Can I apply to a DU college in the second cut off even if I was eligible for the first cut off but did not take admission at that time?

Yes, you can still apply for college admission. All you need to do is bring all necessary documents, but keep in mind that you will be marked as a Defaulter (a Defaulter student fails to appear in the previous cut-off when he was meeting the requirements). 

According to University Regulations, a defaulter can only take admission on the third day of that particular cut-off.

You should go to the college where you want to enroll on the first day and follow the admissions procedure. You are suggested not to tell any teacher about the same because teachers sometimes forget to check if students are defaulters or not. If anyone gets to know, then you will have to come back again on the third day of admission.