Migration of Chromosomal vs. Plasmid DNA

[RPSCOTT]

> From:   IN%"<@CGNET.COM:muriana at aclcb.purdue.edu>"  "muriana"
> Does anyone have a good reference explaining why chromosomal DNA migrates
> in the range of moderately-sized plasmid DNA (bacterial) on agarose gels,
> considering that it's so much larger.  I'm looking for one or more good
> references for graduate students (and myself too).  I can find material on
> CCC vs. OC vs. linear plasmids, but not **why** chromosomal DNA migrates so
> close to ~30-kb plasmids while it may be ~2-4 mb.  Thanks in advance.
> Peter

There is this concept of limiting mobility in sieving separation techniques like 
gel electrophoresis. While light nucleic acid fragments easily traverse the 
agarose matrix because they are small enough to pass thru most of the gel 
pores, huge fragments on the other hand have to alter their conformation 
to literally squeeze out of the gel pores. When the fragments are about 
30-40 kb or more, the gel is practically unable to sieve them off and resolution
is defeated under ordinary electrophoretic condition.  Such  huge fragments 
would then apparently co-migrate with a 20-30 kb marker. Chromosomal
DNA samples are best observed thru pulse-field gel electrophoresis 
(Schwartz & Cantor, 1984, Cell 37: 67). Try looking-up other general 
references on pulse-field techniques. These should give you adequate 
dicsussion on why ordinary agarose gel electrophoresis fails in resolving
heavy nucleic acid fragments. For starters try  Michael Finny's article in the 
Red Book (Current Protocols in Molec. Biol.), "Pulse-field gel 
electrophoresis." 

Have a pleasant day Peter. ;-)

Scott
Intl Rice Res Inst
PHILIPPINES
e-mail: rscott at irri.cgnet.com