The stability of RNA hairpin loops containing A–U–G: An–U–G–Um

✍ Scribed by Eric Wickstrom; Ignacio Tinoco Jr.

• Book ID: 102762593
• Publisher: Wiley (John Wiley & Sons)
• Year: 1974
• Tongue: English
• Weight: 875 KB
• Volume: 13
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1974.360131116

✦ Synopsis

RNA oligomers with the sequence AJJ-G-Urn, n = 7-9, m = 5-10, have been synthesized and found to form hairpin loops in 21 mM or 101 mM Na+. The hairpin loops displayed melting temperatures 13'-29'C greater than that of the hairpin loop AsCs-U6 in the same solvent. The increased stability of these hairpin loops is attributed to the presence of the trinucleotide A-U-G in the loop.

Circular dichroism (CD) spectra were taken of the hairpin loops ATU-G-U~,~,~, As-U-G-U6,7,8, and Ag-U-G-Us in 21 mM Na+, and compared with circular dichroism spectra of A6-U6 in 1 M Na+. Difference spectra were calculated between each A,,-U-G-Urn and 11.5 mM (nucleotide) As& at similar temperatures and identical singlestrand fract,ions to give the "experimental" CD spectrum of the unbase-paired nuclectides in the loop, assuming, five, six, or seven base pairs. CD spectra were calculated for each of the assumed unbase-paired sequences using the measured CD spectra of ApA, A-U-G, A, and U, and compared with the experimental spectra. The best agreement was found for hairpin-loop models containing five base pairs and five to eight unbase-paired nucleotides in the loop.