4030 Nucleic Acids Research, 2008, Vol. 36, No. 12 of the synaptic complex is thought to result in maximal activation of the kinase (23). Our results are consistent with a model whereby dimerization of DNA-PK is inde- pendent of microhomology while kinase activity is greatly inﬂuenced by end annealing. There are two models one can envision for the role of DNA in activation of the kinase once these molecules are brought within proximity. One model involves the frayed 50 DNA end being inserted into the active site of the same DNA-PKcs molecule to which the DNA is bound (19,22). The second model positions the 50 strand interacting with the DNA-PKcs molecule that is bound to the opposite DNA strand (32). This model is supported by recent data suggesting that DNA-PKcs is autophosphorylated in trans (33). An addi- tional caveat is that NHEJ-dependent joining of blunt-end substrates can occur in vitro and in cell culture models whereby joining is independent of microhomology. Consistent with this data, we demonstrate that blunt-end DNA eﬀectors are the most eﬀective activators of the kinase. Thus the potential exists for an alternate kinase activation mechanism that may not necessarily include fraying of the termini or nuclease processing. Direct experimental proof of these diﬀering models remains to be obtained and likely will require high resolution mapping of the DNA-protein and protein-protein contacts needed to support DNA-PK activation and NHEJ. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS This work was supported by US Publich Health Service Grant CA-82741 and an award from the Flight Attendants Medical Research Institute. Funding to pay the Open Access publication charges for this article was provided by National Institutes of Health research grant CA-82741 to JJT. Conﬂict of interest statement. None declared. REFERENCES 1. Lees-Miller,S.P. and Meek,K. 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