Custom LNA mRNA Detection Probes are great for detecting short RNAs and for discriminating between highly similar RNAs. The high affinity of these probes for their target sequences allows use of stringent hybridization and washing conditions, despite the short probe lengths. Our online design tool enables you to easily design highly sensitive LNA probes for your specific mRNA sequence.
Custom LNA mRNA Detection Probes are available with a large selection of 3' or 5' labels or in ready-to-label format for your own custom labeling. Double (5' and 3') DIG-labeled probes are the most sensitive detection probes available, due to the synergistic effect between the two labels. Therefore, we generally recommend this labeling option. The design tool allows you to choose between several different probe synthesis scales and modifiers.
Probe design process
Our online design tool uses a sophisticated algorithm to quickly identify optimal LNA-enhanced probes for your target mRNA. The tool quickly 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 the following:
- Optimization of probe length and the number and positions of LNA bases within the probe: ensures that the probes have the correct melting temperatures and avoids any potential self-hybridization.
- A detailed analysis of the probe's LNA pattern, based on our extensive knowledge of oligonucleotide design rules: ensures that LNA bases are not placed in positions where they could negatively affect the performance of the probe.
- Calculations of the target’s secondary structure: ensures that the probes only target accessible regions of the mRNA.
- BLAST searches: ensure that the probes will only target the relevant mRNA sequence.