A Novel RNA Motif Based on the Structure of Unusually Stable 2‘,5‘-Linked r(UUCG) Loops

• Published in: Journal of the American Chemical Society 2003-09, Vol.125 (38), p.11525-11531
• Main Authors: Denisov, Alexei Yu, Hannoush, Rami N, Gehring, Kalle, Damha, Masad J
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Base Sequence; Biological and medical sciences; Carbohydrate Conformation; Fundamental and applied biological sciences. Psychology; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Nucleic acids; RNA - chemistry; Rna, ribonucleoproteins
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja036207k

We have recently shown that hairpins containing 2‘,5‘-linked RNA loops exhibit superior thermodynamic stability compared to native hairpins comprised of 3‘,5‘-RNA loops [Hannoush, R. N.; Damha, M. J. J. Am. Chem. Soc. 2001, 123, 12368−12374]. A remarkable feature of the 2‘,5‘-r(UUCG) tetraloop is that, unlike the corresponding 3‘,5‘-linked tetraloop, its stability is virtually independent of the hairpin stem composition. Here, we determine the solution structure of unusually stable hairpins of the sequence 5‘-G1G2A3C4-(U5U6C7G8)-G9(U/T10)C11C12-3‘ containing a 2‘,5‘-linked RNA (UUCG) loop and either an RNA or a DNA stem. The 2‘,5‘-linked RNA loop adopts a new fold that is completely different from that previously observed for the native 3‘,5‘-linked RNA loop. The 2‘,5‘-RNA loop is stabilized by (a) U5·G8 wobble base pairing, with both nucleotide residues in the anti-conformation, (b) extensive base stacking, and (c) sugar−base and sugar−sugar contacts, all of which contribute to the extra stability of this hairpin structure. The U5:G8 base pair stacks on top of the C4:G9 loop-closing base pair and thus appears as a continuation of the stem. The loop uracil U6 base stacks above U5 base, while the cytosine C7 base protrudes out into the solvent and does not participate in any of the stabilizing interactions. The different sugar pucker and intrinsic bonding interactions within the 2‘,5‘-linked ribonucleotides help explain the unusual stability and conformational properties displayed by 2‘,5‘-RNA tetraloops. These findings are relevant for the design of more effective RNA-based aptamers, ribozymes, and antisense agents and identify the 2‘,5‘-RNA loop as a novel structural motif.