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A method for estimating the nearest neighbor base-pair content of RNAs using CD and absorption spectroscopy

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

Publisher: Wiley (John Wiley & Sons)
Year: 1991
Tongue: English
Weight: 947 KB
Volume: 31
Category: Article
ISSN: 0006-3525
DOI: 10.1002/bip.360310403

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✦ Synopsis

SYNOPSIS

CD and absorption spectra are sensitive to the secondary structure of RNAs. By fitting the spectra contained in our basis set to the CD and absorption spectra of an RNA of known sequence, we could determine the fractions of base pairs, the fractions of each of the nearest neighbor base pairs, and the fractions of the single-stranded nucleotides in that RNA. The basis set included 58 CD and 58 absorption spectra. The fitting was done with a guided selection routine. The estimated error was about 0.05 for predicting the fractions of the nearest neighbor base pairs, 0.06 for predicting the fractions of A * U, G * C, and G -U base pairs, and 0.04 for predicting the fractions of the single-stranded nucleotides.

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✍ Kenneth H. Johnson; Donald M. Gray 📂 Article 📅 1991 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 742 KB

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, an