Design Guidelines

Design Options

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:

  • LNA will bind very tightly to other LNA residues. Avoid self-complementarity and cross-hybridization to other LNA-containing oligonucleotides.
  • Keep the GC-content between 30–60%.
  • Avoid stretches of more than 4 LNA bases, except when designing very short (9–10 nucleotides) oligos.
  • Avoid stretches of 3 or more Gs or Cs.
  • For novel applications, design guidelines may have to be established empirically.
  • QIAGEN’s in-house LNA experts can help you design the best LNA oligonucleotide for your application and target of interest. Your oligonucleotide will be designed for optimal LNA content and positioning to achieve optimal specificity and minimal secondary structure and self-complementarity. To use this service, please provide us with the details of your request (target sequence and application) in the contact form.
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