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PrimeTime™ LNA® qPCR Probes

Shorter probes with high melting temperatures 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 identification or the differentiation of microbial species. When incorporated into a probe, locked nucleic acids impart heightened structural stability to the target sequence leading to increased hybridization temperature.


*LNA is a registered trademark of Qiagen, Inc.


  • A wide variety of reporter and quencher combinations to choose from 
  • Small scale size available for discovery studies
  • Mismatch discrimination is improved when compared to traditional probes

See the Product details tab on the Affinity Plus™ qPCR Probes product page for design considerations or contact us for design assistance.

Prices listed include probe sequence (10–25 standard bases with up to 6 locked nucleic acid nucleotides), reporter, quencher, and HPLC purification.

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$170.00 USD
HEXIowa Black™ FQ$170.00 USD
YAKIowa Black™ FQ$170.00 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.


Product Details

Locked nucleic acid nucleotides can be incorporated into effective qPCR probes [1–4]. Because these bases significantly increase melting temperature (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 increases the precision 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 on the Affinity Plus qPCR Probes product page or contact us. 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 Yakima Yellow® (YAK) fluorescent dyes, and Iowa Black® FQ quencher
  • Guaranteed normalized yield of 0.5 nmol

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

Frequently asked questions


  1. Davialieva K, Kiprijanovska S, Plaseska-Karanfilska D. Fast, reliable and low cost user-developed protocol for detection, quantification and genotyping of hepatitis C virus. Virol Methods. 2014;196:104-112.
  2. Owczarzy R, You Y, Groth CL, et al. Stability and mismatch of Locked Nucleic Acid–DNA duplexes. Biochemistry. 2011;50(43):9352–9367.
  3. You Y, Moreira BG, Behlke MA, et al. Design of LNA probes that improve mismatch discrimination. Nucl Acid Res. 2006;34(8):e60.
  4. Johnson MP, Haupt LM, Griffiths LR.Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res. 2004;32(6):e55.