RNA world: IR reveals watery shell

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  • Published: Feb 5, 2018
  • Author: David Bradley
  • Channels: Infrared Spectroscopy
thumbnail image: RNA world: IR reveals watery shell

Watery shell

Two-dimensional vibrational spectra of RNA (upper panel) and DNA (lower panel) in the frequency range of the sugar-phosphate vibrations of the backbone. The RNA spectrum displays additional bands (contours) along the frequency diagonal ν1=ν3 and a more complex distribution of off-diagonal peaks. In addition to the frequency positions the line shapes of the individual bands (contours) give insight in details of the interactions with neighboring water molecules.

Two-dimensional infrared spectroscopy allows the ultrashort time-scale evolution of vibrational excitations to be mapped in the interaction of RNA with water molecules to reveal how water molecules at the nucleic acid's surface undergo tipping motions or librations. Theoretical analysis of these librations offers new insights into the molecular dynamics of ribonucleic acid with implications for its role and behaviour in biochemical processes that occur at the cellular level in an aqueous environment.

Ribonucleic acid (RNA) represents is a fundamental component of life. Indeed, it is even considered in some origins of life theories to be the predecessor to the more well-known deoxyribonucleic acid (DNA). DNA, of course, is the carrier of genetic information for most organisms, whereas RNA has a much more complicated biochemical function, including not only the transmission of information in the form of mRNA, messenger-RNA, but also in mediating catalytic activity in ribosomes. It is also the only genetic material involved in the replication of RNA viruses. RNA comprises a string of organic nucleobase molecules held together by a phosphate and sugar backbone. The sequence can exist as a single strand or as a double-helix geometry of two strands entwined. Either way, both single and double strands exist in an aqueous shell with the phosphate and sugar groups acting as distinct docking points for water molecules. The aqueous shell is in constant flux on a timescale of a few tenths of a picosecond. This makes understanding the interactions of RNA and water molecules and the role of water in the three-dimensional structure of RNA difficult to investigate and as such they are only poorly understood at the present time.

Dynamic RNA

Now, a team from the Max Born Institute in Berlin, Germany, have observed the interaction of RNA with its water shell in real time. Using a novel experimental approach, the team has observed vibrations of the RNA backbone as it serves as a sensitive and non-invasive probe of the influence of neighbouring water molecules involved in shaping the structure and dynamics of the RNA. The IR spectra reveal how water molecules at the RNA surface undergo a tipping motion, the aforementioned librations, over a picosecond timescale. Despite these incredibly fast movements, the local spatial arrangement of the RNA and its watery shell is preserved for more than 10 picoseconds.

This behaviour deviates strongly from that of neat water and is governed by the steric boundary conditions set by the RNA surface, the team suggests. Individual water molecules connect the neighbouring phosphate groups and form a partly ordered structure which is mediated by their coupling to the sugar units. Moreover, the librating water molecules produce an electrical force that allows their movements to be transferred to vibrations of the RNA itself. The resulting shivers down the backbone show diverse dynamical behaviour which can be exposed by their local water environment and reflects its heterogeneity.

RNA versus DNA

The team also explains that the RNA vibrations couple mutually and exchange energy among themselves and with the water shell. This leads to an incredibly fast redistribution of excess energy, which precludes local overheating of the delicate macromolecular structure. The team's theoretical calculations and simulations reveal this complex scenario in great detail and show the similarities and differences between the RNA and DNA world. Ultimately, the research highlights the strong potential for non-invasive time-resolved vibrational spectroscopy for unwinding the behaviour of complex biomolecular systems at the molecular level and on such short timescales.

Related Links

J Phys Chem Lett 2018, 9. 583-587: "Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study"

Article by David Bradley

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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