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Updated: Aug 6, 2026

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
Published on: February 27, 2026
Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of
Shenghua Duan1, David H Mathews, Douglas H Turner
1Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
Abstract:
A method to deduce RNA secondary structure on the basis of data from microarrays of 2'-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3' end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides.
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