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The ability to synthesize and propagate genetic information encoded in the framework of xeno-nucleic acid (XNA) polymers would inform a wide range of topics from the origins of life to synthetic biology. While directed evolution has produced examples of engineered polymerases that can accept XNA substrates, these enzymes function with reduced activity relative to their natural counterparts. Here, we describe a biochemical strategy that enables the discovery of engineered polymerases with improved activity for a given unnatural polymerase function. Our approach involves identifying specificity determining residues (SDRs) that control polymerase activity, screening mutations at SDR positions in a model polymerase scaffold, and assaying key gain-of-function mutations in orthologous protein architectures. By transferring beneficial mutations between homologous protein structures, we show that new polymerases can be identified that function with superior activity relative to their starting donor scaffold. This concept, which we call scaffold sampling, was used to generate engineered DNA polymerases that can faithfully synthesize RNA and TNA (threose nucleic acid), respectively, on a DNA template with high primer-extension efficiency and low template sequence bias. We suggest that the ability to combine phenotypes from different donor and recipient scaffolds provides a new paradigm in polymerase engineering where natural structural diversity can be used to refine the catalytic activity of synthetic enzymes.

Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.

Feeding habits of the four most abundant deep-sea demersal trawl-caught macrourids on Chatham Rise, New Zealand, were examined from stomach contents. Two species were predominantly benthic foragers: Coelorinchus bollonsi on infaunal and epifaunal polychaetes, and C. aspercephalus on epifaunal crustaceans; and two species were predominantly mesopelagic foragers; C. oliverianus on calanoid copepods, and Lepidorhynchus denticulatus on mesopelagic crustaceans. The most important predictors of diet variability were identified using distance-based linear models and included areal predictors in all four species, fish size in C. aspercephalus, C. bollonsi and L. denticulatus, and sample year in C. bollonsi. Cluster analyses showed that the diets of C. aspercephalus and C. bollonsi were most distinct. There was a greater interspecific similarity in diet in the spatial and fish size subgroups of C. oliverianus and L. denticulatus, than at the species level. Failing to account for areal, temporal, and ontogenetic variability in diets may bias evaluations of resource competition., Author(s): Darren W. Stevens [sup.1] , Matthew R. Dunn [sup.1] Author Affiliations: (1) grid.419676.b, 0000000092525808, National Institute of Water and Atmospheric Research Ltd, , 301 Evans Bay Parade, Greta Point, [...]