We would like to generate a polyclonal antibody for western and IP work, but we fear that if using Freund's adjuvant, we will dramatically increase the cross-reactivity that our antibody would be useless.
I have successfully raised a number of antibodies to yeast transcription-related proteins using Freund's adjuvant and not had problems with reactivity (the antibodies were primarily used for western blotting).
the use of Freund's adjuvant generally enhances the production of antibodies. Of course, use the complete adjuvant only for the first immunization and the incomplete for the following ones
Most commercial antibodies are produced with Frends adjuvant. You get a higher antibody titre with Freunds than if you do the immunization without adjuvant. Normally we use FCA for the first immunization and FICA for the following immunizations. You should try to get a good mixture (a white, thick mixture that looks like mayonaise) so that it remains at the site of deposition.
Cross-reactivity is not caused by any adjuvant. If the protein you need antibodies to contains conserved domains shared with other proteins from the same species, you should not use the entire protein as the immunogen. Best then is to pick a unique part of the protein for immunizations. Use FCA for first immunization, then FA for the boosts.
Cross reactivity is not caused by adjuvant. The main functions of the Complete Freunds adjuvant are to help in illiciting immune response against immunogen, protect immunogen from proteases and slow release of immunogen from the depot.