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Single-molecule conductance of double-stranded RNA oligonucleotides

Subrata Chandra , Keshani G. Gunasinghe Pattiya Arachchillage , Evgenii Kliuchnikov , Farkhad Maksudov , Steven Ayoub , Valeri Barsegov and Juan M. Artés Vivancos
02/24/2022
Royal Society of Chemistry
 Abstract

RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA[thin space (1/6-em)]:[thin space (1/6-em)]RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA. Microsecond Molecular Dynamics simulations explain this difference and provide structural insights into the higher stability of DNA[thin space (1/6-em)]:[thin space (1/6-em)]RNA duplex with atomic level of detail. The rotations of 2′-OH groups of the ribose rings and the bases in RNA strands destabilize the duplex structure by weakening base stacking interactions, affecting charge transport, and making single-molecule conductance of dsRNA more variable (dynamic disorder). The results demonstrate that a powerful combination of state-of-the-art biomolecular electronics techniques and computational approaches can provide valuable insights into biomolecules’ biophysics with unprecedented spatial resolution.

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