Most of PentaBase’s reagents are based on our own oligonucleotide platform chemistry, a DNA analogue also known as Intercalating Nucleic Acid, INA®. An INA® is comprising standard nucleotides (DNA and/or RNA) with one or more “pentabases” inserted in the sequence during manufacturing. The insertion of a pentabase will have one or more of the following effects:
- Increased affinity towards complementary DNA and RNA
- Increased specificity, reducing off target effects
- Increased stability
- The ability to differentiate between a DNA and RNA of the same sequence
- A defined non-temperature dependent secondary structure when unbound
As said by the Australian scientist George Miklos in Nature Bioentrepreneurs, 23. June 2003: “Anything an oligonucleotide can do, an INA® can do better,”. More importantly, “INA can be utilized in some detection systems where oligonucleotides cannot,” he adds.
Illustration of pentabase modified DNA oligonucleotides hybridising to their complementary DNA targets. The pentabases are shown in red.
A) The pentabase is added to the end of the oligonucleotide and stacks on top of the formed duplex working as a lid that prevents water from unzipping the formed duplex. Among other features, it increases the stability of the formed duplex and the stability against for example 5′-exonucleases.
B) The pentabase is inserted internally in a DNA oligonucleotide. When hybridising to a complementary DNA, it makes room for it self to intercalate. This increases the stacking effect of the formed duplex and thereby the sensitivity, specificity and stability. Please note that the pentabase does not pair with any nucleotides of the target strand and therefore is a true addition of a nucleotide. You can therefore often use the same sequences that you are using now, adding the pentabase as a “gluing” nucleotide introducing extra features into your oligo.
If one of the above features are useful in your approach, then why not try it out? You are always welcome to talk to us with your wishes and if we promise that pentabases can solve a specific problem it can – or it is free of charge.