title: The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region.
abstract: The gene-silencing effect of short interfering RNA (siRNA) is known to vary strongly with the targeted position of the mRNA. A number of hypotheses have been suggested to explain this phenomenon. We would like to test if this positional effect is mainly due to the secondary structure of the mRNA at the target site. We proposed that this structural factor can be characterized by a single parameter called "the hydrogen bond (H-b) index," which represents the average number of hydrogen bonds formed between nucleotides in the target region and the rest of the mRNA. This index can be determined using a computational approach. We tested the correlation between the H-b index and the gene-silencing effects on three genes (Bcl-2, hTF, and cyclin B1) using a variety of siRNAs. We found that the gene-silencing effect is inversely dependent on the H-b index, indicating that the local mRNA structure at the targeted site is the main cause of the positional effect. Based on this finding, we suggest that the H-b index can be a useful guideline for future siRNA design.
authors.affiliation: Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
authors.forename: Kathy Q
authors.initials: KQ
authors.lastname: Luo
authors.forename: Donald C
authors.initials: DC
authors.lastname: Chang
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D019926:Cyclin B / Q000096:biosynthesis / Q000235:genetics; D056744:Cyclin B1; D020868:Gene Silencing; D018390:Gene Targeting; D049452:Green Fluorescent Proteins; D006367:HeLa Cells; D006801:Humans; D006860:Hydrogen Bonding; D008164:Luminescent Proteins / Q000235:genetics; D008856:Microscopy, Fluorescence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019253:Proto-Oncogene Proteins c-bcl-2 / Q000037:antagonists & inhibitors / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012044:Regression Analysis; D013925:Thromboplastin / Q000235:genetics
chemical_list: C534699:CCNB1 protein, human; D019926:Cyclin B; D056744:Cyclin B1; D008164:Luminescent Proteins; D019253:Proto-Oncogene Proteins c-bcl-2; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D049452:Green Fluorescent Proteins; D013925:Thromboplastin