Kolev NG , Hartland EI , Huber PW .

	Figure 1. A manganese-dependent ribozyme in the 3′-UTR of Vg1 mRNA. (A) The secondary structure of the region encompassing residues 210–350 of the Vg1 localization element (VLE). An arrow indicates the site of cleavage and boxes enclose a consensus polyadenylation signal at position 334 and a nonconsensus signal at 272. The structure was generated using mfold version 3.1 (51). (B) Vg1 RNA (radiolabeled at the 3′-end) was incubated overnight in cleavage buffer in the presence (lane 3) or absence (lane 4) of 10 mM manganese and then analyzed on a denaturing polyacrylamide gel alongside ribonuclease T1 and alkaline hydrolysates (lanes 1 and 2, respectively). The doublet in lane 3 is also apparent in the T1 digest (lane 1) and is due to length heterogeneity in the substrate RNA. (C) A 5′ hydroxyl group at the cleavage site. The 3′ cleavage product was incubated with polynucleotide kinase and ATP and compared to untreated fragment and an alkaline hydrolysate. (D) A 3′ phosphate at the cleavage site. A portion of a cleavage reaction containing an equal mixture of substrate and product RNA was incubated with poly(A) polymerase and compared to an untreated sample. Only the substrate RNA is polyadenylated.
	Figure 2. Characterization of the self-cleavage reaction. All reactions were carried out in standard conditions, excepting the indicated variable. The metal dependence of cleavage was tested with the indicated divalent cation at a concentration of 10 mM.
	Figure 3. Kinetics of the cleavage reaction. (A) A trace amount of internally labeled Vg1 RNA was added to the indicated concentration of unlabeled Vg1 RNA. The reactions proceeded in standard conditions overnight. (B) Vg1 RNA (100 nM) was incubated for the indicated amount of time in standard conditions. Reactions were stopped with EDTA and analyzed on a denaturing polyacrylamide gel. (C) The autoradiograph was scanned with a laser densitometer to generate the individual data points. The best-fit curve (solid line) is defined by a kinetic equation that represents a two-step process with both steps being first order. (D) The plot of ln(fraction unreacted) versus time yields an observed first-order rate constant of 6.6 × 10−4 min−1.
	Figure 4. In vivo translation of wild-type and mutant Vg1 mRNA lacking the GAAA ribozyme sequence. Stage VI oocytes were injected with capped mRNA and incubated overnight in OR2 buffer containing [35S]methionine/cysteine. Vg1 protein was immunoprecipitated from whole-cell extract prepared from 20 oocytes and analyzed by SDS–PAGE followed by autoradiography. Lane 1, oocytes injected with water only; lane 2, oocytes injected with wild-type mRNA; lane 3, oocytes injected with mRNA in which the GAAA ribozyme sequence was changed to CCCA.
	Figure 5. A manganese-dependent ribozyme in the zipcode of β-actin mRNA. (A) The predicted secondary structure of the zipcode element in the 3′-UTR of β-actin mRNA (52). An arrow marks the site of manganese-dependent cleavage. (B) Zipcode RNA (radiolabeled at the 3′-end) was incubated overnight in cleavage buffer in the presence (lane 3) or absence (lane 4) of 10 mM manganese and then analyzed on a denaturing polyacrylamide gel alongside alkaline and ribonuclease T1 hydrolysates (lanes 1 and 2, respectively). (C) The metal dependence of self-cleavage in zipcode RNA. RNA was incubated overnight in the presence of the indicated metal. Weak cleavage with Cu2+ has been reported previously for the manganese ribozyme (53); whereas, Zn2+ triggers nonspecific degradation.
	Figure 6. The frequency of GAAA immediately upstream and downstream of the polyadenylation signal. One thousand mRNA sequences from C. elegans and D. melanogaster were scanned in 1-nt increments using a 4-nt window. The frequency of the sequences GAAA, CAAA and TATG are presented as histograms relative to the position of the AATAAA hexanucleotide sequence.
	Figure 7. Predicted base-pairing interactions between the HDE of histone mRNAs and U7 snRNAs. Selected histone mRNAs (top strand) and U7 snRNAs (bottom strand) are presented; only the region immediately flanking the Sm site (designated by a rectangle) of U7 is shown in each case. Adapted from ref. 41.

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