Abstract
A comparison was made of three procedures used for measuring the locations of long range base pairing in single-stranded DNA. All three procedures gave equivalent results for the location of a transposon, Tn903, and for a loop created by pairing between the nut and operator segments on an Eco RI restriction fragment of lambda DNA. DNA molecules prepared by a T4 gene 32 protein procedure had the best contrast. The highest frequency of measurable loops resulted from a procedure which utilized ammonium acetate/formamide spreading conditions. This procedure also appeared to be the simplest and most satisfactory procedure. Only one procedure revealed the fact that the nut r and o r regions are separated by several hundred bases, but this procedure, which involves crosslinking with trioxsalen, gave generally unsatisfactory DNA morphology. None of the procedures revealed the existence of a short “bulge” loop of single-stranded DNA located between nut l and o l and a longer “bulge” loop located between nut r and o r .
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