OligoDesign: Design of LNA oligonucleotides for gene expression arrays

Niels Tolstrup1, Peter S. Nielsen and Sakari Kauppinen
1tolstrup@exiqon.com, Exiqon

OligoDesign is a webservice for the design of DNA/LNA mixmer oligonucleotides. LNA constitutes a novel class of RNA analogs having an exceptionally high affinity and specificity toward their complementary DNA and RNA target molecules. The OligoDesign software features recognition and filtering of the target sequence by genome-wide BLAST analysis in order to minimize cross-hybridisation with non-target sequences. Furthermore it includes routines for prediction of melting temperature, self-annealing and secondary structure for LNA substituted oligonucleotides, as well as secondary structure prediction of the target nucleotide sequence. The poster discusses issues with regard to the design of short oligonucleotides. The OligoDesign program is freely accessible at http://lnatools.com/ Tolstrup et al. OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. to apear in Nucleic Acids Research 2003, Vol. 31. No. 13