The group designed a PrimeTime qPCR LNA Probe targeting a P. armandii SNP sequence.The probe was 24 bases long and contained 6 LNA bases in addition to the 5′ 6-FAM label and 3′ black hole quencher (3BHQ_1). A second PrimeTime qPCR LNA Probe was designed to serve as a blocker probe for species of trees related to the species of interest, Pinus armandii. The probe was also 24 bases long with 6 LNA bases in addition to a 5′ HEX label and a 3′ BHQ. These reporter dyes (HEX and FAM) can be spectrally resolved from each other because they emit at different wavelengths.
PNA (peptic nucleic acid-locked nucleic acid) clamp Primers and LNA (locked nucleic acid) mutant probes from IDT were used in a PNA-LNA PCR clamp assay for EGFR mutation analysis.
New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs.
Improved modified probe design through consideration of modified nucleic acid thermodynamics.