RESEARCH problem

R. Jayakumar jakku at
Fri Oct 20 01:33:23 EST 2000

    I badly need a help on a particular research problem.  A friend of mine
is working on a  genetically associated disorder that affects some human
beings ( I regret not able to mention the disorder due to obvious reasons).
She has done a PCR with certain specific primers developed to amplify a
particular portion of an exon closely found associated with the disease.
The problem is this.  She expects a 250 bp amplicon from these primers.  She
works on two samples of DNA templates, one is form normal healthy persons
and other from the diseased persons having that particular disorder.
Surprisingly, she gets an additional amplicon of 750 bp apart from the
expected 250bp amplicon from the diseased person DNA, and NOT IN THE HEALTHY
person DNA.  On analysis of the sequenced 750bp DNA, the amplicon was found
to have been amplified by the forward primer alone acting as both forward
and reverse.  The sequenced fragment was also found to have some retroviral
repeats in them.  All the DNA analysis was done by me using GCG and webbased
programs. Since I am not a human biologist, I found it difficult to further
interpret the results.  BLAST search also did not yield any interesting
results and did not show the fragment to belong to any particular part of
the human genome and showed low homology to human DNA, even though different
parts of the amplicon showed homology to different areas of the human
genome.  To all possibility, the amplicon seems to be a foreign DNA.  Could
this be true and how do I explain retroviral repeats, and are retroviral
repeats common part of the human genome?
     I am totally confused as to how to interpret the results.  Please help
me out.

Any help would be sincerely acknowledged.

CSIR- Senior Research Fellow
Dept. of Molecular Microbiology,
School of Biotechnology,
Madurai Kamaraj University,
Madurai - 625 021.
email: jakku at
tel: +91-452-858471-374
efax: (603)-688-4665
"YOu harvest what you sow.. so sow happiness everywhere"


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