Figure 1.

Self-Folding of (+)RNA5 A/California/04/2009 (H1N1) and siRNAs Target Regions

Secondary structure of (+)RNA5 A/California/04/2009 (H1N1) was predicted by Dynalign mode in RNAstructure 6.1 based on type A base pairs conservation data calculated from the previously determined (+)RNA5 secondary structure of A/Vietnam/1203/2004 (H5N1) strain. Target regions for designed siRNAs are marked with orange lines. For the RNA secondary structure model, the predicted accessible nucleotides are marked by a color-coded system based on reactiveness to chemical reagents, as well as isoenergetic microarray mapping results obtained for (+)RNA5 A/Vietnam/1203/2004 (H5N1). Symbols: red circles, predicted strong reactivity; green circles, medium reactivity; black squares, high accessibility to microarray probe; blue squares, moderate accessibility to microarray probe.