Loop formation, deletions...with PCR

Kitchen, Chad chad_kitchen at URMC.Rochester.edu
Fri May 18 11:03:23 EST 2001


I am wondering whether anyone has experienced "skipping" of segments flanked
by long, direct repeats while performing PCR.  We used a template (Contig
clone, human genomic, sequence is published), and obtained a pcr product
~100bp less than expected size.  Our sequencing of the resultant clone
indicates a 100bp deletion, flanked by CCagCCCCCC (5'-3').  Could a loop
have formed such that Taq polymerase read right through?  Any experiences
would be helpful.  Thanks!!!!
Chad M. Kitchen
Technical Associate I
Center for Cardiovascular Research, Box 679
University of Rochester Medical Center
Ph. 716-273-1535

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