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.