Integrated DNA Technologies (IDT) is providing free oligo design and analysis tools via its online SciTools suite. These software applications determine the properties of any oligo sequence entered, as well as mediating the intelligent design of assay conditions. The SciTools suite includes IDT’s customised OligoAnalyzer, PrimerQuest and RealTime PCR design tools, in addition to a dilution calculator, a resuspension calculator and an application for analysing oligonucleotide secondary structures.

The OligoAnalyzer calculates the physical properties of any DNA or RNA sequence, including those containing methylated, locked and phosphorylated bases. The tool provides important information for reaction optimisation such as oligo melting temperature range, GC content, length, molecular weight, optical density and extinction coefficient. In addition, users can utilise mFold to investigate the existence of reaction-inhibiting secondary structures. To avoid potential off-target effects and explore oligo specificity, each sequence can be directly compared with all known nucleotide sequences using a link to the NCBI BLAST database.

For PCR and qPCR assay planning, SciTools offers two specialised analysis options. PrimerQuest allows the user to specify the stretch of sequence to be amplified, along with the desired reaction conditions and the positional sequence constraints the primers need to operate under. The program then identifies primer pairs optimised to these specifications, favouring those pairs that reduce the chances of unwanted primer-dimer formation. For users of IDT’s PrimeTime qPCR System, SciTools includes a flexible RealTime PCR design tool, specifically developed to simplify the design of qPCR experiments. Users provide a specific gene sequence or reference database accession number and the system automatically generates several optimised primer sets and probe sequences, spanning different exons where possible. As with all sequences analysed using SciTools, a chosen selection of oligos can be transferred to an order list ready for purchase.