BACKGROUND: Ewing's sarcoma is a malignancy characterized by a specific 11:22 
chromosomal translocation which generates a novel EWS-FLI1 fusion protein 
functioning as an aberrant transcription factor. In the present study, we have 
further characterized the junction region of the EWS-FLI1 fusion protein.
METHODS: In-silico model of EWS-FLI1 fusion protein was analysed for ligand 
binding sites, and a putative region (amino acid (aa) 251-343 of the type 1 
fusion protein) in the vicinity of the fusion junction was cloned and expressed 
using bacterial expression. The recombinant protein was characterized by 
Circular Dichroism (CD). We then expressed aa 251-280 ectopically in Ewing's 
sarcoma cell-line and its effect on cell proliferation, tumorigenicity and 
expression of EWS-FLI1 target genes were analysed.
RESULTS: Our modelling analysis indicated that Junction region (aa 251-343) 
encompasses potential ligand biding sites in the EWS-FLI1 protein and when 
expressed in bacteria was present as soluble form. Ectopically expressing this 
region in Ewing's sarcoma cells inhibited tumorigenicity, and EWS-FLI1 target 
genes indicating a dominant negative biological effect.
CONCLUSIONS: Junction region can be exploited further as target for drug 
development in future to specifically target EWS-FLI1 in Ewing's Sarcoma.