NFkB oscillates between the nucleus and the cytosol. In my experience (and in agreement with the literature, link below), maximum initial translocation is at about 60 minutes. At 2 hours it should be back in the cytosol. At 3 hours approximately 50-60% will have translocated back into the nucleus, and so on.

http://www.ncbi.nlm.nih.gov/pubmed/15499023

Thank you Jordan and Md for the response. After reading your responses and going through the contents of the paper, i feel that it is necessary to look at the time points of 60 90 and 120 minutes. Therefore i feel that i would go for the following time points in one experiment: 5, 10, 15, 20, 30, 60, 90, 120, 150, 180, 210, 240, and 270 minutes. Moreover the activator i am using is il-1alpha. I feel that there is some difference in the timings of these translocations according to the activation agent used. do you think that this may be true ?

Nuclear localization of NF-kB family proteins and activation of NF-kB transcriptional activity depend on several factors, including the cell type, culture conditions, inducer of NF-kB activity and time. Assuming that other factors are well controlled (and cells lack significant constitutive activaty of the NF-kB), the time frame for the nuclear localization of NF-kB sub-units  in most cell types varies between 10 to 30 min (the half-life of IkBa is less than 30 min). Once activated, levels of IkBa, which is a transcriptional target of NF-kB, increase in cells. Notably, nuclear localization of the NF-kB proteins may not correlate well with activation of NF-kB transcriptional activity in some cell types. 

The short answer for you is that you are not waiting long enough. Studies with memory and in my lab show you need to wait at least 45 min and up to 3 hrs to see peaks of NF-kB in contexts of learning, memory, and recall as measured by EMSA and Western blots.

[email protected]