

We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions.

Occurrence of Tourmaline in Metasedimentary Rocks of the Isua Supracrustal Belt, Greenland: Implications for Ribose Stabilization in Hadean Marine Sediments

Abiotic formation of RNA was important for the emergence of terrestrial life, but the acknowledged difficulties of generating and stabilizing ribose have often raised questions regarding how the first RNA might have formed. Previous researchers have proposed that borate could have stabilized ribose; however, the availability of borate on the early Earth has been the subject of intense debate. In order to examine whether borate was available on the early Earth, this study examined metasedimentary rocks from the Isua Supracrustal Belt. Garnet, biotite, and quartz comprise the major constituents of the examined rocks. Field relationships and the chemical compositions of the examined rocks suggest sedimentary origin. The present study found that garnet crystals contain a number of inclusions of tourmaline (a type of borosilicate mineral). All tourmaline crystals are Fe-rich and categorized as schorl. Both garnet and tourmaline often contain graphite inclusions and this close association of tourmaline with garnet and graphite has not been recognized previously. Garnet-biotite and graphite geothermometers suggest that the tourmaline in garnet experienced peak metamorphic conditions (~500 °C and 5 kbar). The mineralogical characteristics of the tourmaline and the whole rock composition indicate that the tourmaline formed authigenically in the sediment during diagenesis and/or early metamorphism. Clay minerals in modern sediments have the capability to adsorb and concentrate borate, which could lead to boron enrichment during diagenesis, followed by tourmaline formation under metamorphic conditions. Clay minerals, deposited on the early Archean seafloor, were the precursors of the garnet and biotite in the examined samples. The studied tourmaline crystals were most likely formed in the same way as modern tourmaline in marine sediments. Therefore, boron enrichment by clays must have been possible even during the early Archean. Thus, similar enrichment could have been possible during the Hadean, providing a stabilization agent for ribose.

The Origin of Life--Out of the Blue

Either to sustain autotrophy, or as a prelude to heterotrophy, organic synthesis from an environmentally available C1 feedstock molecule is crucial to the origin of life. Recent findings augment key literature results and suggest that hydrogen cyanide--"Blausäure"--was that feedstock.

Modulation of reactivity in the cavity of liposomes promotes the formation of peptide bonds

In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide. By contrast, when the activated amino acid is found outside the liposome, hydrolysis is the prevalent reaction, showing that the cavity of the liposomes promotes the formation of peptide bonds. We attribute this result to the large lipid concentration in small compartments from the point of view of a membrane-impermeable molecule. Based on this result, we show how the outcome of the reaction can be predicted as a function of the size of the compartment. The implications of these results on the behavior of biomolecules in cell compartments, abiogenesis, and the design of artificial cell-inspired systems are considered.

Information-Theoretic Considerations Concerning the Origin of Life

Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.

Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

The place of RNA in the origin and early evolution of the genetic machinery

The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness.

Synergism and mutualism in non-enzymatic RNA polymerization

The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.

Hydrolytic Fitness of N-glycosyl Bonds: Comparing the Deglycosylation Kinetics of Modified, Alternative and Native Nucleosides

Nature's selection of the contemporary nucleobases in RNA and DNA continues to intrigue the origin of life community. While the prebiotic synthesis of the N-glycosyl bond has historically been a central area of investigation, variations in hydrolytic stabilities among the N-glycosyl bonds may have presented an additional selection pressure that contributed to nucleobase and nucleoside evolution. To experimentally probe this hypothesis, a systematic kinetic analysis of the hydrolytic deglycosylation reactions of modified, alternative and native nucleosides was undertaken. Rate constants were measured as a function of temperature (at pH 1) to produce Arrhenius and Eyring plots for extrapolation to 37°C and determination of thermodynamic activation parameters. Rate enhancements based on the differences in reaction rates of deoxyribo- and ribo-glycosidic bonds were found to vary under the same conditions. Rate constants of deoxynucleosides were also measured across the pH range of 1 - 3 (at 50°C), which highlighted how simple changes to the heterocycle alone can lead to significant variation in deglycosylation rates. The contemporary nucleosides exhibited the slowest deglycosylation rates in comparison to the non-native/alternative nucleosides, which we suggest as experimental support for nature's selection of the fittest N-glycosyl bonds.

Potential pitfalls in MALDI-TOF MS analysis of abiotically synthesized RNA oligonucleotides

Demonstration of the abiotic polymerization of ribonucleotides under conditions consistent with conditions that may have existed on the prebiotic Earth is an important goal in "RNA world" research. Recent reports of abiotic RNA polymerization with and without catalysis rely on techniques such as HPLC, gel electrophoresis, and MALDI-TOF MS to analyze the reaction products. It is essential to understand the limitations of these techniques in order to accurately interpret the results of these analyses. In particular, techniques that rely on mass for peak identification may not be able to distinguish between a single, linear RNA oligomer and stable aggregates of smaller linear and/or cyclic RNA molecules. In the case of MALDI-TOF MS, additional complications may arise from formation of salt adducts and MALDI matrix complexes. This is especially true for abiotic RNA polymerization reactions because the concentration of longer RNA chains can be quite low and RNA, as a polyelectrolyte, is highly susceptible to adduct formation and aggregation. Here we focus on MALDI-TOF MS analysis of abiotic polymerization products of imidazole-activated AMP in the presence and absence of montmorillonite clay as a catalyst. A low molecular weight oligonucleotide standard designed for use in MALDI-TOF MS and a 3'-5' polyadenosine monophosphate reference standard were also run for comparison and calibration. Clay-catalyzed reaction products of activated GMP and UMP were also examined. The results illustrate the ambiguities associated with assignment of m/z values in MALDI mass spectra and the need for accurate calibration of mass spectra and careful sample preparation to minimize the formation of adducts and other complications arising from the MALDI process.

Possible role of metal(II) octacyanomolybdate(IV) in chemical evolution: interaction with ribose nucleotides

We have proposed that double metal cyanide compounds (DMCs) might have played vital roles as catalysts in chemical evolution and the origin of life. We have synthesized a series of metal octacyanomolybdates (MOCMos) and studied their interactions with ribose nucleotides. MOCMos have been shown to be effective adsorbents for 5'-ribonucleotides. The maximum adsorption level was found to be about 50 % at neutral pH under the conditions studied. The zinc(II) octacyanomolybdate(IV) showed larger adsorption compared to other MOCMos. The surface area seems to important parameter for the adsorption of nucleotides. The adsorption followed a Langmuir adsorption isotherms with an overall adsorption trends of the order of 5'-GMP > 5'-AMP > 5'-CMP > 5'-UMP. Purine nucleotides were adsorbed more strongly than pyrimidine nucleotides on all MOCMos possibly because of the additional binding afforded by the imidazole ring in purines. Infrared spectral studies of adsorption adducts indicate that adsorption takes place through interaction between adsorbate molecules and outer divalent ions of MOCMos.

The algorithmic origins of life

Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation-where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies-may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.

5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution

The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.

Refining the genetic alphabet: a late-period selection pressure?

The transition from genomic ribonucleic acid (RNA) to deoxyribonucleic acid (DNA) in primitive cells may have created a selection pressure that refined the genetic alphabet, resulting from the global weakening of the N-glycosyl bonds. Hydrolytic rupture of these bonds, termed deglycosylation, leaves an abasic site that is the single greatest threat to the stability and integrity of genomic DNA. The rates of deglycosylation are highly dependent on the identity of the nucleobases. Modifications made to the bases, such as deamination, oxidation, and alkylation, can further increase deglycosylation reaction rates, suggesting that the native bases provide optimum N-glycosyl bond stability. To protect their genomes, cells have evolved highly specific enzymes called glycosylases, associated with DNA repair, that detect and remove these damaged bases. In RNA, however, the occurrence of many of these modified bases is deliberate. The dichotomous behavior that cells exhibit toward base modifications may have originated in the RNA world. Modified bases would have been advantageous for the functional and structural repertoire of catalytic RNAs. Yet in an early DNA world, the utility of these heterocycles was greatly diminished, and their presence posed a distinct liability to the stability of cells' genomes. A natural selection for bases exhibiting the greatest resistance to deglycosylation would have ensured the viability of early DNA life, along with the recruitment of DNA repair.

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Mapping the landscape of potentially primordial informational oligomers: (3'→2')-D-phosphoglyceric acid linked acyclic oligonucleotides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements

The (3'→2')-phosphodiester glyceric acid backbone containing an acyclic oligomer tagged with 2,4-disubstituted pyrimidines as alternative recognition elements have been synthesized. Strong cross-pairing of a 2,4-dioxo-5-aminopyrimidine hexamer, rivaling locked nucleic acid (LNA) and peptide nucleic acid (PNA), with complementary adenine-containing DNA and RNA sequences was observed. The corresponding 2,4-diamino- and 2-amino-4-oxo-5-aminopyrimidine-tagged oligomers were synthesized, but difficulties in deprotection, purification, and isolation thwarted further investigations. The acyclic phosphate backbone structure of the protected oligomer seems to be prone to an eliminative degradation owing to the acidic hydrogen at the 2'-position--an arrangement that renders the oligomer vulnerable to the conditions used for the removal of the protecting groups on the heterocyclic recognition element. However, the free oligomers seem to be stable under the conditions investigated.

Primitive genetic polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?

Bioenergetics and life's origins

Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.