Bioinformatics Vol. 17 no. 11 2001
Pages 1058-1061
© 2001 Oxford University Press
Concepts to automate the theoretical design of effective antisense oligonucleotides
1 Medizinische
Universität zu
Lübeck, Institut
für Molekulare Medizin, Ratzeburger
Allee 160, D-23538 Lübeck, Germany
2 A3D GmbH - Antisense Design & Drug
Development, Waldhofer Straße 100, D-69123 Heidelberg,
Germany
Received on January 11, 2001
; revised on August 14, 2001
; accepted on August 16, 2001
Among the large number of possible antisense species against a given target RNA, only a small number shows effective suppression of the target gene in living cells. In the case of short-chain antisense oligonucleotides (asON) which usually comprise less than approximately 25 nucleotides, local structures of the target RNA seem to be of particular importance for the extent of gene suppression. Experimental approaches to identify promising local target sequences and, hence, complementary asON sequences, have provided tools to define asON that are biologically active at higher than statistical probability. However, experimental protocols are expensive, time consuming, and are associated with intrinsic basic and technical limitations. As insights into the structure–function relationship of asON as well as the role of sequence motifs increase, it becomes feasible to consider computer-based theoretical approaches for the design of effective asON. In the following we describe how individual steps of the theoretical design of asON may be automated by establishing and implementing suitable algorithms.
Contact: sczakiel{at}imm.mu-luebeck.de
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  I. Ladunga More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature Nucleic Acids Res., January 28, 2007; 35(2): 433 - 440. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Kusov, T. Kanda, A. Palmenberg, J.-Y. Sgro, and V. Gauss-Muller Silencing of Hepatitis A Virus Infection by Small Interfering RNAs. J. Virol., June 1, 2006; 80(11): 5599 - 5610. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Bo, S. Lou, D. Sun, J. Yang, and S. Wang AOBase: a database for antisense oligonucleotides selection and design Nucleic Acids Res., January 1, 2006; 34(suppl_1): D664 - D667. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Hyyro, M. Juhola, and M. Vihinen Genome-wide selection of unique and valid oligonucleotides Nucleic Acids Res., July 26, 2005; 33(13): e115 - e115. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Deere, P. Iversen, and B. L. Geller Antisense Phosphorodiamidate Morpholino Oligomer Length and Target Position Effects on Gene-Specific Inhibition in Escherichia coli Antimicrob. Agents Chemother., January 1, 2005; 49(1): 249 - 255. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Kretschmer-Kazemi Far and G. Sczakiel The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides Nucleic Acids Res., August 1, 2003; 31(15): 4417 - 4424. [Abstract] [Full Text] [PDF]
|
|