Concepts to automate the theoretical design of effective antisense oligonucleotides

Bioinformatics

Volumn 17, Issue 11, 2001, Pages 1058-1061

  Far, Rosel Kretschmer Kazemi ^a   Nedbal, Wolfgang ^b   Sczakiel, Georg ^a  

^a UNIVERSITY OF LÜBECK   (Germany)

^b A3D GmbH Antisense Design and Drug Development   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; RNA;

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER SYSTEM; CONTROLLED STUDY; GENE REPRESSION; GENE TARGETING; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; RNA SEQUENCE; RNA STRUCTURE; STATISTICAL ANALYSIS; STRUCTURE ACTIVITY RELATION; THEORY; TIME;

EID: 0035182648     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.11.1058     Document Type: Article

References (22)

1. Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes
2. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
3. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries
4. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity
5. Predicting oligonucleotide affinity to nucleic acid targets
6. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
7. Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity
8. Selecting effective antisense reagents on combinatorial oligonucleotide arrays
9. Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase
10. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
11. Inhibition of viral growth by antisense oligonucleotides directed against the IE110 and the UL30 mRNA of herpes simplex virus type-1
12. Sequence specific thermodynamic and structural properties for DNA.RNA duplexes
13. A computer program for choosing optimal oligonucleotides for filter hybridization, sequenceing and in vitro amplification of DNA
14. Theoretical and experimental approaches to design effective antisense oligonucleotides
15. A modified oligodeoxynucleotides as antisense therapeutics
16. Bias in nucleotide composition of antisense oligonucleotides
17. Thermodynamic parameters to predict the stability of RNA/DNA hybrid duplexes
18. Influence of mRNA self-structure on hybridization: Computational tools for antisense sequence selection
19. Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design
20. Effects of RNA secondary structure on cellular antisense activity
21. Calculating nucleic acid secondary structure