title: Optimization of antisense oligodeoxynucleotide structure for targeting bcr-abl mRNA.
abstract: Antisense oligodeoxynucleotides targeted to bcr-abl are potential ex vivo purging agents for use with autologous bone marrow transplantation in the treatment of chronic myeloid leukemia (CML). We investigated, in a cell-free system, the activity and nuclease resistance of phosphodiester, phosphorothioate, chimeric methylphosphonate/phosphodiester, and chimeric methylphosphonate/phosphorothioate antisense octadecamers directed against either b2a2 or b3a2 bcr-abl breakpoint RNAs. Certain chimeric compounds were shown to possess targeted activity broadly equal to the parent phosphodiester or phosphorothioate forms and greater resistance to the nucleases present in cell extracts. Selected chimeric structures were compared with phosphodiester and phosphorothioate analogues for antisense activity in human CML cells containing either b2a2 or b3a2 bcr-abl breakpoint mRNAs. We present results showing that all four structures can suppress bcr-abl mRNA level in vivo. The rank of in vivo activity is chimeric methylphosphonate/phosphodiester > or = phosphodiester > phosphorothioate > methylphosphonate/phosphorothioate. We show that b2a2 breakpoint RNAs can be more effectively targeted than b3a2 sequence RNAs both in vitro and in vivo and suggest that RNA secondary structure may be a possible explanation for this phenomenon.
authors.affiliation: Department of Biochemistry, University of Liverpool, UK.
authors.forename: R V
authors.initials: RV
authors.lastname: Giles
authors.forename: D G
authors.initials: DG
authors.lastname: Spiller
authors.forename: J A
authors.initials: JA
authors.lastname: Green
authors.forename: R E
authors.initials: RE
authors.lastname: Clark
authors.forename: D M
authors.initials: DM
authors.lastname: Tidd
mesh_terms: D001483:Base Sequence; D002474:Cell-Free System; D002851:Chromatography, High Pressure Liquid; D004355:Drug Stability; D004706:Endodeoxyribonucleases / Q000378:metabolism; D016044:Fusion Proteins, bcr-abl / Q000235:genetics*; D015973:Gene Expression Regulation, Leukemic / Q000187:drug effects*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology; D009943:Organophosphorus Compounds / Q000494:pharmacology*; D016133:Polymerase Chain Reaction; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000473:pathology; D012333:RNA, Messenger / Q000037:antagonists & inhibitors* / Q000235:genetics; D012334:RNA, Neoplasm / Q000037:antagonists & inhibitors* / Q000235:genetics; D013873:Thionucleotides / Q000494:pharmacology*; D014407:Tumor Cells, Cultured
chemical_list: D016376:Oligonucleotides, Antisense; D009943:Organophosphorus Compounds; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D013873:Thionucleotides; C032627:methylphosphonic acid; D016044:Fusion Proteins, bcr-abl; D004706:Endodeoxyribonucleases