Genetic Code

Bill_A_Nussbaumer at Bill_A_Nussbaumer at
Wed Nov 3 11:51:26 EST 1999

Bill A Nussbaumer at BDX
11/03/99 11:43 AM

> I referring to a Could someone explain the numbers 5' and 3' in the
> terminal sequence for a given strand of DNA?

I think what your asking is answered by the following:

If you take a look at the chemical structure of DNA you'll see that it's based
on a ribose sugar containing 5 Carbon atoms which are numbered 1' through 5'
according to organic chemistry convention.  (I'm not an organic chemist so I
won't go out on a limb to explain that further).  Attached to the 3' Carbon atom
is a hydroxyl group.  This hydroxyl is the reaction site where the next base in
succession is attached.  This reaction attaches the phosphate group of the next
base to the hydroxyl group of the previous base to form the phosphodiester
linkage.  As you may have guessed, the phosphate group on each base is attached
to the 5' Carbon of the ribose sugar.  I recommend looking at a textbook such as
"Molecular Biology of the Gene" for diagrams that will make what I'm saying much
more clear.  The point is that the 3' end is the end of the DNA base chain
because attachment of the next base occurs at the 3' Hydroxyl (The 5' phosphate
group is already attached to the 3' hydroxyl of the previous base - it may help
to visualize the 5' phosphate of the very first base as unattached to any other
bases).  This should also make it apparent why the extension (i.e. replication
DNA ---> DNA, and transcription DNA ---> RNA) moves in the 5' to 3' direction.

> The two strands of the Double Helix run in opposite direction 5' -> and 3->.
DNA polymerase can
> synthesize DNA in only the 5' - to - 3' direction  - resulting in the
> ("lagging strans") short stretches (5' -> and 3->) with gaps in between,
> which will be filled by the action of DNA polymerase I and sealed with
> ligase. What I think we're talking about is elongation down the chain,
> relating to the ends (5' -> and 3->) the hydroxyl (binding)   or
> nucleotides. I read that when a 5'- protected dinuclotide condensed with
> a 3'- protected mononucleotide forms trinuclotide. This sycle of
> condensation, specific removal from one end until the desired length is
> synthesized. But I would like to get a better grip on the (5' -> and 3' ->

Was there a question in the rest of your post?  You seem to be talking about
synthetic DNA synthesis which is not a natural process and really has nothing to
do with the double helix, DNA polymerase synthesis, or lagging and leading
strands so I'm not sure exactly what you're after.  Chemical synthesis involves
pumping chemicals through a column containing an individual nucleotide attached
to a solid support.  The protecting groups on this nucleotide are manufactured
by organic chemists to ensure that nothing prematurely attaches to the
nucleotide.  Before the synthesis occurs you must chemically remove these
groups, wash them away, and expose the unprotected base to the next nucleotide
(called phosphoramidites due to their own chemical modification and protecting
sites).  This cycle then repeats one base at a time until the desired length is
reached.  Maybe what I said above will help.  Finding the text book I mentioned
above at the library would be your best bet because it has much more info with
diagrams to help explain. There is also an explanation of chemical DNA synthesis
in "Current Protocols in Molecular Biology" which may be more difficult to find
if you don't work in a lab.  Also see for a little more info on DNA

Hope I've been some help.
Hope I wasn't doing a homework assignment but I'm happy to help.


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