Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1046K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Lehmann, M. J.
Right arrow Articles by Sczakiel, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lehmann, M. J.
Right arrow Articles by Sczakiel, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 13 2597-2604
© 2000 Oxford University Press

Theoretical design of antisense genes with statistically increased efficacy

Maik Jörg Lehmann1, Volker Patzel1,* and Georg Sczakiel1,2

1Deutsches Krebsforschungszentrum, Forschungsschwerpunkt Angewandte Tumorvirologie, Im Neuenheimer Feld 242, D-69120 Heidelberg, Germany and 2Medizinische Universität zu Lübeck, Institut für Molekulare Medizin, Ratzeburger Allee 160, D-23538 Lübeck, Germany

Endogenous expression of antisense RNA represents one major way of applying antisense nucleic acids. To express antisense RNA intracellularly, recombinant antisense genes have to be designed and introduced into cells where the target RNA is encountered. Efficient annealing between the antisense RNA and the target RNA is crucial for efficacy and is strongly influenced by RNA structure. Here we extend structural rules for the design of in vitro transcribed antisense RNAs to the design of recombinant antisense genes. Intracellularly expressed antisense RNA transcripts contain a central antisense portion and additional flanking vector-derived sequences. A computer algorithm was generated to compose large sets of antisense genes, to calculate secondary structures of the transcribed sequences and to select for favorable structures of antisense RNA in terms of annealing and efficacy. The biological test system to measure efficiency of antisense genes was human immunodeficiency virus type 1 (HIV-1) replication in 293T cells. When considering the lower intracellular steady-state levels of favorably structured endogenous transcripts, an antisense effect against HIV-1 replication was observed that was up to 60-fold stronger than that measured for predicted unfavorable species. The computational selection was successful for antisense portions of 300 nt but not 100 nt in length. This theoretical design of antisense genes supports their improved application under time- and labor-saving conditions.

* To whom correspondence should be addressed. Tel: +49 6221 424938; Fax: +49 6221 424932; Email: patzel@dkfz-heidelberg.de


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
O. V. Matveeva, D. H. Mathews, A. D. Tsodikov, S. A. Shabalina, R. F. Gesteland, J. F. Atkins, and S. M. Freier
Thermodynamic criteria for high hit rate antisense oligonucleotide design
Nucleic Acids Res., September 1, 2003; 31(17): 4989 - 4994.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Renal Physiol.Home page
M. N. Helms, G. Fejes-Toth, and A. Naray-Fejes-Toth
Hormone-regulated transepithelial Na+ transport in mammalian CCD cells requires SGK1 expression
Am J Physiol Renal Physiol, March 1, 2003; 284(3): F480 - F487.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Sohail, H. Hochegger, A. Klotzbucher, R. L. Guellec, T. Hunt, and E. M. Southern
Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo
Nucleic Acids Res., May 15, 2001; 29(10): 2041 - 2051.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.