Dear John,

For this specific task, I would approach a lab that offers a synthetic library of some sorts (be it scFv, nanobodies, Fabs etc) and a stringent selection process such as phage display. While there are some anti-DNA antibodies out of immunisations, DNA is probably still not the most immunogenic molecule, so a classical mAb campaign may well fail. Also, using in vitro selection, you are able to control buffers etc, which may be helpful for maintaining the specific DNA structure. And you can counter-select against other DNA structures.

Good luck with this project!

Hello John...

Phage display would be rank 1.

Will be difficult with immunization methods

Good luck

Here are two papers on the selection of quadruplex-specific antibody-scFv by phage-display

Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J., and Plückthun, A. (2001). In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. U.S.A. 98, 8572-8577. https://www.bioc.uzh.ch/plueckthun/pdf/APpub0202.pdf

and selection of quadruplex-specific DARPins by ribosome display:

Scholz, O., Hansen, S., and Plückthun, A. (2014). G-quadruplexes are specifically recognized and distinguished by selected designed ankyrin repeat proteins. Nucleic Acids Res 42, 9182-9194. https://www.bioc.uzh.ch/plueckthun/pdf/APpub0364.pdf

out of our lab.

Dear John,

For this specific task, I would approach a lab that offers a synthetic library of some sorts (be it scFv, nanobodies, Fabs etc) and a stringent selection process such as phage display. While there are some anti-DNA antibodies out of immunisations, DNA is probably still not the most immunogenic molecule, so a classical mAb campaign may well fail. Also, using in vitro selection, you are able to control buffers etc, which may be helpful for maintaining the specific DNA structure. And you can counter-select against other DNA structures.

Good luck with this project!

If I recall correctly, pure double-stranded DNA is not immunogenic, however, single stranded one is. Binding the DNA to some carrier, such as a basic protein or poly-peptide (e.g. poly L-lysine) may help.

Perhaps generating monoclonal anti-dsDNA may be achieved by selecting clones from mouse strains, having congenital autoimmune disease, such MRL/l and NZB/NZW.

Hi John

As some of the replies mention, DNA (and RNA) are poor immunogens, because they are self-antigens which would generate an autoimmune response. In fact, the few initially described come from selection of clones of autoimmune mice (as Falk rightly suggest as an alternative), but not elicited to recognize a particular antigen. Of course selection from phage display is a great choice, it depends on the expertise you have, the time you are prepared to invest and what is your goal with those antibodies. I am sure there are a number of labs with that expertise that you could collaborate with, as Christian suggests.

If you want to generate the antibodies naturally, say in mice (that is elicited against a particular epitope), it is obviously non-trivial, but we have succeeded in doing so by immunizing a particular DNA that binds to a DNA binding domain strongly . In fact, it appears that the protein has a lot to do (I noticed that Falk also suggest a polycharged cationic carrier). These days I would try assembling a larger and stable particle, either by an engineered carrier or simply chemical crosslinking. This would ensure long lasting circulation in the system for immunogenic epitopes to te selected. The work is mostly summarized in one of the references I attach (the first, and the most recent).

We obtain what it appears a couple of antibodies with some sequence specificity for double stranded DNA, but they ended up having a strong affinity and specificity against the 5" trinucleotide. The interaction is fundamentally based on stacking between base aromatics and a few trps and tyrs in the right place in the antibody. Given the size of the required contact area for a double stranded B DNA, I suspect sequence specificity with high affininty for such a ligand is not likely to happen. But this is just speculation.

I would not be surprised if some of the existint a-DNAbs work for your particular goal, or, more laborious, using these as frames for selection of particular sequences.

Cheers

Gonzalo

Article Specific Recognition of a DNA Immunogen by its Elicited Antibody

Article Generation of Sequence-specific, High Affinity Anti-DNA Antibodies