Metal-ion-promoted hydrolysis of polyuridylic acid

Kuusela, Satu; Lönnberg, Harri

doi:10.1039/p29940002301

Cited by 45 publications

(52 citation statements)

References 41 publications

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“…Here we found that Zn 2þ catalysis was quite effective in all cases, but diminished by the additional polymers. The binding of Zn 2þ with strong ligands, such as the nitrogen on the polyethylenimine backbone or imidazoles, apparently decreased its Lewis acidity and, therefore, its catalytic activity (9,31).…”

Section: Resultsmentioning

confidence: 99%

Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles

Cheng

Abhilash

Breslow

2012

Proc. Natl. Acad. Sci. U.S.A.

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Four polyimidazoles were used in the binding and cleavage studies with poly(U). The two polydisperse polyvinylimidazoles were previously described by others, while the other two new polymers of polyethyleneimines were prepared by cationic polymerization of oxazolines. The latter had imidazole units attached to each nitrogen of the polymers. They were characterized by gel permeation chromatography and had very low polydispersities. When they were partially protonated they bound to the poly(U) and catalyzed its cleavage by a process analogous to that used by the enzyme ribonuclease A. The kinetics of the cleavage were followed by an assay we had previously described using phosphodiesterase I from Crotalus venom after the cleavage processes. Cleavage of poly(U) with Zn 2+ was also examined, with and without the polymers. A scheme is described in which these cleavages could be made sequence selective with various RNAs, particularly with important targets, such as viral RNAs.

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Section: Resultsmentioning

confidence: 99%

Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles

Cheng

Abhilash

Breslow

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…On the other hand, the pK a s of the aqua complexes of Cd 2+ , Ni 2+ , Co 2+ , Pb 2+ , and Zn 2+ fall within the 7-10 range (31). This fact may contribute to the previously observed nonspecific Zn 2+ -dependent hydrolysis of RNA (32)(33)(34). Third, the geometric requirements of the binding site place a limitation on the size of the bound metal ion.…”

Section: +mentioning

confidence: 99%

Identification and Characterization of a Divalent Metal Ion-Dependent Cleavage Site in the Hammerhead Ribozyme

2001

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We describe a new RNA cleavage motif, found in the hammerhead ribozyme. Cleavage occurs between nucleotides G8 and A9, yielding a free 5′-hydroxyl group and a 2′,3′-cyclic phosphate. This cleavage is dependent upon divalent metal ions and is the first evidence for a metalloribozyme known to show preference for Zn 2+ . Cleavage is also observed in the presence of Ni 2+ , Co 2+ , Mn 2+ , Cd 2+ , and Pb 2+ , while negligible cleavage was detected in the presence of the alkaline-earth metal ions Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ . A linear relationship between the logarithm of the rate and pH was observed for the Zn 2+ -dependent cleavage, which is indicative of proton loss in the cleavage mechanism, either prior to or in the rate-determining step. We postulate that a zinc hydroxide complex, bound to the known A9/G10.1 metal ion binding site, abstracts the proton from the 2′-hydroxyl group of G8, which attacks the A9 phosphate and initiates cleavage. This hypothesis is supported by a previously reported crystal structure [Murray, J. B., Terwey, D. P., Maloney, L., Karpeisky, A., Usman, N., Beigelman, L., and Scott, W. G. (1998) Cell 92, 665-673], which shows the conformation required for RNA cleavage and proximity of the 2′-hydroxyl group to the metal ion complex.The hammerhead ribozyme ( Figure 1A) is an RNA motif that catalyzes the cleavage of an RNA substrate via a transesterification reaction, producing a 2′,3′-cyclic phosphate and a 5′-hydroxyl terminus ( Figure 1B) (1). Divalent metal ions have been implicated directly in the hammerhead ribozyme cleavage mechanism (2-5), and the most popular mechanism has involved the abstraction of the 2′-hydroxyl proton at the cleavage site by a metal ion hydroxide (6). Divalent metal ions can also play a structural role in ribozyme activity by stabilizing the catalytically active tertiary conformation through coordination to heteroatoms, such as oxygen atoms or nitrogen atoms present in the nucleoside bases. The finding that the hammerhead ribozyme is active in the absence of divalent metal ions at high concentrations of monovalent metal ions calls into question the role of divalent metal ions in the mechanism of substrate cleavage (5,7,8).Divalent metal ion binding sites in the hammerhead ribozyme have been found by X-ray crystallography (9-13) and by NMR spectroscopy (14). One of the most extensively studied metal ion binding sites is the A9/G10.1 site which involves coordination of the metal ion to N7 of G10.1 and the pro-R P phosphate oxygen of A9 (Figure 2). The pro-R P oxygen of A9 has been implicated in hammerhead ribozyme function by replacement of the nonbridging, pro-R P oxygen at the A9 phosphate with sulfur. Substrate cleavage studies in the presence of Mg 2+ resulted in reduced † This work was supported by a grant from the National Institutes of Health (GM56947).

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“…All these rate profiles exhibit a marked rate acceleration in the pH range 6.5 ± 7.0 (at 908) and a broad rate maximum at pH 7.0 ± 7. [21]. The retardation observed at pH > 7.5 may be attributed to precipitation of the metal ions as a hydroxo complex.…”

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confidence: 93%

“…The rate-accelerating effect of the mononuclear 2 complex is equal to that of the Zn 2 complex of 1,5,9-triazacyclododecane [20] [21]. In all likelihood, the metal ion in 2 is bound to only one of the azacrown moieties, the other one having no effect on the course of the reaction.…”

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confidence: 97%

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

Wang

Mikkola²,

Lönnberg³

2004

Chemistry & Biodiversity

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The ability of bimetallic homo- and heteronuclear complexes of two spiro-linked ligands, viz. a biazacrown (i.e., 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane (1)) and an azacrown-crown ether (i.e., 14,17,20,23,26-pentaoxa-2,6,10-triaza-spiro[11.15]heptacosane (2)), to promote the cleavage of the phosphoester linkage of dinucleoside 3',5'-phosphates and the phosphoric anhydride bridge of dinucleoside 5',5'-triphosphates was studied. In both reactions, the bimetallic homonuclear Cu2+ and Zn2+ complexes were better catalysts than their monometallic counterparts. The acceleration was two- to five-fold with the phosphoester cleavage and 3- to 20-fold with the phosphoric anhydride cleavage. Interestingly, the most-efficient catalyst of the phosphoester cleavage was the heterodinuclear Ni2+,Zn2+ complex of 1, the catalytic activity of which was up to 5- and 100-fold that of the homodinuclear Zn2+ and Ni2+ complexes, respectively. Moreover, this cooperative acceleration was observed to depend on the identity of the 5'-linked nucleoside: 3',5'-UpU and 3',5'-ApU were cleaved much faster than 3',5'-UpA, and no cooperative acceleration was observed with 3',5'-ApA. The reaction was second-order in hydroxide ion concentration, suggesting that a double deprotonation took place on going from the initial to the transition state. Evidently, in addition to deprotonation of the attacking 2'-OH group, N(3)H of the 5'-linked uridine was displaced by one of the metal ions of the cleaving agent. With the phosphoric anhydride cleavage, no similar cooperativity of two different metal ions was observed, but the greatest rate-acceleration was achieved with the homodinuclear Cu2+ complexes.

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Metal-ion-promoted hydrolysis of polyuridylic acid

Cited by 45 publications

References 41 publications

Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles

Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles

Identification and Characterization of a Divalent Metal Ion-Dependent Cleavage Site in the Hammerhead Ribozyme

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

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