Back to top

LNA Oligonucleotides

 
 
The major advantage of LNA lies in the design options for primers and probes as the Tm can be finetuned according to the needs of a desired oligonucleotide. Due to the enhanced binding affinity shorter probes can be realized and as a result binding specificity to the target DNA and RNA is increased. Hence, LNA oligonucleotides are very well suited for use in antisense protocols, hybridization assays, in situ hybridization probes, dual labeled probes, molecular beacons and qPCR primers.
 

Features and Benefits

 
Increased Thermal Stability of qPCR Probes
  • Improved affinity and specificity
  • Reduced background fluorescence
  • Better signal-to-noise ratio
 
 
Multiplex qPCR Systems
  • Normalization of the Tm across several short sequences with varying GC-content gets accessible
  • Optimal design of highly-specific, shorter probes
  • Particularly beneficial for microarray and multiplex PCR applications
 
Enhanced Single Nucleotide Discrimination
  • Greatly enhanced discrimination between alleles via single nucleotide polymorphism (SNP)
  • Better mismatch discrimination compared to native-state DNA probes
 
Antisense Technology
  • Enhanced binding affinity to complementary nucleic acids 
  • High nuclease resistance
  • Further increase in nuclease resistance by introduction of a phosphorothioate backbone

 

Overview

 
Locked Nucleic Acid (LNA) is a synthetic nucleic acid analogue containing a bridged, bicyclic sugar moiety. The extra methylene group attached between the 2’-O- and the 4’-positions “locks” the ribofuranosyl-ring in its 3’-endo conformation (see Figure 1). This conformation leads to the characteristic structure of A-form RNA. As a consequence of the constraint bicyclic sugar skeleton LNA exclusively forms A-type duplexes. Furthermore, LNA fully complies with Watson- Crick base pairing rules. LNA:DNA hybrid duplexes are formed spontaneously from complementary DNA and LNA-sequences and it was found that LNA:DNA hybrids show strongly improved annealing temperatures compared to their DNA:DNA counterparts. Since the synthesis of LNA is compatible with standard oligonucleotide synthesis, site-selective incorporation of single or multiple LNA nucleotides into DNA sequences can be achieved straightaway. These LNA-containing oligonucleotides anneal with their DNA complements to form chimeric LNA:DNA hybrids. Any such duplex adopt A-form conformation and again Tm are substantially increased compared to analogous DNA:DNA double-strands. As a rough guess the incorporation of LNA nucleotides into short DNA primers (<30 nt) increases the Tm by 3-8 °C for each substituted nucleotide. All in all, the major advantage of LNA lies in the design options for primers and probes as the Tm can be finetuned according to the needs of a desired oligonucleotide. Due to the enhanced binding affinity shorter probes can be realized and as a result binding specificity to the target DNA is increased. Therefore LNA is recommended for use in any hybridization assay that requires high specificity and/or reproducibility, e.g. PCR primers, dual-labeled probes, in-situ hybridization probes, and molecular beacons. Furthermore, but for the same reasons, LNA modified oligonucleotides are equally interesting as candidates in antisense drug development.

Figure 1: LNA 3’-endo conformation

How to Order

 
  • Enter our webshop
  • Click on DNA in the "DNA/RNA Synthesis" domain
  • Select Normal Entry in order to type or copy/paste the desired sequence information
  • With Select under Modification you can place the LNA modifications whereever needed
  • Follow the further instructions