title: Design of LNA-modified siRNAs against the highly structured 5' UTR of coxsackievirus B3.
abstract: This study describes a strategy to develop LNA-modified small interfering RNA (siRNAs) against the highly structured 5' UTR of coxsackievirus B3 (CVB-3), which is an attractive target site due to its high degree of conservation. Accessible sites were identified based on structural models and RNase H assays with DNA oligonucleotides. Subsequently, LNA gapmers, siRNAs, siLNAs and small internally segmented interfering RNA (sisiLNAs) were designed against sites, which were found to be accessible in the in vitro assays, and tested in reporter assays and experiments with the infectious virus. The best siLNA improved viability of infected cells by 92% and exerted good antiviral activity in plaque reduction assays.
authors.affiliation: Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany.
authors.forename: Mariola
authors.initials: M
authors.lastname: Dutkiewicz
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Grunert
authors.forename: Heinz
authors.initials: H
authors.lastname: Zeichhardt
authors.forename: Suzy W
authors.initials: SW
authors.lastname: Lena
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.forename: Jens
authors.initials: J
authors.lastname: Kurreck
mesh_terms: D020121:5' Untranslated Regions / Q000037:antagonists & inhibitors* / Q000235:genetics; D000818:Animals; D000998:Antiviral Agents / Q000737:chemistry / Q000494:pharmacology*; D002470:Cell Survival / Q000187:drug effects / Q000235:genetics; D029822:Enterovirus B, Human / Q000187:drug effects* / Q000235:genetics / Q000502:physiology; D006367:HeLa Cells; D006801:Humans; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics* / Q000494:pharmacology; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics* / Q000494:pharmacology; D014779:Virus Replication / Q000187:drug effects / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D000998:Antiviral Agents; D009841:Oligonucleotides; D034741:RNA, Small Interfering; C527207:amino-LNA