Increased sensitivity for distinguishing DNA base-pair mismatches
A bicyclic nucleic acid is a modified RNA nucleotide that when incorporated into an oligonucleotide sequence, imparts structural rigidity and improves base stacking for greater Tm. This modification is not compatible with PCR, because modified bases are not extendable by Taq polymerase.
Prices listed include probe sequence (up to 25 bases in length), up to 6 BNA base insertions, reporter, quencher, and HPLC purification. Probes are shipped in 4–6 business days.
Submit custom designs directly (see Product details for design considerations), or for design assistance, email email@example.com (design fees may apply).
IDT has licensed from Isis Pharmaceuticals the rights to manufacture BNA oligonucleotides for life sciences research and development activities, excluding therapeutic, diagnostic, in vivo, and mass spectroscopy applications. BNA oligonucleotides are not licensed for resale or transfer to third parties. Diagnostic licenses for BNA oligonucleotides are available from Isis Pharmaceuticals.
BNA bases have a modification to the ribose backbone that locks the base in the C3′-endo conformation, which favors RNA A-type helix duplex geometry. This modification significantly increases Tm and is also relatively nuclease resistant.
BNAs can be incorporated into dual-labeled probes for use in 5′ nuclease assays. Because BNA bases significantly increase Tm, PrimeTime BNA Probes can be designed with shorter lengths than standard dual-labeled probes. Shorter probes are more effectively quenched and have a higher signal-to-noise ratio; therefore, they are more sensitive.
More importantly, these probes offer an improved ability to distinguish mutations or single nucleotide polymorphisms (SNPs). A DNA dual-labeled probe typically has a ΔTm of ~5°C between a perfect-match and mismatched hybridization. In contrast, a BNA dual-labeled probe can have a ΔTm of >15°C, greatly increasing accuracy of allele determination in real-time PCR or other methods that use differential hybridization to distinguish polymorphisms.
Tm calculations can be made using the OligoAnalyzer® Tool. The LNA notation (+T, +A, +G, +C) to estimates Tm or mismatch discrimination potential of BNA bases. BNA probe design points to consider include:
For additional assistance with design of PrimeTime BNA Probes, email firstname.lastname@example.org (design fees may apply).