The beauty of nucleic acids and the scope of their application

Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System

In this study, they coupled DNA replication with gene expression in cell-free system. They performed the experiments in water-in-oil droplets in serial dilution cycles. Circular DNA is replicated through rolling-circle replication followed by homologous recombination catalysed by the proteins, phi29 DNA polymerase, and Cre recombinase expressed from the DNA. Isolated circular DNAs accumulated several common mutations that exhibited higher replication abilities than the original DNA due to its improved ability as a replication template, increased polymerase activity, and a reduced inhibitory effect of polymerization by the recombinase.

https://pubs.acs.org/doi/10.1021/acssynbio.1c00430

Fuel-Driven Dynamic Combinatorial Libraries 

The authors analyse the fuel-driven oligomerisation of isophthalic acid. They determine that while oligomer formation is mainly driven by fuel activation, its relaxation back to equilibrium (isophthalic acid monomers) is not symmetrical. Instead of hydrolysing, the relaxation is produced by the "reshuffling" of the longest oligomers with shorter ones to produce average length oligomers. They also demonstrate that oligomers longer than 3 units can produce some sort of feedback interaction, creating insoluble complexes that resist better the relaxation to equilibrium. Of course, they also have some leak reactions that produce an undesired subproduct with a constant rate. The paper presents an interesting view on a well established far-from-equilibrium assembly reaction as the oligomerisation of isophthalic acid. However, the control over the oligomerisation process is not impressive; the concentration of oligomers decreases exponentially with length.

https://pubs.acs.org/doi/10.1021/jacs.1c01616

A Comparison of Genotype-Phenotype Maps for RNA and Proteins

This paper attempts to identify differences and similarities in the RNA and HP-lattice Protein GP maps. To ensure appropriate comparison, the RNA GP Map has only 2 alphabets. Similarities include the tendency for some simple phenotypes to be highly overrepresented in genotype space. One interesting difference is that whereas most sequences in the RNA GP-Map tend to fold to a unique structure, only a small subset of sequences in the HP GP-Map do so. The average size of genotype sets are much smaller in the HP GP Map, and it takes more mutations from a given sequence to cover the whole phenotype space than in the RNA GP Map.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328697/