What is 3'-5' and 5'-3'?

Peter J. Floriani, Ph.D. floriani at epix.net
Thu Aug 6 22:48:48 EST 1998

```Jeff Heeney wrote:

> A book entitled dictionary of science states "The two strands run in
> opposite directions, 3'-5' on one strand corresponding to 5'-3' on the
> other.
> What the hell are they talking about?!
> Sorry, specifically...what is the meaning of the ' character.
> Thanks.
> You can go back to doing something serious now.

It's a serious question - so I'll try answering it. Seriously!

The numbers are the numbers of the carbons of the deoxyribose (sugar)
part of the DNA (remember that means deoxyRIBOnucleic acid). These carbon
numbers are marked with a prime to distinguish them from the carbons
which are in the purine or pyrimidine part - these are the famous A, C,
G, T "bases" you've heard about. The carbons in those are numbered, but
not marked with a prime. The prime distinguishes the carbons in the ACGT
part from those in the sugar.

Now both the carbon called five-prime and the carbon called three-prime
have OH groups attached. These are the places by which one nucleoside
(that means a purine or pyrimidine stuck to the sugar) is stuck to
another. Either of these places can be connected to a phosphate (PO4),
and then the unit is called a nucleotide.

The three-prime carbon of one base may be connected to a phosphate and
that same phosphate may be connected to the five-prime carbon of another
base. This connection is called a phosphodiester bond. So, DNA is a
string (sorry, that's my computer science showing) DNA is a polymer of
nucleotides.  Clearly, both the five-prime and the three-prime carbons of
each nucleotide (except for the first and last) are connected to other
nucleotides. The "ends" are different, since one has a free five-prime
carbon (the 5' end) and the other has a free three-prime carbon (the 3'
end).

Like this:

base		   base		   base		   base
5'-sugar-3'-PO4-5'-sugar-3'-PO4-5'-sugar-3'-PO4-5'-sugar-3'

(I hope that shows the "base" on top of the "sugar" - if not, just use

For more details, see the nearest available organic chemistry book. One
I've used is "Biochemistry" by J. David Rawn, p. 627-629 and 665-668.

Sincerely,

Peter J. Floriani, Ph.D.
floriani at epix.net
====================================================================
"I have often thanked God for the telephone." G. K. Chesterton, 1910
====================================================================

```