LNA PrimeTime Probes

LNA PrimeTime Dual-Labeled Probes

 
Locked Nucleic Acids (LNAs) dual-labeled probe Ե ֽϴ. LNA bases Tm Ǽ ְ ֱ LNA duallabeled probes (DLPs) standard DNA DLPs ªϴ. ª probes quenching ϰ signal-to-noise Ƽ sensitiveմϴ. ߿ probe SNP(single nucleotide polymorphisms) Ȥ mutation Źϴٴ Դϴ.
DNA DLP perfect match mismatch hybridization Tm ~5 ɻ Դϴ. ϳ LNA DLP Tm 15
־ real time PCR̳ ٸ assay ־ ſ Ȯ polymorphism ֽϴ.
Sequence context LNA base DNA oligo ߰ insertion Tm 3-6 ŵϴ.
IDT 6 LNA bases LNA DLP õϰ LNA bases SNP site base üǾ մϴ. base ߰
Tm ֵ ֽϴ.
 
Note that relative binding affinity (Tm) of LNA bases are LNA: LNA > LNA:DNA > DNA>DNA. It is important to examine the probe sequence for self-dimer and hairpin formation and minimize designs that allow for LNA:LNA pairing.
 

Mini LNA PrimeTime Probes

 
Mini LNA PrimeTime Probes FAM and HEX dyes ϸ 500 reaction 뷮(0.5 nmole) ˴ϴ. Probe optimization Ǵ ϰ ſ ̻ ǰԴϴ.
 
* Ideal for analyzing a small sample set or performing a few reactions to optimize probe designs
* Available with FAM and HEX dyes and Iowa Black FQ
* Guaranteed normalized yield of 0.5 nmoles
* ҿⰣ: 7-10
 

Mini LNA PrimeTime Probes 差

 
5' Reporter Dye(s)
Quencher(s) Delivery Amount
FAM Iowa Black FQ * 0.5 nmole ₩200,000
HEX Iowa Black FQ * 0.5 nmole ₩200,000
 
 

LNA PrimeTime Probes

 
LNA PrimeTime Probes FAM, Cy3, Cy5, TEX, TYE, HEX dyes پ reporter ռ Ϸθ ˴ϴ. (250 nmole, 1 µmole)
 
* Available with FAM, Cy3, Cy5, TEX, TYE, and HEX dyes
* High synthesis scales (250 nmole and 1 µmole) for large-scale and high throughput requirements
* ҿ Ⱓ: 7-10
 

LNA PrimeTime Probes 差

 
5' Reporter Dye
Quencher Synthesis Scale Min Guarantee Price
5' 6-FAM 3' Black Hole Quencher 1 250 nmole 8 nmoles ₩927,000
1 µmole 20 nmoles ₩1,323,000
3' Iowa Black FQ 0.1 0.5 nmoles ₩200,000
250 nmole 8 nmoles ₩600,000
1 µmole 20 nmoles ₩1,080,000
5' Cy3 3' Black Hole Quencher 2 250 nmole 4 nmoles ₩1,026,000
1 µmole 10 nmoles ₩1,458,000
3' Iowa Black RQ-Sp 250 nmole 4 nmoles ₩855,000
1 µmole 10 nmoles ₩1,197,000
5' Cy5 3' Black Hole Quencher 2 250 nmole 4 nmoles ₩1,044,000
1 µmole 10 nmoles ₩1,485,000
3' Iowa Black RQ-Sp 250 nmole 4 nmoles ₩873,000
1 µmole 10 nmoles ₩1,224,000
5' TEX 615 3' Black Hole Quencher 2 250 nmole 4 nmoles ₩1,350,000
1 µmole 10 nmoles ₩1,890,000
3' Iowa Black RQ-Sp 250 nmole 4 nmoles ₩1,224,000
1 µmole 10 nmoles ₩1,719,000
5' TYE 563 3' Black Hole Quencher 2 250 nmole 4 nmoles ₩1,305,000
1 µmole 10 nmoles ₩1,827,000
3' Iowa Black RQ-Sp 250 nmole 4 nmoles ₩1,179,000
1 µmole 10 nmoles ₩1,656,000
5' TYE 665 3' Black Hole Quencher 2 250 nmole 4 nmoles ₩1,305,000
1 µmole 10 nmoles ₩1,827,000
3' Iowa Black RQ-Sp 250 nmole 4 nmoles ₩1,179,000
1 µmole 10 nmoles ₩1,656,000
5' HEX 3' Black Hole Quencher 1 250 nmole 8 nmoles ₩963,000
1 µmole 20 nmoles ₩1,368,000
3' Iowa Black FQ 0.1 0.5 nmoles ₩200,000
250 nmole 8 nmoles ₩650,000
1 µmole 20 nmoles ₩1,125,000
 
 

Design Considerations

 
Depending on sequence context, insertion of an LNA base into a DNA oligo can increase the Tm by 3–6C. However, there are some sequence-specific designs involving GT and CA mismatches where LNA bases actually impair specificity [1].
LNA bases should be placed at the SNP site and adjacent bases. The SNP should be positioned in the center of the probe if possible. Additional LNA bases can be added towards the 3-end of the probe to adjust Tm as needed.
The relative binding affinity (Tm) of LNA bases are LNA:LNA > LNA:DNA > DNA:DNA. Therefore, it is important to examine the probe sequence for self-dimer and hairpin formation and minimize designs that allow LNA:LNA pairing. In addition, IDT recommends up to 6 LNA bases be placed in an LNA DLP.
 
For additional assistance with design of LNA PrimeTime Probes, contact IDT Technical Support.
 

References

 
Davialieva K, Kiprijanovska S, Plaseska-Karanfilska D. (2013) Fast, reliable and low cost user-developed protocol for detection, quantification and genotyping of hepatitis C virus. J Virol Meth, 196:104-112.
Standard desalted IDT Primers and ZEN Double-Quenched Probes were used for HCV detection and genotyping. The primers and probe used in this study were designed based on 45 HCV sequences (obtained from GenBank) correspond to genotypes 1a, 1b, 2a, 2b, 2c, 3a, 3b and 4 according to the HCV genotype nomenclature.The developed assays for HCV detection and genotyping were set up to detect and discriminate four HCV genotypes.
Owczarzy R, You Y, et al. (2011) Stability and mismatch of Locked Nucleic Acid–DNA duplexes. Biochemistry . Biochemistry, 50(43):9352–67.
Johnson MP, Haupt LM, and Griffiths LR . (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res, 32(6):e55.
Ugozzoli LA, Latorra D, et al. (2004) Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Analytical Biochemistry, 324(1):143–152.
Letertre C, Perelle S, et al. (2003) Evaluation of the performance of LNA and MGB probes in 5-nuclease assays. Molecular and Cellular Probes. Molecular and Cellular Probes, 17(6):307–311.
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