Open Access Research article

Side chain modified peptide nucleic acids (PNA) for knock-down of six3 in medaka embryos

Sebastian Dorn1, Narges Aghaallaei1, Gerlinde Jung2, Baubak Bajoghli13, Birgit Werner4, Holger Bock4, Thomas Lindhorst4 and Thomas Czerny12*

Author Affiliations

1 Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria

2 Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria

3 Current address: Director’s Research Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany

4 Ugichem GmbH, Mitterweg 24, A-6020, Innsbruck, Austria

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BMC Biotechnology 2012, 12:50  doi:10.1186/1472-6750-12-50

Published: 17 August 2012



Synthetic antisense molecules have an enormous potential for therapeutic applications in humans. The major aim of such strategies is to specifically interfere with gene function, thus modulating cellular pathways according to the therapeutic demands. Among the molecules which can block mRNA function in a sequence specific manner are peptide nucleic acids (PNA). They are highly stable and efficiently and selectively interact with RNA. However, some properties of non-modified aminoethyl glycine PNAs (aegPNA) hamper their in vivo applications.


We generated new backbone modifications of PNAs, which exhibit more hydrophilic properties. When we examined the activity and specificity of these novel phosphonic ester PNAs (pePNA) molecules in medaka (Oryzias latipes) embryos, high solubility and selective binding to mRNA was observed. In particular, mixing of the novel components with aegPNA components resulted in mixed PNAs with superior properties. Injection of mixed PNAs directed against the medaka six3 gene, which is important for eye and brain development, resulted in specific six3 phenotypes.


PNAs are well established as powerful antisense molecules. Modification of the backbone with phosphonic ester side chains further improves their properties and allows the efficient knock down of a single gene in fish embryos.

PNA; Knock down; Medaka; Six3