B----A transitions within a 5 S ribosomal RNA gene are highly sequence-specific.

Abstract The UV footprinting technique has been used to detect and map, at single nucleotide resolution, the formation of A conformations within a sea urchin 5S ribosomal RNA gene. Increasing amounts of the dehydrating agent, trifluorethanol, were used to induce the B----A transition. Our measurements argue that the B----A transition is highly sequence-specific. Fourteen different sequences within a fragment of DNA bearing the 5 S gene were found to undergo the B----A transition independently of one another. There is a striking relationship between the midpoint of the B----A transition for each stretch of DNA and its (G+C) content. DNA sequences at the boundary between A and B conformations do not appear to be significantly distorted. A (dAdT)8 tract at the 3' end of the 5 S gene undergoes the B----A transition in two cooperative steps suggesting that for some sequences the B----A transition may actually proceed through the formation of a previously unidentified intermediate. Although the sequence specificity of the B----A transition may be exploited by regulatory proteins when they bind DNA, our measurements argue that binding of the Xenopus laevis transcription factor 111A to 5 S genes does not.