Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras

Development of Dipeptide-Based Liquid Droplets and Fibrils as Enzyme-Mimics

Coacervates are liquid droplets formed by liquid-liquid phase separation (LLPS) and are often considered as model protocells. The physicochemical environment inside coacervates has a unique microenvironment that can accelerate the chemical reactions. However, coacervates are generally made of multiple macromolecular components, and designing short peptide analogues capable of self-coacervation has proven difficult. Here a simple dipeptide for phase separation, made of one hydrophobic residue attached with polar histidine residue is presented. This dipeptide can self-coacervate into micrometre-sized liquid droplets. These droplets can act as microreactor for the hydrophobic reactants. This work delineates a minimalistic peptide that can self-assemble to coacervate resembling protocell. The designer peptide also shows fibrillar assembly at relatively low concentration at different pHs. The fibrillar morphologies with appended histidine residues make them an efficient catalyst as esterase mimic. Overall, this study provides a unique strategy for minimalistic design for supramolecular catalysts with applications in enzymology and synthetic biology.

Traces of a Primitive RNA Ring in Current Genomes

(1) Background: Previous theoretical studies have provided arguments for the existence of a circular or hairpin RNA that could have served as a primitive informational and functional molecule at the origin of life. The present article consists of searching in current genomes for RNAs closest to this primitive RNA in terms of the occurrence of similar nucleotide motifs. (2) Methods: In searching for the smallest possible RNA capable of interacting with amino acids in the construction of the peptides of the primitive living world, we found a circular docosamer RNA molecule (length 22), which we called AL (for ALpha or Archetypal Loop). Then, we started to systematically track AL relics in current genomes in the form of motifs like pentamers or pairs of consecutive codons in common with AL. (3) Results: The sequence correspondence between AL and RNA sequences of organisms from different kingdoms of life (Archaea, Bacteria, and Eukarya) was found with high statistical significance, with a frequency gradient depending on both the antiquity of the species and the functional necessity of the genes. (4) Conclusions: Considering the suitability of AL as a candidate for being a primitive sequence, and the evolution of the different species considered, we can consider the AL RNA as a possible actor that favored the appearance of life on Earth.

Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.