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- W2805826204 abstract "The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop-a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids." @default.
- W2805826204 created "2018-06-13" @default.
- W2805826204 creator A5009175551 @default.
- W2805826204 creator A5026399646 @default.
- W2805826204 creator A5028117879 @default.
- W2805826204 creator A5039232730 @default.
- W2805826204 creator A5046990529 @default.
- W2805826204 creator A5071530185 @default.
- W2805826204 date "2018-06-09" @default.
- W2805826204 modified "2023-10-16" @default.
- W2805826204 title "An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch" @default.
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- W2805826204 doi "https://doi.org/10.1093/nar/gky490" @default.