QuantiNova LNA Probe PCR Custom Assays

QuantiNova LNA Probe PCR Custom Assays provide accurate and sensitive gene expression analysis of any RNA target using LNA-enhanced, hydrolysis probe-based detection. Our robust design algorithm provides full Ensembl database support for human, mouse and rat targets and streamlines assay creation. Custom assays are well-suited for targets for which no predesigned assay is available, for discriminating splice variants and for verifying novel mRNAs or lncRNAs. Optimized using QuantiNova chemistry, the simple QuantiNova LNA Probe PCR workflow can be completed in under 2 hours and is robust enough to support room-temperature setup, automation and delayed run of assays. Predesigned assays, pathway-focused panels and custom panels are also available and can be used together in the same experimental setup.

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Highly sensitive and specific LNA-enhanced PCR

QuantiNova LNA Probe PCR Custom Assays are created using stringent design criteria and lab-validated algorithms to deliver the highest real-time PCR specificity and efficiency and the most reliable and accurate gene expression analysis results.

The high binding affinity of LNA bases increases the flexibility of primer and probe placement on the transcript, so we can use intelligent positioning to design assays for otherwise difficult-to-analyze targets. This gives you better target discrimination and robust and reliable quantification, even for AU-rich targets, low-abundance transcripts, targets with high secondary structure and highly complex samples.

The assays’ high sensitivity of ensures excellent amplification efficiencies down to 1 RNA molecule, making it easier for you to detect low-abundance targets such as lncRNAs from less starting material (see figure  QuantiNova LNA Probe PCR Assays provide accurate, sensitive and linear quantification of targets over a wide dynamic range and figure  QuantiNova LNA Probe PCR Assays enable both high-expression and low-expression detection of mRNA). Increased specificity from the clever placement of LNA provides a high signal-to-noise ratio, allowing discrimination of sequences that differ by only a single nucleotide and eliminating non-specific amplification and primer-dimer formation.

Created using a sophisticated LNA design algorithm

Twenty years of LNA design experience has enabled us to develop and optimize our sophisticated LNA design algorithm, which incorporates over 50 different parameters – all thoroughly lab-validated against highly stringent performance criteria – to guarantee the most optimal assay for successful target detection. This proprietary algorithm has been used to design over 1.3 million assays and is available for your specialized requests through our convenient custom assay builder in GeneGlobe.

The custom design process

The QuantiNova LNA Probe PCR Custom Assay design tool lets you easily design highly sensitive and specific, LNA-enhanced PCR assays for any mRNA or lncRNA not available as a predesigned assay. Using the advanced QuantiNova PCR Assay design algorithm, numerous assay combinations are evaluated based on more than 50 different criteria to find the optimal assay for your target within a few minutes. The tool has been designed for human, mouse and rat mRNA and lncRNA targets of at least 55 nucleotides and blasts against the species-relevant databases, including Ensembl and RefSeq. For known gene targets, assays are designed as intron-spanning by default, similar to the predesigned assays, to prevent the risk of gDNA amplification.

Uniquely advanced assay design options

The custom assay design tool includes options to create transcript-specific designs for discriminating splice variants, SNPs or isoforms. Alternatively, designs for assays common to all transcript variants can also be created. You can submit up to 10 different target sequences at once and design either ten different assays, or for related transcripts, you can design a common assay for all.

Note: The preliminary release of the custom design tool can be accessed in GeneGlobe, but some functionalities may not be available. The full version will be released soon. If you need immediate assistance with your advanced design request, please contact our specialist team.

Robust and high-performance hydrolysis probe-based detection

QuantiNova LNA Probe PCR Assays use FAM-labeled hydrolysis probe-based detection, which is highly sensitive and robust, because only the desired PCR product is detected. Probe-based detection still requires high PCR specificity to prevent amplification artifacts such as non-specific PCR products and primer–dimers that can compete for reaction components and compromise performance. However, we’ve already optimized the QuantiNova LNA Probe PCR system for you to eliminate non-specific amplification and give you accurate and sensitive detection every time.

Reference Gene Assays can be easily combined with the custom assays

A wide selection of human, mouse and rat Reference Gene Assays are available to enable high-quality data normalization and ensure reliable results. These assays target endogenous coding RNAs, long non-coding RNA and small nucleolar RNA molecules that are typically constitutively expressed in a wide variety of tissues. The Reference Gene Assays are FAM labeled and have been functionally validated as reference genes for the QuantiNova LNA PCR system and work optimally with the QuantiNova RT and PCR reagents.

Normalization of mRNA/lncRNA qPCR results

Normalization removes technical and biological inter-sample variation unrelated to the biological changes under investigation. Proper normalization is critical for correct analysis and interpretation of results from real-time PCR experiments. Most commonly, stably expressed reference genes are used for normalization.

It is generally recommended to test several endogenous control reference gene candidates before setting up your actual mRNA/lncRNA expression analysis. These candidates should be chosen from genes expected to be stably expressed over the whole range of samples under investigation. They could be stably expressed mRNAs or lncRNAs selected based on literature or preexisting data (e.g., NGS or qPCR panel screening). The QuantiNova LNA PCR system offers validated reference gene assays for RNAs that tend to be stably expressed and are therefore good candidates as reference genes.

All reference gene candidates should be empirically validated for each study. One option for normalizing PCR panel when profiling a large number of mRNAs/lncRNAs is to normalize against the global mean – the average of all expressed mRNAs/lncRNAs. This can be a good option in samples with a high call rate (expressed genes) but should be used with caution in samples with low call rates. It is also not a good option in samples for which the general gene expression level is changed. Further guidance on normalization can also be found in the GeneGlobe Data Analysis Center.

User-friendly data analysis

The complimentary, web-based data analysis tool in the GeneGlobe Data Analysis Center includes a user-friendly wizard to guide you step-by-step through the normalization and analysis of your data and generates publication-ready results figures.

Trusted QuantiNova chemistry

QuantiNova LNA Probe PCR Custom Assays are designed using the time-tested, high-performance QuantiNova chemistry, which offers you the choice between one- or two-step qRT-PCR. Best results are obtained when reverse transcription is performed with the QuantiNova Reverse Transcription Kit. The resulting cDNA is then quantified by qPCR using the master mixes of the QuantiNova Probe PCR Kit combined with your designed QuantiNova LNA Probe PCR Custom Assay.

For one-step qRT-PCR, we recommend using the QuantiNova Probe RT-PCR Kit, which offers quick reaction setup without need for optimization of reaction conditions. Simply add primers, probe and RNA template to the ready-to-use RT-PCR master mix and start the reaction.

Fast and easy workflow

The fast and easy workflow can be completed in under 2 hours with minimal hands-on time and can be automated to save even more time and labor. The simple protocol has been tested for compatibility on all major brand qPCR cyclers (see figure QuantiNova LNA Probe PCR Assays deliver consistent performance across all thermal cycler instruments). Furthermore, the cDNA generated in the RT step can be used across the entire QuantiNova LNA Probe PCR System, allowing seamless transition from assays to panels depending on your research needs, saving you time and sample.

What you need to get started with the QuantiNova LNA Probe PCR system

Reverse transcription: QuantiNova Reverse Transcription Kit

qPCR mastermix: QuantiNova Probe PCR Kit

One-Step qRT-PCR (optional): QuantiNova Probe RT-PCR Kit

Assays or panels:

• QuantiNova LNA Probe PCR Assays
• QuantiNova LNA Probe PCR Reference Assays
• QuantiNova LNA Probe PCR Custom Assays
• QuantiNova LNA Probe PCR Focus Panels
• QuantiNova LNA Probe PCR lncRNA Focus Panels
• QuantiNova LNA Probe PCR Custom Panels
• QuantiNova LNA Probe PCR Flexible Panels

QuantiNova LNA Probe PCR Custom Assays are highly suited for applications including:

• mRNA and lncRNA expression analysis, profiling and quantification
• Validation of RNA-seq gene expression data
• Gene expression profiling
• Signal and pathway analysis
• Confirming gene expression knockdown by LNA GapmeRs or siRNAs
• Biomarker development, including screening, identification and validation of disease-associated biomarkers
• Monitoring phenotypic changes related to gene expression

Multiple assays can also be used to examine a focused panel of genes.