Dataset Information

Exploring the Influence of Intermolecular Interactions in Prebiotic Chemistry Using Laser Spectroscopy and Calculations.

ABSTRACT: One of the most fascinating questions in chemistry is why nature chose CGAT as the alphabet of life. Very likely, such selection was the result of multiple factors and a long period of refinement. Here, we explore how the intermolecular interactions influenced such process, by characterizing the formation of dimers between adenine, theobromine and 4-aminopyrimidine. Using a combination of mass-resolved excitation spectroscopy and DFT calculations, we determined the structure of adenine-theobromine and 4-aminopyrimidine-theobromine dimers. The binding energy of these dimers is very close to the canonical adenine-thymine nucleobases. Likewise, the dimers are able to adopt Watson-Crick conformations. These findings seem to indicate that there were many options available to build the first versions of the informational polymers, which also had to compete with other molecules, such as 4-aminopyrimidine, which does not have a valid attaching point for a saccharide. For some reason, nature did not select the most strongly-bonded partners or if it did, such proto-bases were later replaced by the nowadays canonical CGAT.

SUBMITTER: Camiruaga A

PROVIDER: S-EPMC9299682 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Ceramide is a major actor in the sphingolipid signaling pathway elicited by various kinds of cell stress. Under those conditions ceramide (Cer) is produced in the plasma membrane as a product of sphingomyelin (SM) hydrolysis, and this may lead to apoptosis. Thus, SM and Cer coexist in the membrane for some time, and they are known to separate laterally from the (more abundant) glycerolipids, giving rise to highly rigid domains or platforms. The properties of these domains/platforms are rather well understood, but the underlying SM:Cer molecular interactions have not been explored in detail. Infrared (IR) spectroscopy is a powerful analytical technique that provides information on all the chemical groupings in a molecule, and that can be applied to membranes and lipid bilayers in aqueous media. IR spectra can be conveniently retrieved as a function of temperature, thus revealing the thermotropic transitions of SM and its mixtures with Cer. Four regions of the IR spectrum of these sphingolipids have been examined, two of them dominated by the hydrophobic regions in the molecules, namely the C-H stretching vibrations (2800-3000 cm-1), and the CH2 scissoring vibrations (1455-1485 cm-1), and two others arising from chemical groups at the lipid-water interface, the sphingolipid amide I band (1600-1680 cm-1), and the phosphate vibrations in the 1000-1110 cm-1 region. The latter two regions have been rarely studied in the past. The IR data from the hydrophobic components show a gel (or ripple)-fluid transition of SM at 40 °C, that is shifted up to about 70 °C when Cer is added to the bilayers, in agreement with previous studies using a variety of techniques. IR information concerning the polar parts is more interesting. The amide I (carbonyl) band of pure SM exhibits a maximum at 1638 cm-1 at room temperature, and its position is shifted by about 10 cm-1 in the presence of Cer. Cer causes also a change in the overall band shape, but no signs of band splitting are seen, suggesting that SM and Cer carbonyl groups are interacting tightly, presumably through H-bonds. The 1086 cm-1 band, corresponding to PO2- vibrations, appears more stable in SM than in DPPC, and it is further stabilized by Cer, again suggesting an important role of H-bonds in the formation of SM:Cer clusters. Thus, SM and Cer can interact through their polar headgroups, in a way that is not accessible to other lipid classes.

Dataset Information

Exploring the Influence of Intermolecular Interactions in Prebiotic Chemistry Using Laser Spectroscopy and Calculations.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets