Linker add., PCR amplif., cloning, seq'ng -> degraded R.E. sites?

[Pete Muriana]

After addition of linkers to blunted DNA followed by PCR amplification, 
cloning (via R.E. site in linkers), & sequencing, we've noticed some sequence 
anomalies in the R.E. cloning site (partial site on one end) as well as 
remnants of the entire linker on the end of the cloned fragments rather than 
just the residual?  Has anyone seen anomalies like this or suggest a published 
citation that helps explain similar sequence anomalies?  Very much appreciated.
Regards, Peter
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   Peter M. Muriana 
   Assistant Professor                         317-494-8284   TEL            
   Dept. of Food Science                     317-494-7953   FAX            
   Purdue University                    murianap at foodsci.purdue.edu   
   Smith Hall                                 http://www.foodsci.purdue.edu/ 
   W. Lafayette, IN  47907-1160         personnel/muriana.html        
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The opinions expressed above are mine alone and do not represent 
endorsement by my employer
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