Other forms: punctuated, punctuating, punctuates
To punctuate is to break something up at intervals. Silence broken by a cough, a walk punctuated by stops.
The everyday sense is the figurative one, and it takes by or with. What it always means is that one thing keeps interrupting another at intervals rather than continuously. The original sense belongs to writing, since punctuating a sentence means putting in the commas and full stops. Both come from the same idea of making points in a line. The noun punctuation covers the marks themselves.
Punctuation is pricking. Latin pungō meant to prick or puncture and pūnctus was the point it left, so punctuating a text is marking it with points. The same verb gives punch.
Proto-Indo-European
*pewǵ-
Medieval Latin
pūnctuātus
English, today
punctuate
Built from
Medieval Latin pūnctuātus, of pūnctuō (“to mark with points”), from Medieval Latin pūnctus (“a point, dot”), from pungō (“to prick, punch”); see -ate and -ate. a doublet of punch.
Etymology from Wiktionary, CC BY-SA