Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3-N-methyluridine nucleotide residue in the loop region

Andac C. A., Hornemann U., NOYANALPAN N., Stringfellow T. C.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, cilt.42, sa.7, ss.3659-3681, 2024 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 42 Sayı: 7
  • Basım Tarihi: 2024
  • Doi Numarası: 10.1080/07391102.2023.2214231
  • Dergi Adı: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, MEDLINE
  • Sayfa Sayıları: ss.3659-3681
  • Anahtar Kelimeler: ACSL region of tRNAs, m3U force field, NMR kinetics, RNA hairpin, RNA structure
  • Gazi Üniversitesi Adresli: Evet

Özet

A 17-mer RNA hairpin (5'GGGAGUXAGCGGCUCCC3') 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 (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. H-1-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (similar to 5-6%) ACSL conformations. Exchange rate constant (k(ex)) for interconversion between P and S states is 112 sec(-1) (