A blinking question mark implies the system can't locate a bootable disk.
You stated you were able to boot up under a USB external bootable drive (optical, HD or thumb drive) and were able to run Apple's Disk Utility on your internal drive. So you are able to 'see' the disk which means the drive & the drives SATA cable are in good working order as well as the systems logic board.
Which is all good news! Then the issue is the setup of the disk its self. Can you tell us what happened. Did you try installing some software or upgrade the OS?
Do you have the recovery CD/DVD/USB thumb drive that came with the system? Or, do you have an external disk that has the OS installer present on it.