LNA-modified oligonucleotides Probe

FISH has proven to be a useful technique in many fields, but the increasing requirements for its sensitivity have promoted the application of nucleic acid analog probes. Probes with higher DNA affinity may increase the sensitivity of the technique. Locked nucleic acid (LNA) is a new class of RNA analogs that has a very high affinity for complementary DNA and RNA. Replacing DNA oligonucleotide probes with LNA has been shown to significantly increase their thermal duplex stability and improve the distinction between perfect and mismatched target nucleic acids. LNA follows the Watson-Crick base pairing rule when hybridizing with complementary DNA and RNA, and the LNA bases are connected by the same phosphate backbone as in natural DNA and RNA, allowing the synthesis of scattered LNA/DNA and LNA/RNA mixtures. LNA oligonucleotides are synthesized using traditional phosphoramidite chemistry, allowing the automatic synthesis of pure oligonucleotides and mixed oligonucleotides containing LNA and DNA monomers. The introduction of LNA monomers into oligonucleotides will increase the thermal stability of the heteroduplex. In addition, the conformational limitations and increased thermal stability of heteroduplexes increase the binding affinity of LNA to complementary DNA and RNA sequences.

The structure of LNA, DNA and RNA and the different conformations of LNA.Fig 1. The structure of LNA, DNA and RNA and the different conformations of LNA. (Silahtaroglu A, et al. 2004)

Design Services of LNA-modified FISH Probe

High-affinity LNA replaces short DNA oligonucleotides to produce efficient and sensitive FISH probes, which have a wide range of applications in detecting various repetitive elements in the human genome. Compared with traditional FISH probes, the detection efficiency of modified probes containing LNA) substitution in the structure is more effective. Our LNA/DNA probe design and customization services can solve a major problem in LNA-FISH for customers. The LNA modified FISH probe will be designed for the best LNA content and location to achieve the best specificity and minimal secondary structure and self-complementarity. A variety of customized models provide customers with satisfactory LNA/DNA probe solutions. The length of custom probes is usually 20-25 nucleotides, but the base length can be increased or decreased appropriately. At the same time, we accept the proposal of assisting the customer's design, and a dedicated LNA expert will guide the customer to complete the design.

Advantages of LNA probes

  • LNA probes have higher thermal stability and resistance to degradation,
  • LNA probes can be shorter than the corresponding DNA probes, with higher affinity and specificity;
  • Suitable for fixed cells and chromosome diffusion;

Creative Bioarray provides LNA modified FISH probe construction services to help customers customize probes for LNA-FISH solutions. LNA/DNA probes are better than ordinary oligonucleotides, improve the sensitivity of FISH analysis, and have a wider range of applications. Especially it can be used for in situ visual analysis of small RNA (sRNA). You will benefit from our multiple choices of FISH probe design solutions and provide you with cost-effective LNA/DNA probe customized solutions. If you are interested in this probe customization service, please contact us for customization. We look forward to cooperating with you in the near future.


  1. Silahtaroglu A, Pfundheller H, Koshkin A, et al. LNA-modified oligonucleotides are highly efficient as FISH probes[J]. Cytogenetic and genome research, 2004, 107(1-2): 32-37.
  2. Vilas Boas D, Almeida C, Sillankorva S, et al. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH)[J]. Biofouling, 2016, 32(2): 179-190.
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