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DNA sequencing/info-theory paper in PNAS

S. A. Modena samodena at csemail.cropsci.ncsu.edu
Wed Mar 24 02:22:45 EST 1993


In article <SEB1005.93Mar24020203 at mbfs.bio.cam.ac.uk> you write:
>In article <1993Mar23.220831.23581 at ncsu.edu>, samodena at csemail.cropsci.ncsu.edu (S. A. Modena) writes:
>next comment:
>
>........
>But how exactly does this relate to the decoding scheme?  As I recall,
>in the Meselson-Stahl expermiment, cells were grown in heavy media
>(N15?) for a long time, and then switched to light for a few cell
>divisions.  The ultracentrifugation runs looked like this:

I had to *change* something to get your schematic fully correct:

>
>t=          0       1       2      3               Stage-3 (should be) 
>
>Top                        ----  ====                 ======= 
>(light)     
>
>                   ----    ----  ----  <-- Nope! 
>
>Bottom
>(dense)   ----
>

Yes, it's a two-bit info situation......now let's present the contrasting
experimental result: if conservative replication were true.....

t=                       0        1           2

Top (light)                     -----      =======




Bottom (dense)          =====   ------

The first diagram (which I corrected) is called The Semi-Conservative
Result and it is self-proving, because they could have quenched cell
cultures at time stages 1, 2, and 3 and centrifuged them simultaneously,
and a comparison of the tubes does NOT require any density determination
because there are *three* band positions.

However, the conservative replication results, if they had occurred, would
have required *additional* information.  They would have had to determine
the density of the two zones where the bands occurred in order to *prove*
that the buoyant densities of the DNA species corresponded to all-light 
and all-dense; and so to unequivically rule out a defect in the experiment
or the existance of yet another, unexplained mechanism at work.  :^)


>
>Indicating, of course, that at time zero, all of the DNA is
>heavy-labled.  After one round of replication, all of the molecules
>are half-heavy, half-light (due to having one of each type of strand).
>At time 2, however, there are some all-light molecules, and some
>middling ones.  By time 3, most of the molecules are all-light.

          The words say it correctly, the diagram did not.  :^)
>
>Maybe it relates to the time at which I'm reading, but I assume I'm
>entirely missing the information-encoding point here.  Could you
>explain it further?
>
>Steven E. Brenner               |  Internet    seb1005 at mbfs.bio.cam.ac.uk

Well to my mind it is ISO-morphically the same experimental outcomes as:

      Column labels are mixtures of nucleotide chain terminiators

     SEQUENCE       ( C+A )      ( C+T )

        G
        G
        T                        -------  
        C           -------      -------
        A           -------
        G
        G

     Four outcomes are possible:    A =  band only in left lane
		                    T =  band only in right lane
				    C =  band present in BOTH lanes
			            G =  band absent in both lanes

But the authors claim that detecting G by absence is foolish (and it
doesn't apply in the Messelson-Stahl experiment for the same reason).
To my mind's imagination, the side-by-side bands for C is equivalent to the
radio-labeled heteroduplex.  The A-single band is the fully-labeled
started DNA and the T-single band is the "light" DNA of stage 3.  :^)

Steve
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