Online Analysis Tools Facilitate the Intelligent Design Of Oligos

Integrated DNA Technologies (IDT) provides a number of 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, all at the click of a button. The suite is easy to use and makes it simple to add each optimised oligo to an ongoing order list ready for purchase. The SciTools suite includes IDT’s customised ‘OligoAnalyser’, ‘PrimerQuest’ and ‘RealTime PCR’ design tools, as well as a dilution calculator, a resuspension calculator and an application for analysing oligonucleotide secondary structures.

IDT’s OligoAnalyser 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 easily 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 lets the user 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, favoring those pairs that reduce the chances of unwanted primerdimer formation. For users of IDT’s PrimeTime qPCR System, SciTools includes a highly 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 quickly and simply transferred to an order list ready for purchase.