Design Custom LNA™ mRNA Detection Probes Design your own custom LNA™-enhanced mRNA probe for in situ hybridization or Northern blot analysis by following these three simple steps: Step 1 - Paste the sequence of your target RNA (FASTA DNA format) into the 'Target sequence' form below.
- Enter a probe name
- Select the organism of origin for your target sequence.
- Enter a probe melting temperature (RNA Tm) if the default recommended value is not appropriate for your application.
- Press the 'Design Probe' button to start the design. The design process may take several minutes.
Step 2 - Select one or more detection probes (up to 3 per target)
- Add modifications (Mods) to the 5’ and 3’ ends, respectively. Press the 'Add Double DIG' button to quickly add a 5’ and a 3’ DIG* label or the 'No Mods' button to proceed with an unlabeled probe.
- Press 'Next' to continue the design process.
Step 3 - Select your synthesis scale if the default yield is not appropriate for your application. Learn about our recommended yields.
- Press the 'Add to basket' button. Repeat for each selected probe.
- Press the 'View basket' button to proceed to check-out.
Additional products Learn about our positive and negative control probes. |
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Homo sapiens |
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Designing assay. Please note that the design process can take some minutes.
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Time elapsed: 00:00
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Selecting detection probe candidates.
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Positioning LNA.
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Checking Tm.
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Checking secondary structure.
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Checking general specificity.
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Checking species specificity.
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The 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:
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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.
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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.
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Calculations of the target's secondary structure to ensure that the probes only target accessible regions of the mRNA.
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BLAST searches to ensure that the probes will only target the relevant mRNA sequence.
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A probe could not be designed for this target. Your Design ID is {0}. Contact Exiqon support for help with probe design.
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