Facilitating RNA structure prediction with microarrays.
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.
Kierzek
Elzbieta
E
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Kierzek
Ryszard
R
Turner
Douglas H
DH
Catrina
Irina E
IE
D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D015347:RNA Probes; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry; D013816:Thermodynamics; D013891:Thiouridine / Q000031:analogs & derivatives / Q000737:chemistry
C105273:2-thiouridine; D015347:RNA Probes; D012341:RNA, Ribosomal, 5S; D013891:Thiouridine; D016914:Ribonuclease H