Custom LNA Oligonucleotide FISH Probes

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Benefits of LNA-enhanced FISH probes
Although fluorescence in situ hybridization (FISH) has proven useful in cytogenetics, it has traditionally been a time-consuming method with limitations in sensitivity and resolution. High-affinity LNA-enhanced FISH probes offer fast, sensitive and specific detection of chromosomal DNA.

  • Design your own LNA FISH probes or let us do the design for you
  • Short hybridization time (less than 1 hour)
  • Suitable for both fixed cells and chromosome spreads
  • Multiplexing capability
  • Available with different labels

Let us design LNA FISH probes for you
QIAGEN’s in-house LNA experts can help you design the best LNA oligonucleotide for your DNA FISH analysis. 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.

Design LNA FISH probes yourself
To design and order Custom LNA Oligonucleotides for use as FISH probes, visit the product catalog page and follow the guidelines below.

The following tools and calculators are also available to support you:
Tm Prediction Calculator
LNA Oligo Optimizer
Oligo Dilution Calculator
Oligo Resuspension Calculator
Oligo Concentration Converter
LNA Nomenclature Converter

LNA FISH probe design guidelines
  • Detection probes are typically 20–25 nucleotides in length. However, shorter or longer probes can also be used.
  • Avoid stretches of 3 or more Gs or Cs.
  • Avoid stretches of more than 4 LNA bases, except when designing very short (9–10 nucleotides) oligos.
  • Avoid self-complementarity and cross-hybridization to other LNA-containing oligonucleotides. LNA will hybridize very tightly to other LNA residues.
  • Keep the GC content between 30–60%.
  • A Tm of approximately 75°C is recommended
  • No LNA bases should be placed in palindromes (G-C base pairs are more critical than A-T base pairs).


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