What exactly is the 5 to 3 direction in DNA molecules?

[Mr Rayon]

Tell me about it.

[Kaeroll]

The two ends of a DNA strand are different to one another due to the structure of the phosphate-ribose backbone. The terms 5' and 3' (five-prime and three-prime) refer to the carbon atoms in the ribose; each monomer is attached to the next at these two positions. (Aside: why prime? Why not just 5 to 3? The plain numbers are used to designate carbons in the bases.)

 

DNA is synthesised from the 5' end to the 3' end by DNA polymerase (I think- though the actual enzyme name is irrelevant to this discussion). As such it is conventional to list bases in the 5' to 3' direction, as a form of shorthand. If you've ever studied protein structure this is really quite similar to the N-C convention.

 

Kaeroll

[MedGen]

Correct, both DNA and RNA are synthesis 5' to 3' by adding dNTP's to the free hydroxyl group to the 3' end.

[Fyre4Man]

Its the structure of the DNA strands, in more detail the "backbone" of the DNA strand which contains the phosphate and Sugar (Deoxyribose) so for the Two DNA strands to fit and make a double helix, they have to go different directions, so for an example, DNA strand #1 goes down, while DNA strand #2 goes up and the endings of both of them are related to a 5 to 3, becasue of the number of phosphate and sugars.