you'll have to find literature on Kd values. does depend on the antibody and ligand under question or the oligonucleotide's sequence (GC content) and whether it is modified, such as with LNAs. But ultimately it depends on the application you have in mind that will determine whether you should use an antibody or an oligo.

Do you mean aptamers vs. Ab's? Well, this is very variable and relies on the individual molecules. Nevertheless, many aptamers have Kd values ranging in pM while most Abs range from mM to nM. It is hard to give a general rule as there are also aptamers with Kd in mM. Again, it depends on the individual interaction you are working with. You'll need to actually perform a lot of binding experiments to compare Kd values between aptamers and Ab's against the same target molecule.

But if you're comparing binding strength of antibodies to peptides (which 24 nt would be an 8 amino acid peptide), then typically the antibody will be much stronger. Antibodies are highly specific as well, which gives them an added advantage over peptides. Of course there are many other variables to consider, including size, blood clearance, pharmacokinetics, and application, etc. In vivo, you are going to have a much higher probability of degradation of the small peptide, whereas the antibody should remain more stable over longer time periods. Hope this helps.

Or perhaps Sebastien you are asking what the affinity (Kd) is of a 25-mer duplex DNA as compared to the typical Kd for an antibody (0.1 to 100 nM). Can you elaborate on your question please?

Apologies, I'll elaborate. As George Jackson already mentioned, I'd be keen to know what the general difference in binding strength is between a oligo-RNA interaction and an antibody-protein interaction.

Thanks

Sebastien, that's what I thought you were asking. I used to wonder about the same. Mainly because stability of DNA:DNA and DNA:RNA hybrids is usually expressed in terms of "melting temperature, Tm" instead of Kd. Here's something I wrote on the subject some time ago with some of the few refs I could find:

" ... an 8-mer DNA duplex has an equilibrium dissociation constant (Kd=koff/kon) of ~10 x 10-9 M [84]. A 24-mer at the same temperature has a Kd of ~1 x 10-19 [85]. A “very good” monoclonal antibody might have an affinity (Kd) of 1 nM."

84. Christensen U, Jacobsen N, Rajwanshi VK, Wengel J, Koch T: Stopped-flow kinetics of locked nucleic acid (LNA)-oligonucleotide duplex formation: studies of LNA-DNA and DNA-DNA interactions. Biochem J 2001, 354:481-484.

85. Carrillo-Nava E, Busch L, Mejía-Radillo Y, Boehm K, Hinz H: Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers. J Phys Chem B 2010, 114:16087-16098.

base-pairing is one of the most specific and predictable biological interactions. That's an impressive Kd for a 24 mer. Thanks George.

Thanks for that information George, this gave me a good picture.