An estimate of the nearest neighbor base-pair content of 5S RNA using CD and absorption spectroscopy

✍ Scribed by Kenneth H. Johnson; Donald M. Gray

• Publisher: Wiley (John Wiley & Sons)
• Year: 1991
• Tongue: English
• Weight: 742 KB
• Volume: 31
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360310404

✦ Synopsis

We analyzed the CD and uv absorption spectra of 5s RNA from Escherichia coli using the method developed in the preceding paper. The analysis of spectra of 5 s RNA at 20°C in O.1M NaClO,, 2.5 m M N a + (phosphate), pH 7.0, and 0.5 m M MgS04 gave 7 f 3.6 A * U base pairs, 25 f 3.6 G -C base pairs, and 7.5 k 3.6 G * U base pairs. Estimates of nearest neighbor base pairs were more consistent with the Pieler-Erdmann and the Gewirth-Moore secondary structure models than with the Fox-Woese or the Burns-Luoma-Marshall models.

We also examined the structure of 5s RNA as a function of temperature. The melting profile exhibited two transitions-one at about 35°C and one above 50°C. Our spectral data showed that helices I and I1 were stable during the first transition, and agreed with other data that helix I11 was the most likely helix to have melted. The results from this in-depth study of 5 s RNA indicate that our method of analysis should be useful for studying the secondary structures of other small, unmodified RNAs.