How can I strengthen my knee muscles/tendons?

I'm running half marathons and having issues with my knees, I just can't find the right pair of trainers so sticking to neutral ones for the moment. I have no problems running uphill but when I run down hill I feel like I'm going to blow my knee out at any time. There is a fair bit of pain but only downhill. If the 13 miles were flat I would be fine!! I'm doing double step knee ups on the stairs( liftting my bodyweight up two stairs with just one leg) is there anything else I can do to strengthen my knees?