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Custom LNA mRNA Detection Probes

For detecting short RNAs and discriminating highly similar RNAs by in situ hybridization with LNA-enhanced probes
  • Sensitivity and specificity superior to DNA probes and riboprobes
  • Online tools provide optimally designed LNA-enhanced probe in minutes
  • Available with a wide selection of labels
  • No cloning expertise required
  • Excellent tissue penetration
Custom design your own LNA-enhanced detection probes for any mRNA or lncRNA target in just minutes using our advanced online design tools. Custom LNA mRNA Detection Probes allow you to easily detect short RNAs and discriminate between highly similar RNAs. High affinity for their target sequences allows use of stringent hybridization and washing conditions, despite short probe lengths.

Please contact us for further product information, or technical questions.
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Product Product no. Cat. no. List price:
Custom LNA mRNA Detection Probes (1 µmol)
1 µmol Custom LNA mRNA Detection Probes with option of different labels, provided in tube format
339501 Varies Create and order
Custom LNA mRNA Detection Probes (250 nmol)
250 nmol Custom LNA mRNA Detection Probes with option of different labels, provided in tube format
339500 Varies Create and order
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Custom LNA mRNA Detection Probes are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.


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Custom LNA mRNA Detection Probes give higher signal and lower background than DNA probes.
Detection of SSA4 RNA in ∆rip1 fixed yeast cells using a single-labeled Cy3 Custom LNA mRNA Detection Probe (left) or a single-labeled Cy3 DNA oligonucleotide (right) of same length. The results show improved signal and less background staining with the Custom LNA mRNA Detection Probe. Pictures were taken after 20 min hybridization time in 50% formamide. From Thomsen et al., RNA, Nov 2005; 11(11): 1745–1748; reprinted by permission of CSHL Press.
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Custom LNA mRNA Detection probes produce a nuclear signal from an RNA.
Detection of a poly(A)+ RNA in fixed wild-type yeast cells using a single-labeled Cy3 T 20 Custom LNA mRNA Detection Probe (left) at 37ºC shows a nuclear signal that could not be detected using a single-labeled Cy3 T 70 DNA oligonucleotide (right). Both probes have identical Tm. Pictures were taken after 30 min hybridization time. From Thomsen et al., RNA, Nov 2005; 11(11): 1745–1748; reprinted by permission of CSHL Press.
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Detection of an mRNA transcription site using a Custom LNA mRNA Detection Probe.
Fixed Rat 9G cell hybridized with an HCMV-IE mRNA-specific Custom LNA mRNA Detection Probe. The bright red dot in the nucleus (stained blue with DAPI) represents the transcription and possibly RNA processing site of HCMV-IE mRNA. The mRNA is also detectable in the cytoplasm as red staining. Image kindly provided by Dr. R. W. Dirks, Leiden University, Leiden, The Netherlands.
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Custom LNA mRNA Detection Probes give stronger signals than DNA probes.
The intensities of four probes targeting rRNA from E. coli were compared. All probes had the same 19 nucleotide sequence, but the Custom LNA mRNA Detection Probes had 1–3 LNA subsitutions. The LNA Probe 3 produced 22 times higher intensity than the DNA probe. Data from Kubota et al. Appl. Environ. Microbiol. 2006. 72: 5311–7.
Performance
mRNAs can be detected using either specific LNA mRNA Detection Probes, or with an LNA-enhanced poly(T) probe, which detects the poly(A) tail of mRNA transcripts (see figures Custom LNA mRNA Detection Probes give higher signal and lower background than DNA probes, Custom LNA mRNA Detection probes produce a nuclear signal from an RNA, undetectable by the DNA probe, and Detection of an mRNA transcription site using a Custom LNA mRNA Detection Probe).

Custom LNA mRNA Detection Probes can also be used to discriminate between different splicing variants, isoforms and to detect the trinucleotide repeats associated with some diseases. In addition, the probes are great for detecting short non-coding RNAs and have been widely used for miRNA detection. In some cases, LNA Detection Probes give a signal intensity over 20 times higher than that from DNA probes (see figure Custom LNA mRNA Detection Probes give stronger signals than DNA probes).
Principle
Features
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.

Product description
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.
Applications
Custom LNA mRNA Detection Probes are great for in situ hybridization applications requiring a short probe, such as in the detection of short sequences or for discriminating between closely related sequences.
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