Enzymatic synthesis of DNA employing pyrophosphate-linked dinucleotide substrates

Comparative Analysis of Object Digitization Techniques Applied to the Characterization of Deformed Materials in Ballistic Tests

Several three-dimensional scanning methods have been developed and improved over the past 40 years. The peculiarities of each technique, associated with the computational advances of the period, allowed the increasing application and diffusion of the technology in several sectors, among them those related to metrology in ballistics and the testing of protective materials. The specific goal of such ballistic tests is to estimate the depth of indentation caused by projectiles. In particular, this study presents a comparative analysis between two three-dimensional optical scanning methods, taking into account the same object of interest. The comparative analysis was based on reference planes detected by Random Sample Consensus methodology in each cloud. By comparing the results of the different techniques, it was found for this case that three-dimensional reconstruction by stereo images estimated values closer to the real ones in comparison to those estimated by the structured light scanner, mainly due to the fact that, for three-dimensional reconstruction, the image acquisition was conducted statically.

The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA

Hypotheses of the origins of RNA and DNA are generally centred on the prebiotic synthesis of a pristine system (pre-RNA or RNA), which gives rise to its descendent. However, a lack of specificity in the synthesis of genetic polymers would probably result in chimeric sequences; the roles and fate of such sequences are unknown. Here, we show that chimeras, exemplified by mixed threose nucleic acid (TNA)-RNA and RNA-DNA oligonucleotides, preferentially bind to, and act as templates for, homogeneous TNA, RNA and DNA ligands. The chimeric templates can act as a catalyst that mediates the ligation of oligomers to give homogeneous backbone sequences, and the regeneration of the chimeric templates potentiates a scenario for a possible cross-catalytic cycle with amplification. This process provides a proof-of-principle demonstration of a heterogeneity-to-homogeneity scenario and also gives credence to the idea that DNA could appear concurrently with RNA, instead of being its later descendent.

Heterogeneous Pyrophosphate-Linked DNA-Oligonucleotides: Aversion to DNA but Affinity for RNA

Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by pyrophosphate as backbones of primordial oligomers, DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) were synthesized and investigated for their base-pairing properties. As expected, pyrophosphate inserts into the backbone compromised the thermal stability of ppDNA-DNA duplexes. In contrast, the ppDNA-RNA duplex exhibited, remarkably, duplex stability, even with accumulation of pyrophosphate linkages. This seems to be a consequence of an increase in the diameter of the double-helix with eight-bond-repeat units, and higher inclination of the base-pair axis with respect to the backbone in RNA (A-form), compared with that in DNA (B-form). These results suggest that pyrophosphate-linked oligonucleotides could harbor functional capabilities with implications for their roles in the origins of life and chemical biology.

Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach

TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.

Theoretical Analysis of a Self-Replicator With Reduced Template Inhibition Based on an Informational Leaving Group

The first non-enzymatic self-replicating systems, as proposed by von Kiedrowski (Angew Chem Int Ed Engl 25(10):932-935, 1986) and Orgel (Nature 327(6120):346-347, 1987), gave rise to the analytical background still used today to describe artificial replicators. What separates a self-replicating from an autocatalytic system is the ability to pass on structural information (Orgel, Nature 358(6383):203-209, 1992). Utilising molecular information, nucleic acids were the first choice as prototypical examples. But early self-replicators showed parabolic over exponential growth due to the strongly bound template duplex after template-directed ligation of substrates. We propose a self-replicating scheme with a weakly bound template duplex, using an informational leaving group. Such a scheme is inspired by the role of tRNA as leaving group and information carrier during protein synthesis, and is based on our previous experience with nucleotide chemistry. We analyse theoretically this scheme and compare it to the classical minimal replicator model. We show that for an example hexanucleotide template mirroring that is used by von Kiedrowski (Bioorganic chemistry frontiers, 1993) for the analysis of the classical minimal replicator, the proposed scheme is expected to result in higher template self-replication rate. The proposed self-replicating scheme based on an informational leaving group is expected to outperform the classical minimal replicator because of a weaker template duplex bonding, resulting in reduced template inhibition.

A synthetic substrate of DNA polymerase deviating from the bases, sugar, and leaving group of canonical deoxynucleoside triphosphates

The selection of artificial nucleic acids to be used for synthetic biology purposes is based on their structural and biochemical orthogonality to the natural system. We describe the example of a nucleotide mimic that functions as a substrate for polymerases and in which the carbohydrate moiety as well as the base moiety and the leaving group are different from that of the natural building blocks. The nucleotides themselves have two anomeric centers, and different leaving group properties of substituents at both anomeric centers need to be exploited to perform selective glycosylation reactions for their synthesis. In addition, the reversibility of the polymerase reaction at the level of the template has been demonstrated when pyrophosphate functions as leaving group and not with the alternative leaving groups.