NMR-based analysis of nucleotide π-stacking in a crowded environment: Implications for prebiotic reactions
The inherent heterogeneity of the prebiotic milieu is often overlooked when studying nonenzymatic reactions. However, it is important to note that the prebiotic soup of a putative ‘RNA World’ would have been replete with a plethora of molecules resulting from complex chemical syntheses, as well as exogeneous delivery. The presence of such background molecules could lead to pertinent phenomena such as molecular crowding, which can potentially affect how a reaction would advent in a crowded milieu. In the current study, we have analyzed the effect of crowding on the stacking ability of the RNA monomers, using Nuclear Magnetic Resonance (NMR) spectroscopy. In particular, DOSY and 13C-T1 relaxation studies are carried out to understand the formation of pseudo-oligomeric species at higher nucleotide concentrations and the effect of crowding agents on such oligomers. Our findings corroborate that the purine monomers possess better stacking efficiency than pyrimidine based monomers. Significantly, this competence is further enhanced in the presence of a crowding agent. Interestingly, this enhanced stacking could result in higher sequestration of the purine monomers, putting their ready availability for relevant nonenzymatic polymerization and replication reactions into question. Taken together, this study demonstrates the need for systematic biophysical characterization of molecular crowding in the context of prebiotically pertinent processes. Unraveling such phenomena is essential to gather a real understanding of how the transition from abiotic to biotic, would have happened during the origin of life.
Steps to reproduce
This data set contains all the raw NMR data used in the manuscript. The data are grouped as per experiment types which are: 1) T1, 2) DOSY and, 3) 1H-GMP. Each of these contains the folders for nucleotide which contain subfolders labeled with numbers, details of which are available in the info.docx file included in the main folder of the data-set. The NMR data in the data-set can be processed using NMR data processing software (I have used Topspin3.2 or 3.5) using standard processing protocols. The Diffusion coefficients and the 13C-T1 rates are calculated by fitting the intensity data to the appropriate equations as mentioned in the manuscript.