A hybridization method for autoradiographic visualization of small unique sequence fragments resolved on polyacrylamide gels

A useful method is described for sequence-specific visualization of small nucleic acid fragments on polyacrylamide gels. Excess highly radioactive probe is annealed in solution to smaller fragments. The resulting hybrids are trimmed (under appropriate conditions) with S1 nuclease to yield duplex fragments whose sizes are determined by the strand contributed by the smaller unlabeled fragment, but which also contain a labeled strand from the radioactive probe. These fragments can then be resolved on polyacrylamide gels and visualized by drying the gel and subjecting it to autoradiography. This method is shown to visualize fragments as small as 40 base pairs.