Locked nucleic acids are modified RNA monomers. The “locked” part of their name comes from a methylene bridge bond linking the 2′ oxygen to the 4′ carbon of the RNA pentose ring (Figure 1). The bridge bond fixes the pentose ring in the 3′-endo conformation.
Because of the afforded increase in Tm, locked nucleic acid qPCR probes can be designed with shorter lengths than standard probes. Shorter probes are more effectively quenched and have a higher signal-to-noise ratio. They are, therefore, more sensitive, providing robust target detection regardless of sequence GC content.
These probes also show greater mismatch discrimination compared to traditional qPCR probes. This improves their ability to distinguish mutations or single nucleotide polymorphisms (SNPs) . By including locked nucleic acid bases, you can design a probe with ΔTm >15°C. By varying the number of these modified bases, you can essentially control the Tm of a nucleotide duplex. Use these probes in methods that use differential hybridization to distinguish polymorphisms.
Other applications of locked nucleic acid probes include transcript variant identification; verification of microbial species; and improved target detection in FFPE tissue, biofluids, and other challenging samples.
Locked nucleic acid oligonucleotides are useful in template switching oligo designs and for strengthening target oligo binding in challenges sequence regions, such as AT-rich areas. As with locked nucleic acid qPCR probes, hybridization Tm can be manipulated by the number of locked nucleic acid bases incorporated.
IDT provides 2 types of locked nucleic acid products: Custom Affinity Plus DNA & RNA Oligonucleotides, and Affinity Plus qPCR Probes. While Affinity Plus modified sequences provide identical performance to traditional LNA® sequences, PrimeTime Affinity Plus qPCR Probes and custom Affinity Plus DNA & RNA Oligonucleotides are a better value.
*LNA is a registered trademark of Qiagen, Inc.
Use Affinity Plus qPCR Probes for SNP genotyping, transcript variant identification, and sensitive target detection in challenging samples (FFPE tissue, biofluids).
Use Affinity Plus DNA & RNA Oligonucleotides for increased hybridization Tm, stability, and nuclease resistance over standard oligonucleotides.