DNA extracted from conventionally fixed human tissues is damaged. Template (base) damage is likely to be greater than chain damage because formalin reacts with bases but not sugar or phosphate groups. DNA from fixed tissues is generally longer on agarose gels than targets amplified by PCR, and can even be used for Southern blot analysis. Base damage can stop PCR because of polymerases stalling. Recently discovered error-prone or by-pass DNA polymerases can bridge damaged templates by adding non-templated bases. """"""""Repair"""""""" of damaged DNA by an error-prone polymerase will cause """"""""in vitro"""""""" mutations but rescue subsequent PCR. However, PCR products can retain the information of original templates because the correct base would be present in the majority of amplified molecules. For example, very low levels of base damage can significantly reduce stretches of intact template. At 3 percent random base damage, less than 1 percent of templates would be longer than 200 bases but 97 percent of amplified molecules would retain the correct base at each site. PCR after """"""""repair"""""""" by error prone polymerases should yield more and longer products, and may further unlock the utility of this ubiquitous clinical resource.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21CA091301-02
Application #
6515082
Study Section
Special Emphasis Panel (ZCA1-SRRB-Y (J2))
Program Officer
Bledsoe, Marianna
Project Start
2001-07-01
Project End
2004-06-30
Budget Start
2002-09-26
Budget End
2004-06-30
Support Year
2
Fiscal Year
2002
Total Cost
$162,500
Indirect Cost
Name
University of Southern California
Department
Pathology
Type
Schools of Medicine
DUNS #
041544081
City
Los Angeles
State
CA
Country
United States
Zip Code
90089