According to me, the problem starts at question, what killed Engineers. It is showed that they were running, from what?
Also there is no prove that the thing to which Fifield (the geologist played by Sean Harris) turned would became also from Dr. Charlie Halloway (played by Logan Marshall-Green). We also saw that after the intimate act with Dr. Elizabeth Shaw (played by Noomi Rapace) he saw something in his eye, something what was moving and looked like a small worm to me.
Why would Engineers put the black liquids forms into the chamber if it would be so dangerous for them? They were running also to that chamber.
According to me the "DARK LIQUIT" project was infected by Allien DNA and that is what killed them one way or another. We should keep in mind that Engineers died 2000 years ago, so there is a plenty of time to mutate. Maybe this is not the origin of Alien, maybe this is just let's say the first encounter with humans.
So to answer the question. The "dark liquid" manipulates with DNA, but obviously, the Alien DNA has it own manipulation method. The Aliens infected the "dark liquid". That turned the small worms in the chamber ground to big breaking-arms creatures. That is how the small worm appeared in the Dr. Charlie Halloway eye and why Dr. Elizabeth Shaw had to make that very nice surgery on herself. Whatever was the purpose of the "dark liquid", it was altered by Alien DNA. The "dark liquid" has the ability to destroy DNA, however Alien one has the ability to survive in any conditions. Put these together and you have a movie of many answersquestions : D