The activity of DNA polymerase underlies numerous biotechnologies, cell division, and therapeutics, yet the enzyme remains incompletely understood. We demonstrate that both thermostable and mesophilic DNA polymerases readily utilize deoxyribonucleoside diphosphates (dNDPs) for DNA synthesis and inorganic phosphate for the reverse reaction, that is, phosphorolysis of DNA. For Taq DNA polymerase, the s of the dNDP and phosphate substrates are ∼20 and 200 times higher than for dNTP and pyrophosphate, respectively. DNA synthesis from dNDPs is about 17 times slower than from dNTPs, and DNA phosphorolysis about 200 times less efficient than pyrophosphorolysis. Such parameters allow DNA replication without requiring coupled metabolism to sequester the phosphate products, which consequently do not pose a threat to genome stability. This mechanism contrasts with DNA synthesis from dNTPs, which yield high-energy pyrophosphates that have to be hydrolyzed to phosphates to prevent the reverse reaction. Because the last common ancestor was likely a thermophile, dNDPs are plausible substrates for genome replication on early Earth and may represent metabolic intermediates later replaced by the higher-energy triphosphates.
A series of N-alkoxybenziminoyl chlorides were synthesized and reacted with tributyltin hydride in the presence of AIBN to generate the corresponding N-alkoxybenziminoyl radicals. This methodology successfully generates the desired radicals, which undergo a rapid and highly efficient β-scission reaction, as shown by the formation of the corresponding nitriles and products derived from alkoxy radicals. The intermediate N-alkoxybenziminoyl radical could not be trapped by employing high concentrations of Bu3SnH or by using a hydrogen atom donating solvent such as toluene. The fast β-scission reaction was found to be independent of the structure of the iminoyl chloride. These results are different from studies on the similar N-alkyliminoyl radicals, which typically give products from both β-scission hydrogen atom transfer pathways. Using the data from this study as well as some reported rate constants for different hydrogen atom transfer (HAT) processes, we conclude that the lower limit for the rate constant for the β-scission process (k β) in N-alkoxybenziminoyl radicals is 2.5 × 107 s−1.
Metabolite-responsive RNA regulators with kinetically-controlled responses are widespread in nature. By comparison, very limited success has been achieved creating kinetic control mechanisms for synthetic RNA aptamer devices. Here, we show that kinetically-controlled RNA aptamer ribosensors can be engineered using a novel approach for multi-state, cotranscriptional folding design. The design approach was developed through investigation of 29 candidate p-aminophenylalanine-responsive ribosensors. We show that ribosensors can be transcribed in situ and used to analyze metabolic production directly from engineered microbial cultures, establishing a new class of cell-free biosensors. We found that kinetically-controlled ribosensors exhibited 5-10 fold greater ligand sensitivity than a thermodynamically-controlled device. And, we further demonstrated that a second aptamer, promiscuous for aromatic amino acid binding, could be assembled into kinetic ribosensors with 45-fold improvements in ligand selectivity. These results have broad implications for engineering RNA aptamer devices and overcoming thermodynamic constraints on molecular recognition through the design of kinetically-controlled responses.
Ribonucleic acid (RNA) molecules have diverse roles in biological systems. Although some code for proteins or act to translate codons to amino acids, others fold into specific shapes that endow them with the ability to catalyse specific chemical transformations. These catalytic RNAs, ribozymes, are responsible for protein synthesis, transfer RNA (tRNA) processing, self‐splicing of certain introns, self‐scission during rolling circle replication of some single‐stranded RNA viruses and cofactor‐dependent gene regulation in bacteria. Other ribozymes have been evolved in vitro to perform a wide variety of transformations. Two of these, tRNA aminoacylase and RNA polymerase ribozymes, are featured here because molecules with such capabilities are thought to have existed on early Earth, before proteins took over as the dominant biological catalysts. Most of the ribozymes have been shown to perform multiturnover catalysis and thus act as true enzymes, either in their natural, biological form or as engineered constructs. Key Concepts: RNA molecules can fold into specific conformations and accelerate chemical transformations, thus acting as catalytic biomacromolecules, ribozymes. Ribozymes can accelerate chemical reactions by many orders of magnitude. Many ribozymes are capable of multiturnover catalysis, acting as enzymes. Protein synthesis templated by mRNA is catalysed by ribosomal RNA. Most ribozymes are phosphoryl transferases. In vitro selected ribozymes have been shown to catalyse a wide variety of reactions. The existence of ribozymes supports the RNA World hypothesis.
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