The collection of software tools within MOPS give you the option of checking your oligos before you order. It also facilitates the set up of experiments by calculating the adequate amounts and dilution factors for your oligo solutions. You can enter DNA as well as RNA sequences and you can attach or insert modifications to your oligos.
Just enter the sequence and check:
1. Properties – specifies all physical attributes of your oligo such as GC content, annealing temperature, molecular weight, extinction coefficient etc.
2. Structure - the secondary structure of an oligo is calculated. For DNA secondary structure prediction the mfold is used, which is an adaptation of the mfold package (version 2.3) by Zuker and Jaeger that has been modified to work with the Wisconsin Package. The RNAfold program (Vienna RNA Package) is used for prediction of RNA secondary structures.
3. BLAST – provides a number of databases to align your oligo against human, murine and rat sequence databases.
Example of BLASTn report:
4. Dimer/PCR – tests your oligos against itself or another oligo for dimer formation or performs a PCR viability check for a primer pair.
Example of a dimer formation check:
Example of a PCR viability check:
5. OD Calc - calculates the optical density of your oligo using a setup of experimental conditions. This tool is designed to show the relationship between OD and amount of your oligo. You can set the OD and calculate the mass or molar amount of your oligo and vice versa. Another feature is the calculation of the appropriate scale of the oligo which is needed for your experiments. In relation to the number of experiments and the amount of oligo to be used in the experiment, the respective OD is derived. This will help you to figure out the scale of oligo you should order.
6. Dilu Calc - This tool is designed to determine how much volume is needed to dilute an oligo stock solution of higher concentration down to a specific lower concentration. Stock volumes and final volumes (default 100 µl) can be defined as well.
