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From 2011.igem.org

Contents 1 Introduction 1.1 Adjacent Regions 1.2 Design Primers 1.2.1 General Overview 1.2.2 How to interpret the results

Introduction

With these tools we would like to ease the design of primers for a Biobrick.

In case you find any bugs or have any comments, suggestions or questions please feel free to email us at lmuprimer@googleemail.com

We provide two main functions and hope that these can help you during primer design.

Adjacent Regions

The main idea behind Adjacent Regions is that in case you would like to design a non coding Biobrick you can easily find adjacent regions of your Biobrick in the original host genome.

As options we provide the host genome as well as cutoff rates for the adjacent regions. The input would be the sequence of your Biobrick.

Click here to use this tool.

Design Primers

General Overview

Design Primers will provide you with several suggestions for primers and name soem of their properties which it determines. Only those primers are named which are not selfannealing and do not have a G or a C at the end of the sequence. Tm values are determined based on the Wallace Rule, potential Loop sites are named and the GC content of the annealing part of the primer is determined.

You will have to give either the Coding sequence of your Biobrick as an input in case you would like to create primers for a coding Biobrick or the flanking sequences of your Biobrick in case you would like to design a non codign Biobrick.

As options you can choose the length of the annealing part of the primers and the Biobrick format: Either the "classic" Biobrick or the Freiburg standard. You can also have your input sequences checked for restriction enzyme binding sites. Here you can choose whether to check for all known restriction enzymes, only those used in Biobricks or non at all.

How to interpret the results

You will be given a set of potential primers for both the forward primer as wells as the reverse primer. Next to the primer is the determined value of Tm. Next to the Tm value is the GC content. And as the very last value a potential Hairpin is being named. E.g. HAIRPIN?!7-4 would mean that there are 4 nucleotides at the very end of the sequence of the primer which might bind 4 other nucleotides after a loop of 7 nucleotides.