Well we know there was one common ancestor going back hundreds of millions of years because we share genes with sponges and other simple organisms. Prior to that, DNA could have developed more than once on earth, although just once would be enough. Also, the very first lifeforms on earth wouldn't have used DNA as it's kind of difficult to make and preserve. Presumabley they would have used even simpler molecules. Just what we don't know, although there are lots of good ideas. In a few years very simple living cells will be created from scratch in the laboratory and these will help give us insights into what very early life may have been like.

As for DNA being different, if we ran the earth over again from the start we wouldn't get the same DNA, it would be different even if the end result was much the same. This is how we will be able to detect truely alien DNA life. However, we don't know if DNA is the only molecule suited for complex biological life as we know it. I wouldn't be surprised if something else could work, but DNA is the only one we know will work at the moment.