In apoptosis, genomic DNA is usually partially degraded, with a hallmark
"nucleosomal ladder" of 190-200 bp and multiples thereof appearing, although
in many systems only a minority of the genomic DNA is degraded this far,
much of it remaining in 50+-kilobase fragments.
To analyze apoptotic DNA, it would seem to be desirable to isolate genomic
DNA of all sizes rather than just small ladder DNA. Standard DNA isolation
procedures accomplish this, but there are often problems in redissolving
ethanol-precipitated high-molecular weight DNA without extensive shearing.
Several companies sell genomic DNA purification kits involving ion-exchange
columns and protocols that do not include ethanol precipitation. Has anyone
had experience with these kits in purifying apoptotic DNA? If so, how does
column-kit-purified DNA compare with DNA purified by non-column methods? How
do the recoveries of ladder-size DNA vs. 50+-kilobase DNA compare in these
Steven L. Sabol
Lab. of Biochemical Genetics
sabol at codon.nih.gov