LINE inserts.

[John Ladasky]

In article <34DBE24F.2D189955 at columbia.edu>,
Joel Guss  <jg183 at columbia.edu> wrote:
>Hi,
>We are trying to find a PCR to genotype mutant mice with a LINE element
>insert.  The primers to detect presense of a WT gene are on either
>sides of where the insert is and work well.  One of the primers used
>to detect the LINE insert is obviously in the LINE element.  PCR with
>this primer, though, gives many nonspecific nonreproduceable bands
>in both wild type and mutant mice!
>This is most likely due to the presense of large numbers of these
>inserts that contain very homologous sequences thorughout the genome.
>Any primer we select even has at least three good anealing sites just
>within the one LINE element we have!
>Does anyone have any experience with this and might be able to lend
>some advice?  We would prefer not to have to use Southerns to genotype
>the mice.
>Thanks.
>                                                        Joel

	LINE elements are typically about 6 kB long, correct?  I have
recently experienced something similar.  I have cloned a fragment which
contains an Alu repeat.  I placed one of my sequencing primers inside
the Alu repeat, and for this purpose the primer works fine.  But when I
try PCR with it, I get a huge smear.

	If you're feeling a little ambitious, you could try doing a long
PCR assay.  In order to pull this off you will need to know a bit of se-
quence clear on the other side of the LINE sequence from where you're
working now.  Maybe it's the same as the sequence opposite the break-
point in the wild-type animal?  Do you know this already?  Maybe you can
use the primers that you're using for the wild-type analysis, just with
long PCR conditions.  If not, I would just genotype using a Southern
blot -- it will take you more work to isolate the new sequence you need
and develop a reliable long PCR.  But, if you have this information, try
a long PCR; in the animals that have the insert, you will get a 6 kB+
band.  In animals that lack the insert, you will get the band you already
have, probably a few hundred bases.  Heterozygous animals might be dif-
ficult to call, because the small fragment will amplify much more effici-
ently than the large fragment and will compete for polymerase, dNTP's and
primers.

-- 
Rainforest laid low.
"Wake up and smell the ozone,"
Says man with chainsaw.					- John Ladasky