B----A transitions within a 5 S ribosomal RNA gene are highly sequence-specific.
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.
Becker
M M
MM
Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260.
Wang
Z
Z
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004274:DNA, Recombinant; D004275:DNA, Ribosomal / Q000528:radiation effects / Q000648:ultrastructure*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010777:Photochemistry; D012335:RNA, Ribosomal / Q000648:ultrastructure*; D012341:RNA, Ribosomal, 5S / Q000528:radiation effects / Q000648:ultrastructure*; D012617:Sea Urchins; D013816:Thermodynamics; D014466:Ultraviolet Rays
D004274:DNA, Recombinant; D004275:DNA, Ribosomal; D012335:RNA, Ribosomal; D012341:RNA, Ribosomal, 5S