Jing Sun

Nature Chemistry, Published online: 26 July 2021; doi:10.1038/s41557-021-00749-4

Elucidating the origin of translation—the process that produces a specific peptide from an RNA sequence—is one of the most difficult challenges in prebiotic chemistry and evolutionary biology. Now, it has been shown that aminoacylated nucleotides couple to amino-acid-bearing oligoribonucleotides, directed by an RNA template, forming specific di- and tripeptides in the absence of ribosomal machinery.

The diastereoselectivity of the peptide coupling between aminoacidylnucleotides and amino acid esters in aqueous condensation buffer was determined by NMR spectroscopy. Homochiral dipeptides were found as the preferred products.

Abstract

Proteins are composed of l-amino acids, but nucleic acids and most oligosaccharides contain d-sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate-linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Here we report how the diastereoselectivity of the first peptide coupling of the peptido RNA pathway can be determined in situ by NMR spectroscopy. When a racemic mixture of an amino acid ester was allowed to react with an 5′-aminoacidyl nucleotide, diastereomeric ratios of up to 72 : 28 of the resulting dipeptido nucleotides were found by integration of ³¹P- or ¹H-NMR peaks. The highest diastereomeric excess was found for the homochiral coupling product d-Ser-d-Trp, phosphoramidate-linked to adenosine 5′-monophosphate with its d-ribose ring. When control reactions with an N-acetyl amino acid and valine methyl ester were run in organic solvent, the diastereoselectivity was found to be lower, with diastereomeric ratios≤62 : 38. The results from the exploratory study thus indicate that the ribonucleotide residue not only facilitates the coupling of lipophilic amino acids in aqueous medium but also the formation of a homochiral dipeptide. The methodology described here may be used to search for other stereoselective reactions that shed light on the origin of homochirality.

Life from crystals? Crystallization on mineral surfaces could be a decisive moment at the emergence of the first informational polymers from cyclic nucleotide precursors. It is shown that H-form 3’,5’ cyclic guanosine monophosphate could accumulate from millimolar solutions in a crystalline form upon drying of droplets on various mineral surfaces on the early Earth. These organic crystals could provide favorable steric conditions for the subsequent polymerization step yielding short oligonucleotide sequences.

Abstract

Previous studies on the polymerization of 3’,5’ cyclic guanosine monophosphate (cGMP) demonstrated the potential of the compound in the abiotic generation of the first oligonucleotide sequences on the early Earth. These experiments were conducted under idealized laboratory conditions, which logically raises the question whether the same chemistry could take place in the harsh environment present on our planet in its earliest days. In the current study, we focus on the mineralogical context of this chemistry and show that numerous, but not all, common minerals assumed to be present on the early Earth could host the polymerization of H-form 3’,5’ cGMP. In particular, we have found that quartz varieties are especially suitable for this purpose, similar to andalusite, amphibole or micas. On the contrary, olivine, calcite, and serpentine-group minerals interfere with the studied polymerization chemistry. Our results show that crystallization on mineral surfaces, which is mainly a diffusion controlled process, determines the ability of 3’,5’ cGMP to polymerize. The observation that numerous amorphous and crystalline SiO₂ forms are compatible with the oligomerization chemistry suggests that the process could commonly occur in a wide range of primordial environments allowing for crystallization of the cyclic monomers from a dropping solution.

Nature Communications, Published online: 11 June 2021; doi:10.1038/s41467-021-23850-1

A major goal in Engineering Biology and Materials Science is the development of active, autonomous scaffolds that mimic those present in biological cells. Here the authors report a toolkit for programming the dynamic behaviour of nucleic acid scaffolds in minimal cell-like compartments.

We report on a set of rotaxanes with symmetrical axles equipped with a central amide group that installs E/Z stereoisomerism owing to the ring position along the axle. Isomerization by concomitant rotation about the amide bond and ring shuttling along the axle was thoroughly characterized in different solvents. The results trigger a discussion on core concepts, such as microscopic reversibility and transition state theory, and provide insights for designing molecules capable to transform and transmit motion between subcomponents.

Nature, Published online: 23 April 2021; doi:10.1038/d41586-021-01101-z

Don’t get bogged down in technical details, and balance the professional and the personal.

Volume 33, Issue 1-2, January - February 2021, Page 1-7
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The weak interlamellar interaction of covalent organic framework (COF) nanocrystals inhibit the construction of highly efficient ion/molecular sieving membranes owing to the inferior contaminant selectivity induced by defects in stacked COF membranes and stability issues. Here, a facile in situ molecularly soldered strategy was developed to fabricate defect-free ultrathin COF membranes with precise sieving abilities using the typical chemical environment for COF condensation polymerization and dopamine self-polymerization. The experimental data and density functional theory simulations proved that the reactive oxygen species generated during dopamine polymerization catalyze the nucleophilic reactions of the COF, thus facilitating the counter-diffusion growth of thin COF layers. Notably, dopamine can eliminate the defects in the stacked COF by soldering the COF crystals, fortifying the mechanical properties of the ultrathin COF membranes. The COF membranes exhibited ultrafast precision sieving for molecular separation and ion removal in both aqueous and organic solvents, which surpasses that of state-of-the-art membranes.

Phosphorylation of deoxyribonucleosides under plausible prebiotic conditions with diamidophosphate gives rise to 5′‐amidophosphorylated nucleotides and concomitantly to the 3′,5′‐linked DNA oligomers. This direct conversion of deoxynucleosides to DNA oligonucleotides in a single pot scenario—under conditions compatible with ribonucleosides—sets the stage for the potential emergence of RNA and DNA from mixtures of nucleosides.

Abstract

Recent demonstrations of RNA–DNA chimeras (RDNA) enabling RNA and DNA replication, coupled with prebiotic co‐synthesis of deoxyribo‐ and ribo‐nucleotides, have resurrected the hypothesis of co‐emergence of RNA and DNA. As further support, we show that diamidophosphate (DAP) with 2‐aminoimidazole (amido)phosphorylates and oligomerizes deoxynucleosides to form DNA—under conditions similar to those of ribonucleosides. The pyrimidine deoxynucleoside 5′‐O‐amidophosphates are formed in good (≈60 %) yields. Intriguingly, the presence of pyrimidine deoxynucleos(t)ides increased the yields of purine deoxynucleotides (≈20 %). Concomitantly, oligomerization (≈18–31 %) is observed with predominantly 3′,5′‐phosphodiester DNA linkages, and some (<5 %) pyrophosphates. Combined with previous observations of DAP‐mediated chemistries and the constructive role of RDNA chimeras, the results reported here help set the stage for systematic investigation of a systems chemistry approach of RNA–DNA coevolution.

A team has shown that slight alterations in transfer-RNA molecules (tRNAs) allow them to self-assemble into a functional unit that can replicate information exponentially. tRNAs are key elements in the evolution of early life-forms.

Nature Chemistry, Published online: 18 February 2021; doi:10.1038/s41557-020-00633-7

Enzymatic reactions involving mononuclear metal hydrides are unknown in nature, despite the prevalence of such intermediates in synthetic transition-metal catalysed reactions. Now, it has been shown that zinc-containing carbonic anhydrase enzymes can catalyse hydride transfers from silanes to ketones with high enantioselectivity and there is evidence to support the intermediacy of a mononuclear zinc hydride.

The marriage of a switchable rotaxane and an AIEgen gave rise to the successful construction of a novel chiral [3]rotaxane‐based CPL switching system with large g _lum values, remarkable difference in the g _lum values, and excellent cycling ability.

Abstract

The construction of circularly polarized luminescence (CPL) switches with multiple switchable emission states and high dissymmetry factors (g _lum) has attracted increasing attention due to their broad applications in diverse fields such as the development of smart devices and sensors. Herein, a new family of AIE‐active chiral [3]rotaxanes were designed and synthesized, from which a novel CPL switching system was successfully constructed. The switching process was realized through the controlled motions of the chiral pillar[5]arene macrocycles along the axle through the addition or removal of the acetate anions, which not only modulated the chirality information transfer but also tuned the aggregations of the integrated [3]rotaxanes, thus resulting in reversible transformations between two emission states with both high photoluminescence quantum yields (PLQYs) and high dissymmetry factors (g _lum) values.

This Minireview unveils the story of ATP in the natural realm, its journey into the synthetic world for the realization of amazing structures and functions and its promises for next‐generation materials.

Abstract

Adenosine triphosphate (ATP) is a molecular unit of energy that drives various processes in the cellular environment. In this Minireview, we discuss the potential of physical and chemical properties of ATP for the development of bio‐inspired, synthetic ATP‐induced supramolecular systems with dynamic, stimuli‐responsive and active assembly characteristics. Molecular design rules for ATP‐induced assemblies with various architectures and their stimuli‐responsive structural and functional response are categorized. Special attention is given to the immense potential of ATP‐fuelled designs in the nascent field of transient/non‐equilibrium supramolecular polymerization for the synthesis of lifelike temporally programmable soft materials. Finally, the existing dearth and fate of ATP‐driven systems for future challenges are discussed.