DNA-FINGERPRINTING INVOLVING FLUORESCENCE-LABELED TERMINI OF ANY ENZYMATICALLY GENERATED FRAGMENTS OF DNA

We have developed a new fluorescence-based method for DNA fingerprinti ng that does not require a fluorescent linker or a synthetic oligonucl eotide primer, both of which are normally used for labeling of DNA. Co smid DNAs are digested with appropriate restriction enzymes and the 3' termini of DNA fragments are labeled with the corresponding, fluoresc ent dye-conjugated dideoxynucleotide triphosphate terminator (dye-ddNT P) by the Klenow fragment of DNA polymerase I from Escherichia coli, w hich has 3'-->5' exonuclease and replacement activities as well as its main 5'-->3' polymerase activity. Samples are separated on a DNA-sequ encing gel and data are analyzed by application of both the Version 0. 3.8a mapper program (Applied Biosystem Inc., Foster City, CA) and our Overlap I program that facilitate rapid analysis of the frequency of o verlapping of cosmid DNAs. Using this method we have determined the ov erlap frequency of DNA fragments of each cosmid clone from the mouse M HC class I gene cluster.