Custom LNA™ Probes for in situ Hybridization  Whether you choose to do the probe design yourself or let Exiqon’s LNA™ experts do the design for you, LNA™ in situ hybridization probes are ideal for the detection of short or highly similar RNA sequences.
Carsten Alsbo, Ph.D., Product Manager | |
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- 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
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.
You can choose to design your own probes or let us do the work. If you choose to do your own designs, please see our design guidelines at the bottom of this page.
If you choose to let us do the designs for you, our in-house experts will ensure that the probes have optimal LNA™-content and positioning, resulting in efficient target recognition and minimal self-annealing.
Let Exiqon design your probes We are happy to design LNA™ probes targeting customer-defined RNA targets. Simply send us the sequence of your target using this form.
Generally, we ask our customers to provide us with as long a target sequence as possible, since this gives us the best design options. If you would like the probe to bind a specific section of the target sequence, please highlight this area. Also, to ensure that there are no misunderstandings in the design process, we ask you to provide the target sequence and not a database access number. In addition, we ask our customers to indicate what organism the sequence comes from, as we perform BLAST searches to ensure the specificity of the probe sequences. You will be asked to approve the final design of the probe prior to synthesis.
Typically, we design oligonucleotides that are 20-25 nucleotides in length. Probes of this length have high melting temperatures (between 70-85°C), good mismatch discrimination, and high binding specificity, while avoiding high secondary structure and self-complementarity. However, we can accommodate requests for shorter or longer probes as well.
Our custom 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 recommend this labeling option for low abundance targets.
For ordering, price information and requests for alternative labels, please contact us . Please also indicate if you have any special requests regarding the probes.
Design your own probes
Use the guidelines below to design your own probes for in situ hybridization. When you are ready to order, just click the "Order this product" button at the bottom of this page.
Probe design
- 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 very short (9-10 nt) oligonucleotides are designed.
- Avoid LNA™ self-complementarity. LNA™ hybridizes very tightly to other LNA™ residues. Check your design using these tool.
- Keep the GC-content between 30-60 %.
- A T m of approximately 75 °C is recommended. Calculate T m using these tool.
- No LNA™ bases should be placed in palindromes (G-C base pairs are more critical than A-T base pairs).
* Licensed from Roche Diagnostics GmbH |
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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). |
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Figure 1
LNA™ probes give higher signal and lower background than DNA probes. (Click to learn more)
Figure 2 LNA™ produces a nuclear signal from an RNA undetectable by the DNA probe. (Click to learn more)
Figure 3
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) |
 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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