LNAtools

LNAtools designs Locked Nucleic Acid (LNA)-substituted oligonucleotides to select and rank capture probes for functional genomics applications.

Key Features:

• Genome-wide target sequence analysis: Performs BLAST analysis to identify and filter target sequences across the genome and minimize cross-hybridization.
• Melting temperature prediction (Tm): Computes melting temperature using dedicated algorithms to predict hybridization stability of LNA oligonucleotides.
• Secondary structure analysis: Predicts self-annealing and secondary structures of LNA-substituted oligonucleotides and of target nucleotide sequences.
• Fuzzy logic scoring system: Evaluates and combines predicted properties into a fuzzy logic score to rank probe suitability.
• Probe design and ranking (OligoDesign): Returns top-scoring LNA capture probes tailored for applications such as expression arrays, real-time PCR, and SNP genotyping.

Scientific Applications:

• Microarray design for Caenorhabditis elegans: Enables design of microarrays to monitor gene expression related to stress responses and toxicological pathways.
• Expression arrays: Provides probe selection and ranking for high-throughput expression profiling.
• Real-time PCR: Supports design of LNA-containing probes for quantitative PCR assays.
• SNP genotyping: Facilitates selection of LNA probes optimized for single-nucleotide polymorphism discrimination.

Methodology:

Uses BLAST-based genome-wide analysis, melting temperature (Tm) prediction algorithms, secondary structure prediction routines for LNA oligonucleotides and targets, and a combined fuzzy logic scoring system integrated with predictive modeling of thermodynamic properties and structural configurations.