Flexibility and arrangement—the interaction of ribonucleic acid and water

Flexibility and arrangement -- the interaction of ribonucleic acid and water
On the left is a structure of a RNA double helix. The blue spheres represent sodium counterions. On the right is an enlarged segment of the sugar-phosphate backbone of RNA, including bridging water molecules. Vibrations of the RNA backbone serve as sensitive real time probes for mapping the influence of the neighboring water molecules on RNA's structure and dynamics. Credit: MBI

Ribonucleic acid (RNA) plays a key role in biochemical processes that occur at the cellular level in a water environment. Mechanisms and dynamics of the interaction between RNA and water were now revealed by vibrational spectroscopy on ultrashort time scales and analyzed by in-depth theory.

Ribonucleic acid (RNA) represents an elementary constituent of biological cells. While deoxyribonucleic acid (DNA) serves as the carrier of genetic information, RNA displays a much more complex biochemical functionality. This includes the transmission of information in the form of mRNA, RNA-mediated catalytic function in ribosomes, and the encoding of genetic information in viruses. RNA consists of a sequence of organic nucleobase molecules held together by a so-called backbone consisting of phosphate and sugar groups. Such a sequence can exist as a single strand or in a paired double-helix geometry. Both forms are embedded in a water shell and their phosphate and sugar groups are distinct docking points for . The structure of the water shell fluctuates on a time scale of a few tenths of a picosecond. The interactions of RNA and water and their role for the formation of three-dimensional RNA structures are only understood insufficiently and difficult to access by experiment.

Scientists from the Max Born Institute have now observed the interaction of RNA with its water shell in real time. In their new experimental method, vibrations of the RNA backbone serve as sensitive noninvasive probes of the influence of neighboring water molecules on the structure and dynamics of RNA. The so-called two-dimensional infrared spectroscopy allows for mapping the time evolution of vibrational excitations and for determining molecular interactions within RNA and between RNA and water. The results show that water molecules at the RNA surface perform tipping motions, so-called librations, within a fraction of a picosecond whereas their local spatial arrangement is preserved for a time range longer than 10 ps. This behavior deviates strongly from that of neat water and is governed by the steric boundary conditions set by the RNA surface. Individual water molecules connect neighboring phosphate groups and form a partly ordered structure which is mediated by their coupling to the sugar units.

Flexibility and arrangement -- the interaction of ribonucleic acid and water
The 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. Credit: MBI

The librating water generate an electrical force by which the water fluctuations are transferred to the vibrations of RNA. The different backbone vibrations display a diverse dynamical behavior which is determined by their local water environment and reflects its heterogeneity. RNA vibrations also couple mutually and exchange energy among themselves and with the water shell. The resulting ultrafast redistribution of excess energy is essential for avoiding a local overheating of the sensitive macromolecular structure. This complex scenario was analyzed by detailed theoretical calculations and simulations which, among other results, allowed for the first complete and quantitative identification of the different vibrations of the RNA backbone. Comparative experiments with DNA reveal similarities and characteristic differences between these two elementary biomolecules, showing a more structured arrangement around RNA. The study highlights the strong potential of non-invasive time-resolved for unraveling the interplay of and dynamics in complex biomolecular systems on molecular length and time scales.


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More information: Eva M. Bruening et al, Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study, The Journal of Physical Chemistry Letters (2018). DOI: 10.1021/acs.jpclett.7b03314
Provided by Forschungsverbund Berlin
Citation: Flexibility and arrangement—the interaction of ribonucleic acid and water (2018, January 24) retrieved 27 June 2019 from https://phys.org/news/2018-01-flexibility-arrangementthe-interaction-ribonucleic-acid.html
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