screen -S session_name -X at window_number stuff $'\003'
# or
screen -S session_name -X -p window_number stuff $'\003'If you want to send something to all the windows, use # (needs to be quoted) as the window_number.
UPDATE:
Screen's stuff command also supports ^X (or ^x) to mean CTRL-X so the following command can also be used to send CTRL-C.
screen -S session_name -X at window_number stuff ^C