Using modern punctuation to help in clarifying and explaining the meanings of the Qur’an is allowed as long as there is nothing that affects its true meaning such as using parenthetical dashes which imply that the sentence between them is not original. This is not allowed since every word and letter in the Qur’an is from Almighty Allah.
Responding to this issue, the prominent Muslim scholar Sheikh Yusuf Al-Qaradawi, states the following:
There is no harm in using punctuation such as commas, semicolons, question marks and exclamation marks when citing some Qur’anic verses. Personally, I like and approve of using punctuation marks as they help people to understand the meanings of the Qur’anic text. Actually, I personally use them when I cite verses from the Qur’an in my books, lectures, private letters and anything else that I write. I have been doing so for many years and I advise all writers to do the same.
My only objection lies in the use of parenthetical dashes, as they imply that the sentence between them is not originally in the text and this may cause unaccepted confusion to the reader.
I would like to remind you that scholars in the past permitted Qur’anic verses to be written in the common style of writing, even if it was in contrast to the traditional Ottoman style, when citing parts of the Qur’an in an article or a research paper. They did not make it obligatory to follow the traditional Ottoman style except when writing the mushafor complete parts of it.
Accordingly, I believe that there is no harm in using such marks for the purpose of clarification and attaining a clearer meaning. Finally, may Almighty Allah confer mercy upon the person who helps his fellow Muslim achieve goodness!