How does Mikoto know about the Sisters before the Sister's Arc? Misaka Mikoto seems to know about the sisters before the Sister's-arc, as she says both in the prologue of the first LN and the Railgun-manga:


  Have you heard how my DNA map was supposedly analyzed and military Sisters were created based on it?


How did Mikoto know about the Sisters back then? She found out during the Sisters Arc (which happened later) that the Sisters exist and the rumor just spread then, too (at least it seems to me). How could she tell Touma about them?
After Mikoto meets Nunotaba Shinobu, she starts investigating her and finds her connection with the 7th Medical Research Center, who were researching her DNA map to create an army of level 5 clones.

This is covered in the Railgun manga and Railgun S anime.

Initially she thought the Sisters project was abandoned because the clones would only be Level 3 (thus not realizing the plan for an army of Level 5 clones), but it's not until later that she realizes the Sisters were utilized for the Level 6 Shift project.