Abstract: Determining the base sequence of DNA broken site is quite crucial for the study on the cleavage site specificity and mechanism of various natural or synthetic DNA cleavage regents, and on developing novel therapeutic drugs targeting at DNA. The most frequently used method depending on chemical reactions of the Maxam-Gilbert procedure, and the late arising methods used by Rui Ren et al. which were based on Sanger's DNA sequencing strategy, all had some deficiencies, either the pollution of radioactive materials, or really complicated and difficult to operate. In the present paper, a new method for DNA cleavage site sequence determination was developed. The fluorescence FAM-labeled primer was annealed to the DNA fragments, which has been cleaved by restriction enzymes or other regents, and extended along the template sequence. The products then loaded onto the polyacrylamide electrophoresis gel of ABI 377 DNA Sequencer. Data was collected and analyzed by using ABI PRISM Data Collection Software and ABI PRISM Sequencing Analysis Software. It is proved to be a credible and simple new approach to determine the base sequence of DNA broken sites.

Key words: DNA cleavage, Broken site, Sequence specificity, Fluorescence labeled primer, ABI 377 DNA Sequencer