Design Guidelines
Design Options
Design your own LNA oligo
Incorporation of LNA into a sequence strongly affects the properties of the oligonucleotide, and great care must be taken to find the right design for your experimental purpose. While you will want to take advantage of the properties of LNA to achieve high target specificity, it is important not to use too much LNA, because this can result in a very "sticky" oligonucleotide that is difficult to handle experimentally. The design must be optimized by varying the length and LNA content of the oligonucleotide, such that you achieve good mismatch discrimination and high binding specificity, while avoiding unacceptable secondary structure and self-complementarity.
General design guidelines: