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Custom microRNA LNA™ PCR primer sets

Design custom LNA™-enhanced microRNA primer sets for your own microRNA. Use our web tool to design super sensitive primers compatible with the miRCURY LNA™ Universal RT microRNA PCR System.

  • Design LNA™-enhanced microRNA PCR primer sets for any microRNA in minutes using our online software tool
  • Fully compatible with the miRCURY LNA™ Universal RT microRNA PCR System

Features

Design LNA™-enhanced qPCR primer sets for any microRNA using Exiqon’s online Custom miRCURY LNA™ Universal RT microRNA PCR Assay design software .

The designed primers are compatible with the miRCURY LNA™ Universal RT microRNA PCR System. Please make sure that pre-designed validated primer sets are not available for your microRNA before proceeding with custom primer design.

Coverage

PCR primer sets designed with Exiqon’s online software tool are provided in amounts sufficient for 100 PCR reactions using the miRCURY LNA™ Universal RT microRNA PCR System.

Ordering

The primer sets can be ordered directly online or by contacting us with the reference number received from the design software. Prices can be found by placing the designs in the shopping basket.

The design process

The Custom miRCURY LNA™ Universal RT microRNA PCR Assay design software is ideal for designing highly sensitive and specific LNA™-enhanced PCR primer sets for any microRNA not available as a pre-designed product.

In a process which typically takes about two minutes, an advanced algorithm evaluates approximately 3,000 primer pair designs based on more than 60 different criteria to find LNA™ optimal primer sets for your microRNA. Note, the design software has been designed for microRNAs but can also be used for other small RNAs (14-27 nt in length).

The design criteria include:
  • Optimization of melting temperatures by varying the LNA™ distribution of the primers to ensure high amplification efficiency and specificity.
  • Calculations and adjustments of self-hybridization and cross-hybridization scores for efficient PCR reactions.
  • Adjustments to avoid potential primer-dimer formation in the PCR reaction.
  • Intelligent positioning of LNA™ bases in the primers based on Exiqon’s vast knowledge of LNA™ oligonucleotide design.
  • miRBase searches to identify potential microRNAs with high sequence similarity. This ensures that the designed primer sets are highly specific for the small RNA for which they were designed.

View experimental data for our standard miRCURY LNA™ Universal RT microRNA PCR Primer Sets

A unique system developed specifically for microRNA profiling

The miRCURY LNA™ Universal RT microRNA PCR System offers the best available combination of performance and ease-of-use on the market because it unites two important features (Figure 2):
  • One cDNA reaction for all microRNAs – One single Universal first strand cDNA synthesis reaction is used as template, regardless of the number of microRNAs being profiled. This saves precious sample, reduces technical variation, means less pipetting and saves time in the laboratory.
  • Two LNA™-enhanced microRNA qPCR primers – Both qPCR primers are microRNA-specific and optimized with LNA™. LNA™ primers bind with high affinity, and are shorter than standard PCR primers, so that both primers can fit on the microRNA without overlapping. The result is unrivalled sensitivity and specificity, and extremely low background.

Unmatched sensitivity

Universal RT combined with LNA™-enhanced and Tm normalized primers enables accurate and reliable quantification of individual microRNAs from as little as 1 pg total RNA (Figure 3). In comparison to other microRNA real-time PCR systems using either stem-loop or standard DNA primers, the LNA™-enhanced primers offer significantly increased sensitivity, especially for AU-rich microRNAs.

Exceptional sensitivity as well as extremely low background enables accurate quantification of very low levels of microRNA without the need for pre-amplification. This makes the miRCURY LNA™ Universal RT microRNA PCR System suitable for all sample types, and especially samples with low RNA content e.g. biofluids such as serum/plasma.

Fully validated and optimized

All miRCURY LNA™ Universal RT microRNA PCR primer sets have been optimized for maximum sensitivity and thoroughly validated either by wet lab testing or in silico. In wet lab validation, over 95% of assays detect 10 microRNA copies or less in the PCR reaction (Figure 4). The primer sets have also been validated for specific amplification of the target and for minimal background signal.

Truly specific – no false positives

The incorporation of LNA™ in the qPCR primers facilitates the design of assays that can distinguish between microRNA sequences that differ by a single nucleotide. This makes it a truly specific microRNA qPCR platform – the only microRNA platform that gives no false positive signals (Figure 5). In addition, the assays can discriminate between mature microRNA sequences and precursor microRNA (Table 1).

Fast, easy and reproducible

Save time and effort in the laboratory with the 3 hour easy-to-follow protocol that minimizes pipetting. By using the same cDNA as template in all subsequent PCR reactions, the procedure is greatly simplified compared to systems that require microRNA-specific cDNA synthesis.

With fewer pipetting steps, technical variation is also reduced. As a result, it is possible to achieve extremely high reproducibility from day-to-day (Figure 6) and even site-to-site.

Flexible qPCR system

Tailor your experimental setup to your specific need using individual assays or fully flexible custom Pick-&-Mix panels . Using the same cDNA reaction, shift seamlessly between individual primers, pre-designed miRNome and Focus panels, or custom Pick-&-Mix panels.
Figure 1 Overview of the miRCURY LNA™ Universal RT PCR workflow
Overview of the miRCURY LNA™ Universal RT PCR workflow. (Click to learn more)

Figure 2 Schematic outline of the miRCURY LNA™ Universal RT microRNA PCR System
Schematic outline of the miRCURY LNA™ Universal RT microRNA PCR System. (Click to learn more)

Figure 3 Accurate quantitation from down to 1 pg total RNA starting material
Accurate quantitation from down to 1 pg total RNA starting material. (Click to learn more)

Figure 4 Serial dilution of hsa-miR-181a
Serial dilution of hsa-miR-181a. (Click to learn more)

Figure 5 Specificity results from the miRQC Study
Specificity results from the miRQC Study. (Click to learn more)

Table 1 Discrimination between mature and precursor microRNAs
Discrimination between mature and precursor microRNAs. (Click to learn more)

Figure 6 Excellent day-to-day reproducibility
Excellent day-to-day reproducibility. (Click to learn more)



NOTICE TO PURCHASER: DISCLAIMER OF LICENSE No license is conveyed with the purchase of this product under any of US Patents Nos. 5,210,015, 5,487,972, 5,804,375, 5,994,056, 6,171,785, 6,214,979, 5,538,848, 5,723,591, 5,876,930, 6,030,787, and 6,258,569, and corresponding patents outside the United States, or any other patents or patent applications, relating to the 5’ Nuclease and dsDNA-Binding Dye Processes. For further information contact the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
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