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From Xu et al 2004, they have anti-KaiC polyclonal antibodies which they used to do a phosphorylated KaiC assay; we can use this method to analyse KaiC fluctuation.

From the paper:

 KaiC Phosphorylation Assay. Cyanobacterial cultures were grown to
 an OD750 of 0.2. After a 12-h dark pulse, the cultures were treated
 with 10�MIPTGfor 3 h at 30°C in light with air bubbling, and�40
 ml of the cultures were collected for preparation of total extracts.
 Immunoblot analysis for KaiC was performed on 5 �g of total
 proteins per lane according to the previous description (20), except
 that we used a highly specific mouse polyclonal antibody to KaiC
 and a SuperSignalWest Pico Chemiluminescent Substrate (Pierce).
 The phosphorylated KaiC signals were quantified as before (16)
 and analyzed by Student’s t test.
"Image of figure shown in Xu paper"