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Custom LNA™ Detection Probes for mRNA and lncRNA

Design LNA™-enhanced detection probes in minutes for any mRNA or lncRNA target using our advanced online design software.

  • Superior sensitivity and specificity compared to DNA probes and riboprobes
  • Designed using proprietary algorithms developed by Exiqon’s LNA™ experts
  • No cloning expertise needed
  • Excellent tissue penetration
  • Available with a wide selection of labels
  • Optimal LNA™-enhanced probe designed in minutes using advanced online tools

Features

LNA™ probes are ideal for detection of short RNAs and for discriminating between highly similar RNAs. The high affinity of these probes for their target sequences means that stringent hybridization and washing conditions can be used, despite the short lengths of the probes.

Use Exiqon’s Custom LNA™ mRNA Detection Probe design tool to design highly sensitive LNA™ probes specifically targeting your mRNA sequence.

Product description

The Custom LNA™ mRNA Detection Probes are available with a large selection of 3’ and 5’ labels. Ready-to-label probes designed for custom labeling are also available. Double (5’ and 3’) DIG-labeled probes are the most sensitive detection probes available due to a synergistic effect of the labels. For this reason, we generally recommend this labeling option.

The design software will allow you to choose between several different probe synthsis scales. Prices and oligonucleotide yield depend on the synthesis scale and choice of modifiers. This information is shown once the designs have been made. You can order the probes directly from our webpage or contact us for a quote. 

Probe design process

Exiqon’s Custom LNA™ mRNA Detection Probe design tool uses a sophisticated algorithm to quickly identify optimal LNA™-enhanced probes for your target mRNA.

In less than a minute, the software evaluates more than 5,000 probe designs based on over 20 design criteria. This process ensures that high-quality probes can be designed for any mRNA sequence.

The design criteria include:
  • Optimization of probe length and the amount and positions of LNA™ bases within the probe. This ensures that the probes have the correct melting temperatures and that any potential self-hybridization is avoided.
  • A detailed analysis of the LNA™ pattern of the probe based on Exiqon’s extensive knowledge of oligonucleotide design rules. This ensures that LNA™ bases are not placed at positions where they could negatively affect the performance of the probe.
  • Calculations of the target’s secondary structure to ensure that the probes only target accessible regions of the mRNA.
  • BLAST searches to ensure that the probes will only target the relevant mRNA sequence.




LNA™ probes can be used for a number of applications. These probes are ideal whenever a short probe is needed, such as in the detection of short sequences or when discriminating between closely related sequences.

Messenger RNAs can be detected using specific probes or using an LNA™ poly T probe, which detects the poly A tail of the transcripts (Figures 1-3). LNA™ detection probes can also be used to discriminate between different splicing variants, isoforms and to detect the trinucleotide repeats associated with some diseases.

LNA™ probes are also ideal for detecting short non-coding RNAs. This is apparent from the wide use of LNA™ probes in the detection of microRNAs. In some cases, LNA™ probes give over 20-times higher signal intensity than DNA probes (Figure 4).  
  Figure 1
Detection of SSA4 RNA LNA™ probes give higher signal and lower background than DNA probes. (Click to learn more)

Figure 2 Detection of poly(A)plus RNA LNA™ produces a nuclear signal from an RNA undetectable by the DNA probe. (Click to learn more)

Figure 3 Fixed Rat 9G cell hybridised
Detection of an mRNA transcription site using an LNA™ probe. (Click to learn more)

Figure 4 Figure 4. LNA™ probes give stronger signals than DNA probes.
(Click to learn more)

Dr. Catia Andreassi Dr. Antonella Riccio Gene Expression Control in Neurons

“I enjoyed very much my collaboration with Exiqon. Their technical support is very efficient, the turnaround time for the production of the LNA™ oligos quite good, and I believe they strive to give the best possible service to their customers.”

Antonella Riccio’s lab at the MRC Laboratory for Molecular and Cellular Biology, UCL, in London studies neuronal gene expression and local protein synthesis in axons. Her group is trying to understand the triggers that induce translation of axonal mRNAs. With these questions in mind, Catia Andreassi, Senior Research Associate, has been working on mRNA localization in axons of primary sympathetic neurons using ISH, together with other approaches.


Maša Milatovič Finding new ways of degrading cellulose

"We got beautiful results repeatedly and could even detect the probes fluorescently."

Maša Milatovič is a PhD student at the University of Ljubljana in Slovenia. She has been using LNA™ detection probes from Exiqon to detect cellulase mRNA transcripts in P. scaber.

 
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