Desperately need accurate Legal Advice for Son in NY?

Son 28 charged w/ raping 13 yr old stepdaughter, he's raised last 10 yrs, married mom 2 years ago, they have 7 yr old girl. Over the last yr teen has gone downhill fast as she's gotten into trouble at school and at home repeatedly, smoking, making out with boys etc. She has always been argumentative and defiant of all authority figures. The night this accused took place my son had grounded her for having a hissy fit cuz she couldn't go to the store with her mom. Time frame from when this happened is 13 minutes from when Mom left till teen was at friend's calling Mom. Teen has been in dire need of psych care but was only recently commited 3 times, which she blames on the She was taken to the hospital - kit showed nothing except that she wasn't a virgin. DA says there is a mix of son's dna & hers on her shorts. Son & wife had hrs before & teen sat on bed. My son is innocent, girls were removed to an uncle's & it is killing son not to see his lil girl. HELP PLEASE