Here is a schematic for a possible solution. Since you still haven't said, I've assumed you are using the 5V version of the Q50 and that 8-bit resolution is sufficient. You will need to increase the PWM frequency if you want the settling time to be lower than a few seconds.
The transistor passes the power (up to 250mA) to the HV multiplier. The op amp cannot supply enough current by itself.The high voltage output is on the right hand side of the schematic. The positive side is marked "+ 0-5 kV", and the negative side is marked Gnd. The negative side is common with Arduino ground. If you wanted negative output instead of positive output, then you would need to use model Q50N and change the arrangement of the voltage divider.