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

0495518 - BFÚ 2019 RIV GB eng J - Journal Article
Krepl, Miroslav - Voegele, J. - Kruse, Holger - Duchardt-Ferner, E. - Woehnert, J. - Šponer, Jiří
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.
Nucleic Acids Research. Roč. 46, č. 13 (2018), s. 6528-6543. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GBP305/12/G034; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : trna(asp) anticodon hairpin * amber force-field * stem-loop-v * molecular-dynamics * watson-crick * transfer-rna * nucleic-acids * active-site * base-pairs * rapid identification
OECD category: Biochemistry and molecular biology
Impact factor: 11.147, year: 2018

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.
Permanent Link: http://hdl.handle.net/11104/0288484