The term comes from Shelley herself, and is based on the Greek myth of the titan Prometheus, who gave fire to humans against the will of the gods, which allowed humans to develop civilization. In the Gothic literature, the Modern Prometheus (a title first given to Victor Frankenstein himself) is a man who madly turns to science to make the unnatural possible. Usually by reanimating a corpse.
In films, this is Dr. Caligari and his creation Cesare (or at least, the Dr. Caligari and Cesare that insane Francis imagines up) or Henry Frankenstein and the Bride.
Why is this trope so prevalent in Gothic fiction?
Part of it may have to do with when the Gothic is said to originate. The genre comes from England in the first half of the 18th Century. This was right in the middle of the Industrial Revolution. So, like my generation, the original writers who grew up in England at that time were being raised during some very quick and abrupt changes in technology.
I don't think it's surprising that authors of the time were interested in how this rise of technology (and with it, science) would affect how they interacted with nature. I think this movement is similar to how now we have a lot of stories (like 'Black Mirror') that are about dystopias where technology is the driving force.
Greek mythology has always been interesting to me because of how human-like the gods were. They made bad decisions and they broke rules and sometimes were punished unfairly. I think that the gods who were most like us are the ones we latch on to. Its not surprising that during the Gothic period, where humans for the first time could really change nature around them on a massive scale, that the authors would become interested in exploring what we may do, and what it would mean for us morally.
'Frankenstein' is a story majorly focused on this topic, and is a good representation of the Gothic genre in general. Looking at the story and the trope through modern lenses-- with an eye towards the history of the time-- makes it clear why this trope is prominent in Gothic literature.