Facilitating RNA Structure Prediction with Microarrays

• Published in: Biochemistry (Easton) 2006-01, Vol.45 (2), p.581-593
• Main Authors: Kierzek, Elzbieta, Kierzek, Ryszard, Turner, Douglas H, Catrina, Irina E
• Format: Article
• Language: English
• Subjects: Base Pairing; Base Sequence; Binding Sites; Computational Biology - methods; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Methylation; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Ribonuclease H - chemistry; RNA Probes; RNA, Ribosomal, 5S - chemistry; RNA, Ribosomal, 5S - genetics; RNA, Ribosomal, 5S - metabolism; Thermodynamics; Thiouridine - analogs & derivatives; Thiouridine - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi051409+

Determining RNA secondary structure is important for understanding structure−function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2‘-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2‘-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.