Lon protease has been well studied in many aspects; however, the DNA-binding specificity of Lon in prokaryotes has not been clearly identified. Here we examined the DNA-binding activity of Lon protease alpha-domains from Brevibacillus thermoruber (Bt), Bacillus subtilis (Bs), and Escherichia coli (Ec). MALDI-TOF mass spectroscopy showed that the alpha-domain from Bt-Lon binds to the duplex nucleotide sequence 5'-CTGTTAGCGGGC-3' (ms1) and protected it from DNase I digestion. Surface plasmon resonance showed that the Bt-Lon alpha-domain binds with ms1 double-stranded DNA tighter than Bs- and Ec-Lon alpha-domains, whereas the Bt-Lon alpha-domain has dramatically lower affinity for double-stranded DNA with 0 and 50% identity to the ms1 binding sequence. Our results indicated that Bt-Lon alpha-domain plays a critical role with ms1 sequence in the DNA-binding specificity. (C) 2009 Elsevier Inc. All rights reserved.