In order to investigate the geometry of a self-cleaving hammerhead domain, an RNA heteroduplex has been constructed in which two of the three helix stems of the domain have each been elongated to 76 duplex base pairs (bp), resulting in an RNA molecule of ca. 160 bp. The heteroduplex molecule is capable of undergoing self-cleavage at neutral pH, upon addition of either Mg2+ or Mn2+, but does not dissociate following cleavage. Using a combination of electrophoretic and hydrodynamic methods, as employed earlier to define the geometry of a four-way DNA branch [Copper & Hagerman (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 7336–7340], we have determined that the elongated hammerhead stems are nearly collinear prior to self-cleavage. Following self-cleavage, and in the absence of Mg2+, the angle between the two stems becomes much more acute and/or flexible; however, in the presence of Mg2+, the cleaved structure appears to retain the geometry of the precleaved form (at least with respect to the interstem angle). It is also observed that the self-cleavage reaction is promoted by Mn2+ to a much greater extent than by Mg2+, consistent with earlier observations. Finally, although the elongated helices appear to be nearly collinear in the uncleaved molecule, the electrophoretic mobility of that species is dramatically reduced with respect to linear control RNAs, indicating that caution should be exercised in the quantitative assignment of branch angles solely from gel retardation experiments.
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