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PrimeTime LNA® qPCR Probes

Shorter probes with high Tm and increased specificity compared to traditional 5′ nuclease probes

These locked nucleic acid probes are commonly used for genotyping and custom applications such as transcript variant detection or differential detection of microbial species. A locked nucleic acid is a modified nucleic acid monomer (learn more about them on the technology education page, Locked nucleic acids). When incorporated into a probe, locked nucleic acids impart heightened structural stability to the target sequence leading to increased hybridization temperature.

  • Choose from a wide variety of reporter and quencher combinations
  • Available in small scale for discovery studies
  • Improve mismatch discrimination compared to traditional probes


PrimeTime Mini LNA qPCR Probes

PrimeTime Mini LNA qPCR Probes are ideal for screening a small sample set or performing a few reactions to optimize probe designs.

5' Reporter Dye(s)Quencher(s)Delivery Amount
0.5 nmol
FAMIowa Black FQ *$165.00 USD
HEXIowa Black FQ *$165.00 USD
YAKIowa Black FQ *$165.00 USD

PrimeTime LNA qPCR Probes

PrimeTime LNA qPCR Probes are offered with a wider selection of dyes and quenchers than PrimeTime Mini LNA qPCR Probes, and are best-suited for large-scale or high-throughput applications.


Locked nucleic acid nucleotides can be incorporated into effective qPCR probes[1–4]. Because these bases significantly increase Tm, PrimeTime LNA qPCR Probes can be designed with shorter lengths than standard qPCR probes. Shorter probes have better quenching and a higher signal-to-noise ratio and are, therefore, more sensitive. More importantly, these probes offer an improved ability to distinguish mutations or single nucleotide polymorphisms (SNPs) [1]. A locked nucleic acid probe can be designed to have a ΔTm of >15°C, which greatly increases accuracy of allele determination in real-time PCR or other methods that use differential hybridization to distinguish polymorphisms.

For design strategies and tips, see the Product details tab of the Affinity Plus qPCR Probes product page or contact Design fees may apply.

PrimeTime LNA qPCR Probes can be ordered either at a guaranteed yield of 0.5 nmol or at defined synthesis scales to suit your research needs:

PrimeTime Mini LNA qPCR Probes

  • Ideal for analyzing a small sample set or performing a few reactions to optimize probe designs
  • Available with FAM, HEX™ or YAK® fluorescent dyes, and Iowa Black® FQ quencher
  • Guaranteed normalized yield of 0.5 nmol
  • Shipped in 4–6 business days

PrimeTime LNA qPCR Probes

  • Available with FAM, Cy® 3, Cy 5, TEX, TYE™, YAK, and HEX dyes
  • High synthesis scales (250 nmol and 1 µmol) for large-scale and high throughput requirements
  • Shipped in 4–6 business days


  1. Davialieva K, Kiprijanovska S, Plaseska-Karanfilska D. (2013) Fast, reliable and low cost user-developed protocol for detection, quantification and genotyping of hepatitis C virus. J Virol Methods, 196:104–112.
  2. Owczarzy R, You Y, et al. (2011) Stability and mismatch of Locked Nucleic Acid–DNA duplexes. Biochemistry, 50(43):9352–9367.
  3. You Y, Moreira BG, et al. (2006) Design of LNA probes that improve mismatch discrimination. Nucl Acid Res 34(8): e60, doi:10.1093/nar/gkl175.
  4. Johnson MP, Haupt LM, Griffiths LR. (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res, 32(6):e55.

Frequently asked questions