Fis protein can bend DNA chain with length much shorter than its persistence length. We applied single-molecule fluorescence resonance energy transfer method to probe these conformational changes. A broad distribution of end-to-end distances correlates well with the molecular dynamics simulation. The flexibility of DNA upon Fis binding is attributed to the breakages of hydrogen bonds between base pairs. DNA kinks at specific sites, instead of continuous bending. The loosening of DNA structures might have biological implications for the functions of Fis-proteins as transcription cofactors. (C) 2010 Elsevier B.V. All rights reserved.