Stability of free and mineral-protected nucleic acids: Implications for the RNA world

Abstract

Using molecular dynamics simulations we study the structural stability of three different nucleic acids intercalated within a magnesium aluminium layered double hydroxide (LDH) mineral, at varying degrees of hydration, and free in aqueous solution. The nucleotides investigated are ribose nucleic acid (RNA), deoxyribose nucleic acid (DNA) and peptide nucleic acid (PNA), all in duplex form. Our simulations show that DNA has enhanced Watson-Crick hydrogen-bonding when intercalated within the LDH clay interlayers, compared with intercalated RNA and PNA, whilst the reverse trend is found for the nucleic acids in bulk water. The tendency for LDH to alter the stability of the three nucleic acids persists for higher temperature and pressure conditions. The uncharged protein backbone of PNA is found to have a detrimental effect on the overall stability of the duplex, as it experiences a greatly reduced electrostatic interaction with the charged LDH sheets compared to RNA and DNA. Assuming an RNA world, in which RNA preceded the DNA/protein world, at some point in time DNA must have taken over the role as the information storage molecule from RNA. These results suggest that a mineral based origin of life may have favoured DNA as the information-storage biomolecule over potentially competing RNA and PNA, providing a route to modern biology from the RNA world.

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

“…12B and C exhibit a right handed B-form which we can see from the incline of the base pairs to the axis (À1.21), the number of base pairs per turn (10.5) and the size of the major and minor grooves (22, 12 Å). 45 RNA, with its longer persistence length, does not display any A-or B-form helical style, but rather adopts many shorter kinks and grooves (as shown in Fig. 12D-F).…”

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

“…[ 49 ] and Swadling et al . [ 50 ] calculated the stability of RNA, DNA, and PNA in the interlayer of LDH and showed that DNA was the most stable. The authors also simulated the bonding between RNA and the surface of LDH composed of Mg 2+ and Al 3+ .…”

Inorganic nanolayers: structure, preparation, and biomedical applications

“…164 Previously, Swadling et al also proved the higher stability of DNA after intercalation by molecular dynamic simulation. 165 Zhang et al studied the structural stability of ribonucleic acid (RNA) before and after intercalation into LDHs by molecular simulation, and their study revealed that RNA had higher stability in LDHs compared to its free form. 166 …”