Abstract
This chapter discusses the techniques for the sequence analysis of short DNA fragments. The method for sequencing short DNA fragments from the labeled termini, up to 20 bases long, consists of in vitro terminal labeling of the DNA fragments, followed by controlled E. coli exonuclease III digestion, and/or by strand separation on homochromatography or gel electrophoresis. Then, the sequences can be obtained after partial enzymatic digestions, 2-D fractionation by electrophoresis and homochromatography, and mobility-shift analyses. With the base-sequence specific restriction endonucleases, homogeneous populations of small DNA segments from many regions of a large DNA molecule can be easily isolated. There is also an increasing need to determine the recognition sequences of new restriction endonucleases. The methods described help in determining a short DNA sequence immediately adjacent to the labeled ends at the cleavage site.
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