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I was reading base pairing sequence in DNA and found 5-3 direction but my question is why we are using word prime with 5 or 3 such as 5 prime 3prime. Prime stand for?

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  • $\begingroup$ The answer to this requires a proper chemical representation of the sugar and base rings, which is not present in the answer to " What does 5' and 3' mean in DNA and RNA strands?", but can be found in the custom diagram in my answer to another question. $\endgroup$
    – David
    Apr 21 at 16:35
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It comes from Lagrange's notation in math, where "prime" denotes a derivative. So if you have a function x and then a derivative function of x, you'd call it x' (x primer) and if you have another one then it's x'' (x prime prime). So basically you are adding prime to say "another one of x". In DNA this refers to Carbons. DNA is composed of nucleotides which are composed themselves of a sugar + a nitrogenous base (or nucleobase) + a phosphate. Both the sugar and the nucleobase have Carbons and those carbons are called with numbers. The nucleobase gets the first "round" of names: Carbon 1, Carbon 2, etc. while the sugar gets the prime ones: Carbon 1 prime (that is, another Carbon 1), Carbon 2 prime (another Carbon 2), etc. So the 5' means Carbon 5 from the sugar in the nucleotide.

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  • $\begingroup$ Welcome to Biology.SE! Please provide references supporting your assertion that this use in Chemistry is derived from Lagrange's notation — in general, on this site we expect answers to be backed up by supporting references. Thanks! $\endgroup$
    – tyersome
    Apr 21 at 17:27
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"Prime" is how you enunciate '.

e.g. "five prime" is the enunciation of the written 5'.

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