Anomalous PCR product

Hiranya Roychowdhury hroychow at NMSU.EDU
Fri Dec 13 10:58:28 EST 1996

At 08:43 PM 12/12/96 GMT, The Great American Gene Company wrote:
>Dear Folks:
>I was just contacted by a colleague with the following question.  It is
>not my field of expertise, but I believe that it is similar to a topic
>recently discussed here.  Can we have your comments and/or
>observations?  Both Neal and I would greatly appreciate any help you
>can provide.
>Posted for Neal Cornell:
>>        I have used an oligo for PCR which resulted in a major,
>>product of 600 bp.  The same  600 bp product was generated when no
>second primer >and no template DNA was put through the "PCR".  Do you
>have any experience to >suggest what might be causing this?
>Thank you kindly,
>Michael T. MacDonell, Ph.D.
>| "Stupidity is the basic building block of the Universe" |
>|                                           -Frank Zappa  |
Apparently the one primer that generates the 600bp fragment has some sort of a palindrome in its sequence that allows it to anneal to each other and extend. the so-called 'primer dimers' are known to go up to 200bp. The other possibility is that the control tube was contaminated with 'some' template DNA that was primed by the single primer. Single primer amplification occurs more frequently than  we would like to believe.

HiranyaDr. Hiranya Sankar Roychowdhury
Plant Genetic Engineering Lab.
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at

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