Biology subjects

Mast, C. B.

Publications and source records attributed to Mast, C. B..

4 recordsLinked to original sources

bioRxiv2024

Heat flows solubilize apatite to boost phosphate availability for prebiotic chemistry

Phosphorus is an essential building block of the most prominent biomolecules, such as polynucleic acids, and has likely played that role since the beginning of life. Despite this importance for prebiotic chemistry, phosphate could not be supplied by the atmosphere, and had to be fueled mainly by geological phosphate sources. However, phosphorus was scarce in Earths rock record and often bound in poorly soluble minerals, with the calcium phosphate mineral apatite as key example. While specific chemical boundary conditions that bind calcium have been used to address this so-called phosphate problem, a fundamental process that solubilizes and enriches phosphate from geological sources remains elusive. Here, we show that ubiquitous heat flows through rock cracks can liberate phosphate from apatite by the selective removal of calcium. Phosphates surprisingly strong thermophoresis not only achieves its 100-fold up-concentration in aqueous solution, in particular it also boosts its solubility by two orders of magnitude. We show that the heat-flow-solubilized phosphate can feed the synthesis of trimetaphosphate, increasing the conversion 260-fold compared to the thermal equilibrium case. Heat flows thus enhance solubility as a geological parameter to unlock apatites as phosphate source for prebiotic chemistry, providing a key element in solving early lifes phosphate problem.

biophysics↗

bioRxiv2024

Prebiotic gas flow environment enables isothermal nucleic acid replication

Nucleic acid replication is a central process at the origin of life. On early Earth, replication is challenged by the dilution of molecular building blocks and the difficulty of separating daughter from parent strands, a necessity for exponential replication. While thermal gradient systems have been shown to address these problems, elevated temperatures lead to degradation. Also, compared to constant temperature environments, such systems are rare. The isothermal system studied here models an abundant geological environment of the prebiotic Earth, in which water is continuously evaporated at the point of contact with the gas flows, inducing up-concentration and circular flow patterns at the gas-water interface through momentum transfer. We show experimentally that this setting drives a 30-fold accumulation of nucleic acids and their periodic separation by a 3-fold reduction in salt and product concentration. Fluid dynamic simulations agree with observations from tracking fluorescent beads. In this isothermal system, we were able to drive exponential DNA replication with Taq polymerase. The results provide a model for a ubiquitous non-equilibrium system to host early Darwinian molecular evolution at constant temperature.

biophysics↗

bioRxiv2022

Selection of the Early Genetic Code by Ultraviolet Light

The DNA sequences available in the prebiotic era were the genomic building blocks of the first life forms on Earth and have therefore been a matter of intense debate.1,2 On the surface of the Early Earth, ultraviolet (UV) light is a key energy source3, which is known to damage nucleic acids4. However, a systematic study of the sequence selectivity upon UV exposure under Early Earth conditions is still missing. In this work, we quantify the UV stability of all possible canonical DNA sequences and derive information on codon appearance under UV irradiation as selection pressure. We irradiate a model system of random 8mers at 266 nm and determine its UV stability via next-generation sequencing. As a result, we obtain the formation rates of the dominant dimer lesions as a function of their neighboring sequences and find a strong sequence selectivity. On the basis of our experimental results, we simulate the photodamage of short proto-genomes of 150 bases length by a Monte Carlo approach. Our results strongly argue for UV compatibility of early life and allow the ranking of codon evolutionary models with respect to their UV resistance.

biophysics↗

bioRxiv2022

Sequence Dependent UV Damage of Complete Pools of Oligonucleotides

Understanding the sequence-dependent DNA damage formation requires to probe a complete pool of sequences over a wide dose range of the damage causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA with ultraviolet radiation at 266 nm and doses of up to 500 photons per base. At the dimer level our results confirm existing literature values, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow to predict their survival chances in high-UV environments.

biophysics↗