LNA-Oligonucleotide Production

specific – robust – stable – sensitive

Locked Nucleic Acids (LNA) are a class of synthetic nucleic acid analogues that contain a “locked” bicyclic sugar moiety. This linkage between the 2’-O- and the 4’-C-position locks the ribose in the 3´-endo conformation (see Figure 1) which leads to the characteristic structure of A-form RNA and forms exclusively A-type duplexes.

Compared to traditional DNA or RNA oligonucleotides, the use of LNA modified oligos exhibit enhanced hybridization affinity towards complementary DNA or RNA.1) LNA oligos can be synthesized using conventional phosphoramidite-chemistry to increase the Tm by 3-8°C for each substituted nucleotide at simultaneously shorter length compared to traditional DNA or RNA oligonucleotides.2) This helps e.g. to detect shorter or very similar target sequences.

Fig. 1: Structures of DNA, RNA and LNA with its C3′-endo, Northern, A-form conformer

Why use LNA

  • Finetuning of melting temperature and Tm normalization
  • Enhanced binding affinity at simultaneously shorter length
  • Improved signal to noise ratio in qPCR Assays
  • Increased target specificity and high sensitivity compared to traditional DNA or RNA probes
  • Enhanced single nucleotide mismatch detection
  • High in-vitro and in-vivo stability due to increased endo- and exonuclease resistance
  • Easy cell entering of antisense LNA oligonucleotides due to negatively charged backbone (combined with cationic transfection agents)
  • Potent & nontoxic building blocks in antisense drug development3)

Applications for LNA4)-5)

  • Gene silencing with antisense LNA oligonucleotides
  • qPCR/PCR applications and Multiplexing
  • Methylation analysis
  • Aptamers
  • Allele discrimination
  • Gene expression analysis
  • Microarray analysis

Design Guidelines

  • Avoid stretches of more than 4 LNA bases, except when very short (9-10 nt) oligonucleotides are designed
  • 3 +G and 3 +C stretches should be also avoided
  • If just one LNA base is positioned at the 5´end, there won´t be any influence on Tm
  • Keep the GC-content between 30-60 %
  • LNA bases should not be positioned at the 3´end or near the 3´terminus
  • Not more than 15 LNA bases should be incorporated because it increases the risk of self-hybridization
  • Single LNA base increases Tm by 2-6°C (DNA) and 3-9°C (RNA) upon binding

Ordering information

  • All standard scales and customized final yields are available
  • LNA should be marked in the sequence with + (e.g. +A, +C, +G, +T)
  • Full compatibility for all additional modifications in our DNA/RNA Portfolio
  • For any further information please enquire

1) Harleen Kaur,Amit Arora, Jesper Wengel, Souvik Maiti, Biochemistry 2006, 45, 7347-7355
2) Singh, S.; Nielsen, P.; Koshkin, A.; Wengel, J. LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chemical Communications, 1998, No. 4, 455-456
3) Wahlestedt, C., Salmi, P., Good, L., Kela, L., Johnsson, T. Hökfelt, T., Broberger, C., Porreca, F., Lai, L., Ren, K., Ossipov, M., Koshkin, A., Jakobsen, N., Skouv, J., Oerum, H., Jacobsen M.H. and Wengel, J. (2000).Potent and nontoxic antisense oligonucleotides containing locked nucleic acids Proc. Natl Acad. Sci. USA. 2000, 97, 5633 – 5638.
4) Letertre, C.; Perelle, S.; Dilasser, F.; Arar, K.; Fach, P. Evaluation of the performance of LNA and MGB probes in 5’-nuclease PCR assays. Molecular and cellular probes 2003, 17 (6), 307-311
5) Karin E.Lundin, Torben Højland, Bo R.Hansen, Robert Persson, Jesper B. Bramsen, Jørgen Kjems Troels Koch, Jesper Wengel, C.I. Edvard Smith, Advances in Genetics, Volume 82, 2013, Pages 47-107.


RNA-Oligonucleotide Production
fast – reliable – customized – high quality standards

We can offer you the full range of RNA Oligonucleotides. Standard-RNA, modified, O-Methyl, DNA/RNA Chimera as well as Duplex-RNA.
Our RNA-Production follows our high quality standards and all produced RNA Oligos will be QC´d by Maldi or according to the customer's request.


Custom RNA Oligos

  • length up to 60 bases
  • standard scale and customized final yields
  • wide range of 5´and 3´modification available - please enquire

Custom 2´-O-Methyl RNA Oligos

  • length up to 60 bases
  • standard scale and customized final yields
  • wide range of 5´and 3´modification available - please enquire

Custom DNA/RNA Chimera

  • length up to 60 bases
  • standard scale and customized final yields
  • wide range of 5´and 3´modification available - please enquire

Duplex RNA

  • setup-costs for annealing: EUR 50,00/single-strand
  • additional HPLC after annealing: EUR 50,00/duplex


  • length up to 150 bases
  • wide range of 5´and 3´modification available
  • please enquire

Additional service

  • normalizing, aliquoting, customized wobble-mixes, customized QC

Turnaround time

  • unmodified RNA: ~ 5 working days
  • modified and Duplex RNA: ~5-7 working days

Scales and Yields

Large Scale

Large Scale - Oligonucleotide Production
high quality – competitive service

Let us help you determine the best large-scale solutions for your projects, so you can focus on generating informative results instead of spending time and money on troubleshooting.
Our production capacity and synthesis expertise allow us to manufacture highly complex oligos for in vivo, high-throughput, or commercial applications. If needed, we can supply you with grams of highly pure siRNAs/DsiRNAs, aptamers, antisense oligos, ribozymes, miRNAs, decoy oligos, next generation sequencing products, and qPCR primers and probe sets.

Bulk Synthesis of DNA and RNA Oligos

  • final yields up to several 100µmol final yield (purity guarantees and synthesis options may vary depending on scale)
  • standard and modified bases
  • almost any chemical modification, fluorophore, or dark quencher
  • custom oligo mixtures available


  • flexible ordering methods (e.g., use the units that work best for your projects)
  • customer-dedicated purification columns available
  • choice of aliquoting and vialing formats
  • independently verified product compliance and release prior to shipment (Certificates of Analysis)
  • hardcopy of analytical QC documentation provided

Turnaround Time

We need at least 10 working days for standard oligos depending on project size