title: A potent inhibitor of prothrombin gene expression as a result of standardized target site selection and design of antisense oligonucleotides.
abstract: The development of antisense oligonucleotides (AS-ODN) always had the limitation that because of complex mRNA secondary structures, not every designed AS-ODN inhibited the expression of its target. There have been many investigations to overcome this problem in the last few years. This produced a great deal of theoretical and empirical findings about characteristics of effective AS-ODNs in respect to their target regions but no standardized selection procedure of AS-ODN target regions within a given mRNA or standardized design of AS-ODNs against a specific target region. We present here a standardized method based on secondary structure prediction for target site selection and AS-ODN design, followed by validation of the antisense effect caused by our predicted AS-ODNs in cell culture. The combination of theoretical design and experimental selection procedure led to an AS-ODN that efficiently and specifically reduces prothrombin mRNA and antigen.
authors.affiliation: Institute of Biochemistry, Technical University Dresden, Bergstrasse 66, D-01069 Dresden, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Böhl
authors.forename: Bernd
authors.initials: B
authors.lastname: Schwenzer
mesh_terms: D045744:Cell Line, Tumor; D003627:Data Interpretation, Statistical; D004587:Electrophoresis, Agar Gel; D004797:Enzyme-Linked Immunosorbent Assay; D005786:Gene Expression Regulation / Q000187:drug effects*; D006801:Humans; D007700:Kinetics; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D011516:Prothrombin / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D021281:Quantitative Structure-Activity Relationship; D012333:RNA, Messenger / Q000737:chemistry / Q000187:drug effects / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D016376:Oligonucleotides, Antisense; D012333:RNA, Messenger; D011516:Prothrombin