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Doube-Dye LNA Probes

LNA bases have a modification to the ribose backbone that locks the base in the C3'-endo position, which favors RNA A-type helix duplex geometry. By changing the conformation of the helix and by increasing the stability of the duplex, the integration of LNA® bases into Double-Dye probes opens great perspectives to improve techniques requiring high affinity probes as specific as possible like SNP detection, expression profiling, and in situ hybridization. LNA® bases can be readily incorporated into Double-Dye oligonucleotides. 

Double dye probes
During the elongation phase, the DNA polymerase cleaves the fluorescent dyes from the probe which starts to emit a fluorescent signal. The signal is then recorded in real time.

Since LNA® bases significantly increase Tm, LNA® Double-Dye probes are shorter than standard DNA Double-Dye oligonucleotides. Shorter probes exhibit better quenching, a higher signal-to-noise ratio and are therefore more sensitive. More importantly, LNA® Double-Dye probes offer an improved ability to distinguish mutations or single nucleotide polymorphisms (SNPs). DNA Double-Dyes probes typically have a ?Tm of 4-5 °C between perfect match and mismatch hybridizatiom. Similar probes containing LNA® bases can have a ?Tm > 15 °C, greatly increasing accuracy of allele discrimination in Real-Time qPCR assays. Compared to DNA Double-Dye probe, LNA® Double-Dye probes have several advantages : They exhibit unprecedented thermal stabilities towards complementary DNA and RNA. LNA® bases show better mismatch discrimination. The high-binding affinity of LNA® oligonucleotides allows the use of shorter probes. They offer high specificity and/or reproducibility. Furthermore, LNA® offers the possibility to adjust Tm values of primers and probes in multiplex assays. Depending on sequence context, insertion of a LNA® base into a DNA oligo can increase the Tm by 3-6 °C. Usually 3 to 5 LNA® bases are placed in LNA® Double-Dye probes. Based on its experience in probe design and by means of collaborations with experienced scientists, Eurogentec is able to design LNA® Double-Dye probes for any type of applications including MGB Taqman® probe replacement, gene expression and SNP analysis. Our team of design specialists is always available to answer any questions you may have. Please contact us at All LNA® Double-Dye Oligonucleotides are HPLC purifed. They are controlled by analytical HPLC and MALDI-TOF Mass Spectrometry. The optimal recommended length of LNA® Double-Dye probes is 20-25 bases. For optimal results, longer probes should be avoided. Double-Dye Oligonucleotides are provided lyophilized in individual tubes.


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