PCR Calculator

Biometra has developed a useful Excel (2003) tool that helps to simplify the setup of new PCR reactions. Download the Excel tool.

PCR protocol designer

The protocol designer allows to create PCR programs for different applications like conventional PCR, fast-PCR or long-range PCR. Just enter the general parameters for the protocol design as recommended by the manufacturer and target specific PCR parameters like primer annealing temperature, product length and number of cycles and a suitable PCR program is created automatically. The protocol can be modified by special settings like a gradient function or touchdown PCR.

PCR mastermix designer

Calculating PCR mastermixes can be a time cunsuming and error prone task. Simply enter the number of reactions, reaction volume and stock concentrations and the finally PCR mastermix is calculated automatically. Additionally, the mastermix volume can be adjusted by a pipetting error. For the documentation of results a printout of the PCR mastermix designer sheet with an inserted gel picture can be generated.

PCR multiplex-mix designer (NEW!)

Similar to the PCR mastermix designer but in this tab mastermixes for a multiplex PCR (up to 10 different targets) can be designed. For reactions less than a 10-plex the filter function serves for a clear representation of the used primer pairs.

Primer calculator

The primer calculator uses an algorithm developed by Marmur & Doty (1962) to calculate annealing temperatures. Just enter the primer sequence and the amount of lyophilzed primer to obtain the melting temperature and a suggestion how to prepare a stock solution. Primer dilutions can be calculated based on OD260 measurements.

Marmur & Doty, Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol. 1962 Jul;5:109-18.