RESUMEN
Chemical reaction networks (CRNs) have been proposed as an abstraction for molecular computing. DNA strand displacement (DSD) reactions are good candidates to realize this endeavor, since DNA strands can be wired to implement the desired dynamic behavior in a test tube. Specialists use simulators to help them design such chemical systems before experimental implementation. In this sense, we present the DNAr package, an alternative open-source tool, developed in R language, for users from multidisciplinary areas. The current version of our tool offers functions to simulate CRNs, convert a formal CRN into a DSD network, interpret results, export to Visual DSD, and create libraries. Here, we use the consensus CRN to show DNAr features and a neural network model to demonstrate scalability, simulating more than 600 chemical reactions in a few minutes.
Asunto(s)
ADN/metabolismo , Programas Informáticos , Algoritmos , Simulación por ComputadorRESUMEN
Plant mitochondrial and chloroplast genomes encode essential proteins for oxidative phosphorylation and photosynthesis. For proper cellular function, plant organelles must ensure genome integrity. Although plant organelles repair damaged DNA using the multi-enzyme Base Excision Repair (BER) pathway, the details of this pathway in plant organelles are largely unknown. The initial enzymatic steps in BER produce a 5'-deoxyribose phosphate (5'-dRP) moiety that must be removed to allow DNA ligation and in plant organelles, the enzymes responsible for the removal of a 5'-dRP group are unknown. In metazoans, DNA polymerases (DNAPs) remove the 5'-dRP moiety using their intrinsic lyase and/or strand-displacement activities during short or long-patch BER sub-pathways, respectively. The plant model Arabidopsis thaliana encodes two family-A DNAPs paralogs, AtPolIA and AtPolIB, which are the sole DNAPs in plant organelles identified to date. Herein we demonstrate that both AtPolIs present 5'-dRP lyase activities. AtPolIB performs efficient strand-displacement on a BER-associated 1-nt gap DNA substrate, whereas AtPolIA exhibits only moderate strand-displacement activity. Both lyase and strand-displacement activities are dependent on an amino acid insertion that is exclusively present in plant organellar DNAPs. Within this insertion, we identified that residue AtPollB-Lys593 acts as nucleophile for lyase activity. Our results demonstrate that AtPolIs are functionally equipped to play a role in short-patch BER and suggest a major role of AtPolIB in a predicted long-patch BER sub-pathway. We propose that the acquisition of insertion 1 in the polymerization domain of AtPolIs was a key component in their evolution as BER associated and replicative DNAPs.