A widely accepted mark for DNA double stranded breaks is yH2AX. This is phosphorylated form of Histone 2A.X. You can use an antibody raised against the phospho-epitope for IHC and IF. 

Here is an example of yH2AX staining in brain of mice (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637871/)

This is the antibody we use most often in the lab (http://www.cellsignal.com/products/primary-antibodies/phospho-histone-h2a-x-ser139-antibody/2577)

^^^ Her paper is one of the most widely cited when discussing Alzheimer's.

Here is another paper:

http://www.redjournal.org/article/S0360-3016%2808%2902398-5/abstract

The other big one is DSBs in response to Xrays:

http://rsif.royalsocietypublishing.org/content/11/100/20140783

Though this uses 53BP1 foci analysis in embryonic brain and I'm not entirely sure that will help you as much as the above suggestion.

yH2AX foci is a good indication (several antibodies are giving quite good results: millipore 05-636, abcam 11174, cell signaling 2577) however depending of the fixation and unmasking you could have a lot of background.  The best is to have as a control a P5 cerebellum irradiated with 5-10 Gy and recovery of 1 hour as a positive control, the egl in this case will be positive. The best results are obtained with fixation overnight (perfusion even better) at 4 degrees in PFA 4%, cryosections 10 um and unmasking 40 min at 95 degrees in citrate buffer . I would suggest also to perform TUNEL assay to exclude the small fraction of yH2AX foci which are associated with DNA fragmentation. For 53BP1 i will be more careful, the foci are not always there but rather and increase of expression and 53BP1 is tissue/cell -specific. Some people were using also comet assay which can provide good information

Thanks everyone.