Locked nucleic acid probes

Enhance your assay with a locked nucleic acid probe or locked nucleic acid primer

Improve assay sensitivity and specificity with locked nucleic acid (LNA) oligonucleotides. LNAs are modified RNA bases in which the ribose is “locked” with a methylene bridge, connecting the 2' oxygen atom to the 4' carbon atom, fixing it in the C3'-endo conformation.

LNAs enable a shorter probe, which supports assay design for:

Improved assay sensitivity
- Higher quenching efficiency (lower background)
- Greater signal-to-noise ratio
Increased hybridization specificity
Targeting A-T rich sequences
Better mismatch discrimination in SNP genotyping assays

Locked nucleic acid probes usually ship in 8 business days More details

Oligos for North America, South America, and APAC will be supplied out of our Petaluma, US manufacturing facility while oligos for EMEA will be supplied out of our Lystrup, Denmark manufacturing facility unless you have an agreement in place.
Our advertised turnaround time applies to orders received before 12PM for the local manufacturing site. Turnaround time is defined as the time of checkout until shipment.

Order Dual-labeled LNA Probes

LNAs from LGC Biosearch Technologies for commercial use

As the original manufacturer of Black Hole Quencher (BHQ) dyes, we are ready to help you take full advantage of the performance improvement power of LNA technology combined with our best-in-class BHQ quenchers. Use this Excel template to communicate your exact specifications to our manufacturing team.

Additional benefits include:

Access to LNA probes in a wide range of fluorophores for multiplexing.
We can add up to seven LNA bases in the probe.
Our sequences are dual-HPLC purified, MS and uHPLC verified.

Our global commercial capabilities are structured to deliver you with the highest quality oligonucleotides formulated to your exact specifications. With more than 40 years of oligonucleotide synthesis expertise, we pride ourselves on partnering with you from early-stage research through commercial launch.

Our oligonucleotides are made under our robust Quality Management System (QMS) to comply with ISO 9001:2015 and ISO 13485:2016, whereby our stringent processes continually drive industry leading quality, transparency, and reliability every step of the way.

Save time and resources with pre-mixed LNA probes and primers

Simplify assay setup by ordering LNA probe and primer pairs as a ValuMix assay.

For gene expression and qPCR assays, you provide the specifications, including your probe-to-primer ratio, and we send you a custom, dual-labled LNA probe and primer pair in a single tube. For SNP genotyping applications, we offer a ValuMix assay comprised of two custom LNA probes and a primer pair delivered in exact quantities.

order ValuMix gene expression assays

Order ValuMix SNP genotyping assays

Customise your LNA oligo with LGC Biosearch Technologies’ extensive menu of custom modifications

Interested in LNA-enhanced primers for SYBR Green Assays? In addition to offering LNA probes, LGC Biosearch Technologies also synthesizes custom oligos with internal LNA modifications. Use the order form to create your oligo with 1-20 LNA base insertions. Add + before the base to indicate where to insert LNA (+A, +T, +C, +G).

Order Custom LNA oligos

*LNA is a registered trademark of QIAGEN Group.

How locked nucleic acids enhance your assay

LNA oligos are a game-changer for assays to detect short or similar sequences.

The bases in LNA oligos follow Watson-Crick base-pairing rules. When incorporated into a probe, LNA nucleotides provide increased duplex stability by inducing a conformational change in the surrounding DNA causing it to adopt a similar C3'-endo conformation. This leads to an increased local organization of the phosphate-sugar backbone, enhancing the strength of base stacking interactions, leading to increased overall duplex stability observed as an increase in the melting temperature (T_m).

LNA probes benefit from being sequence agnostic and allow for an exact fine-tuning of Tm thermodynamics. For each LNA monomer added into the DNA or RNA strand, the Tm of the duplex increases by 2 - 8 °C. Increased Tm allows for a shorter probe, which supports greater assay sensitivity, higher quenching efficiency, greater signal-to-noise ratio, increased hybridization specificity, improved mismatch discrimination in SNP genotyping assays, and accommodating A-T rich sequences.

Additionally, LNA monomers provide significantly increased resistance to endonucleases and exonucleases, resulting in high stability in vitro and in vivo. LNA probes are also a great option for detecting targets in a complex sample matrix like serum/plasma, FFPE sections, and laser capture microdissection (LCM) samples.

Important design considerations for LNA oligos

LNAs bind very tightly to other LNA residues. Avoid self-complementarity and cross-hybridization to other LNA-enhanced oligonucleotides.
Design for GC content between 30-60%
Avoid stretches of more than four LNA bases, except when the final sequence is less than 10 nucleotides.
Avoid stretches of three or more Gs or Cs.

Contact customer service to order

Locked nucleic acid (LNA) probe product specifications

LNA bases	Up to 7 LNA bases in probe sequence
DYES AVAILABLE	FAM, TET, CAL Fluor Gold 540, CIV-550, JOE, HEX, CAL Fluor Orange 560, Quasar 570, Cy3, TAMRA, CAL Fluor Red 590, ROX, CAL Fluor Red 610, CAL Fluor Red 635, Cy5, Quasar 670, Quasar 705
YIELD	5, 20, or 50 nmols delivered
PURIFICATION	Dual-HPLC
DELIVERY FORMAT	Dry or In Solution
QUALITY CONTROL	MALDI-TOF MS and uHPLC
QUALITY STANDARD	ISO 9001 or ISO 13485
SHELF LIFE	12 months from date of manufacture
SHIPPING CONDITIONS	Ambient Temperature or Dry Ice (In Solution)

LNA-enhanced primers and modified oligos product specifications

LNA bases	Up to 20 LNA bases in the custom oligo, priced per base
PURIFICATION	Desalted, RPC, RP-HPLC, AX-HPLC, or Dual-HPLC
DELIVERY FORMAT	Dry or In Solution
QUALITY CONTROL	MALDI-TOF MS and uHPLC
QUALITY STANDARD	ISO 9001 or ISO 13485
SHELF LIFE	12 months from date of manufacture
SHIPPING CONDITIONS	Ambient Temperature or Dry Ice (In Solution)

ValuMix assays for SNP genotyping

LNA bases	Up to 7 LNA bases in probe sequence
DYES AVAILABLE	FAM/TET FAM/CAL Fluor Gold 540 FAM/CIV-550 FAM/CAL Fluor Orange 560
YIELD	2 nmol probe/9 nmol primer 5nmol probe/22.5 nmol primer 12 nmol probe/54 nmol primer
PURIFICATION	Probes - RP HPLC Primers - RPC
DELIVERY FORMAT	Dry
QUALITY CONTROL	MALDI-TOF MS and uHPLC
QUALITY STANDARD	ISO 9001 or ISO 13485
SHELF LIFE	12 months from date of manufacture
SHIPPING CONDITIONS	Ambient Temperature

ValuMix assays for gene expression and qPCR

LNA bases	Up to 7 LNA bases in probe sequence
DYES AVAILABLE	FAM, CIV-550, CAL Fluor Orange 560, CAL Fluor Red 610, Quasar 670
YIELD	0.5 nmol probe/0.5-2.5 nmol primer 5 nmol probe/5-22.5 nmol primer 20 nmol probe/20-90 nmol primer
PURIFICATION	Probe - RP HPLC Primers - salt-free
DELIVERY FORMAT	Dry
QUALITY CONTROL	MALDI-TOF MS and uHPLC
QUALITY STANDARD	ISO 9001 or ISO 13485
SHELF LIFE	12 months from date of manufacture
SHIPPING CONDITIONS	Ambient Temperature

LNA FAQs

Q1: Are locked nucleic acids (LNA™) available through LGC Biosearch Technologies?

A1: Yes. LGC Biosearch Technologies is licensed to synthesise oligos with LNA modifications for both research and commercial use.

Incorporate up to 7 LNA bases in a probe and up to 20 LNA bases in a primer sequence, denote using +A, +G, +C, +T with no spaces or brackets, e.g. ga+ttac+a+gatta+ca.

Q2: Are our LNA bases different to those from other suppliers?

A2: No. We offer standard LNA bases whereby LNA users can incorporate our like-for-like probes/primers directly into their assays.

Q3: Do we need to get a license from Qiagen to use LGC Biosearch Technologies’ LNA for commercial purposes?

A3: No. Customers may use our LNAs for commercial purposes without obtaining a license. We have an agreement with Qiagen to commercially license their technology. Customers will be able to work with us from early-stage research to commercialisation.

Q4: Can LGC Biosearch Technologies make LNA gapmers?

A4: No.

Q5: What is the difference between LNA and BHQplus™ Probes?

A5: In BHQplus Probes, all Cs and Ts are modified with propynyl groups to enhance duplex stabilisation. With LNA oligos there is more design flexibility; any of the bases may be modified with LNA, just one or ALL the bases.

Q6: Do we offer LNA added to RNA oligos (LNA/RNA chimeras)?

A6: No, not currently.

Q7: Can LNAs be used in digital PCR, are there specific order specs?

A7: Yes, LNA oligos can be used in dPCR. Residual organic compounds in oligo preps can possibly negatively affect the emulsions used during droplet-based applications (BioRad ddPCR, Stilla). It is therefore recommended to order only dry oligos for droplet digital PCR.

Q8: Are LNA probes available as ValuMix™ Assays?

A8: Yes, LNA probes are available as Valumix Assays for qPCR and gene expression as well as for SNP genotyping.