| Autor: |
Andac CA; Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul, Turkiye., Hornemann U; Department of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA., Noyanalpan N; Department of Medicinal Chemistry, School of Pharmacy, Gazi University, Ankara, Turkiye., Stringfellow TC; NMR Facility, School of Pharmacy, University of Wisconsin-Madison, WI, USA. |
| Jazyk: |
angličtina |
| Zdroj: |
Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2024 Apr; Vol. 42 (7), pp. 3659-3681. Date of Electronic Publication: 2023 Jun 06. |
| DOI: |
10.1080/07391102.2023.2214231 |
| Abstrakt: |
A 17-mer RNA hairpin (5'GGGAGU X AGCGGCUCCC3') carrying 3- N -methyluridine (m3U) at position X (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. 1 H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (∼5-6%) ACSL conformations. Exchange rate constant (k ex ) for interconversion between P and S states is 112 sec -1 (<Δω ∼454 rad/sec), confirming a slow exchange regime between the two states. Forward (k PS ) and backward (k SP ) rate constants are 49.166 sec -1 and 62.792 sec -1 , respectively, leading to a longer life-time (20.339 msec) for the P-state and a shorter life-time (15.926 msec) for the S-state. In accordance with conformational populations determined by 1 H-NMR, dynamics of the P/S/tertiary states of m3U7-RNA and its wild-type counterpart (wt-RNA) were studied by three independent MD production simulations. Cluster analysis revealed that wt-RNA reflects the structural characteristics of the ACSL region of tRNAs. The P-state of m3U7-RNA was found to be structurally similar to wt-RNA but lacks an intraloop H-bond between m3U7 and C10 (U33 and nt36 in tRNAs). In the S-state of m3U7-RNA, m3U7 flips out of the loop region. O-state loop conformations of m3U7-RNA were also clustered (4.8%), wherein the loop nucleotides m3U7.A8.G9.C10.G11 stack one after another. We propose that the O-state of m3U7-RNA is the most suitable conformation that makes the loop accessible for complementary nucleotides and for non-enzymatic primordial replication of small circular RNAs.Communicated by Ramaswamy H. Sarma. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
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