ZNA® in comparison with MGB-conjugated or LNA-modified oligonucleotides
MGB (Minor Groove Binder) and LNA (Locked nucleic acids) bases are known to alter the Tm of a oligo sequence. ZNA® shows similar properties concerning increased affinity to their target (Tm increase), especially when it comes to short sequence probes. Additionally, ZNA® has unique features like the enhanced/accelerated target recognition, which can be used to shorten cycling times or for improved quantification accuracy of low abundant transcripts.
You will find approximations about the Tm increasing effect of MGB and LNA, but an exact calculation of the final Tm is not possible, and cannot be provided a priori. The effect of Tm increase is highly dependent on sequence composition and GC content; therefore, each assay has to be optimized.
MGB is often supported by “Superbases”, which increase affinity.
The same applies to ZNA, and metabion offers Tm modifying bases to complement the use of ZNA primers and probes:
- C-5 propynyl-dC (pdC) raising melting temperature by ~2.8 °C per substitution
- C-5 propynyl-dU (pdU) raising melting temperature by ~1.7 °C per substitution.
In summary, ZNA probes provide broad flexibility in assay design and represent therefore an effective alternative to MGB- and LNA -containing oligonucleotides.
Of course ZNA® will not be the solution for all your needs and applications, nor do MGB or LNA. It is a wonderful and promising technology, which has to be explored. Be a part of it!