RNA catalytic properties of the minimum (-)sTRSV sequence

Hampel, Arnold; Tritz, Richard

doi:10.1021/bi00438a002

Cited by 378 publications

(267 citation statements)

References 11 publications

(16 reference statements)

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“…An Arrhenius plot for the freezing ligation reaction (Fig. 3C) in that temperature range gives an approximate value for the activation energy of 11 kcal/mol, which is similar to the range of 13-19 kcal/ mol reported for the HPR cleavage and ligation reactions in normal solution (Hampel and Tritz 1989;Fedor 1999;Nesbitt et al 1999).…”

Section: Temperature Effects On the Cleavage-ligation Equilibriumsupporting

confidence: 79%

Ligation of the hairpin ribozyme in cis induced by freezing and dehydration

Kazakov¹,

Balatskaya²,

Johnston³

2006

RNA

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Although reducing the temperature slows most chemical reactions, freezing can stimulate some reactions by mechanisms that are only partially understood. Here we show that freezing stimulates the self-ligation (circularization) of linear forms of the hairpin ribozyme (HPR) containing 2¢,3¢-cyclic phosphate and 5¢-OH termini. Divalent metal ions (M 2+ ) are not required, but monovalent cations and anions at millimolar concentrations can have various effects on this reaction depending on the specific ion. Under optimal conditions, the observed rate of M 2+ -independent self-ligation reaches a peak (0.04 minC with a yield of~60% after 1 h. In contrast, no ligation occurs either at above 0 C or in solutions that remain unfrozen when supercooled to subzero temperatures. Under freezing conditions, the cleavage-ligation equilibrium strongly favors ligation. Besides freezing, evaporation of the aqueous solvent as well as the presence of ethanol at levels of 40% or above can also induce M 2+ -independent HPR ligation at 25 C. We argue that partial RNA dehydration, which is a common feature of freezing, evaporation, and the presence of ethanol, is a key factor supporting HPR ligation activity at both above-and below-freezing temperatures. In the context of the RNA world hypothesis, freezing-induced ligation is an attractive mechanism by which complex RNAs could have evolved under conditions in which RNA was relatively protected against degradation.

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Section: Temperature Effects On the Cleavage-ligation Equilibriumsupporting

confidence: 79%

Ligation of the hairpin ribozyme in cis induced by freezing and dehydration

Kazakov¹,

Balatskaya²,

Johnston³

2006

RNA

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“…Certain hairpin-like structures are endowed with ribozyme activity able to catalyze RNA cleavage/ligase reactions in a reversible way, as originally described in plant virus satellite RNAs (Buzayan et al 1986;Hampel and Tritz 1989). The typical hairpin ribozyme consists of a 35-nt-long hairpin structure (as topologically defined in the previous paragraph), with a 59 dangling end of 14 nt (the substratebinding site) and one overhanging nucleotide in 39 (reviewed in Puerta-Fernández et al 2003).…”

Section: A Stepwise Model For the Origin Of The Rna Worldmentioning

confidence: 99%

The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

Briones¹,

Stich²,

Manrubia³

2009

RNA

100

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A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.

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“…2A). Two of the four helices that compose the 4WJ of the natural hairpin ribozyme (Hampel and Tritz 1989) were removed, although the regions of the hinged construct at H2 and H3 closely mimicked the 4WJ packing environment as a result of engineered intermolecular contacts afforded by crystallographic symmetry (MacElrevey et al 2007).…”

Section: Hairpin Ribozyme Constructsmentioning

confidence: 99%

Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme

MacElrevey¹,

Salter²,

Krucinska³

et al. 2008

RNA

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The hairpin ribozyme requires functional groups from Ade38 to achieve efficient bond cleavage or ligation. To identify molecular features that contribute to catalysis, structures of position 38 base variants 2,6-diaminopurine (DAP), 2-aminopurine (AP), cytosine (Cyt), and guanine (Gua) were determined between 2.2 and 2.8 Å resolution. For each variant, two substrate modifications were compared: (1) a 29-O-methyl-substituent at Ade-1 was used in lieu of the nucleophile to mimic the precatalytic state, and (2) a 39-deoxy-29,59-phosphodiester linkage between Ade-1 and Gua+1 was used to mimic a reactionintermediate conformation. While the global fold of each variant remained intact, the results revealed the importance of Ade38 N1 and N6 groups. Absence of N6 resulting from AP38 coincided with failure to localize the precatalytic scissile phosphate. Cyt38 severely impaired catalysis in a prior study, and its structures here indicated an anti base conformation that sequesters the imino moiety from the scissile bond. Gua38 was shown to be even more deleterious to activity. Although the precatalytic structure was nominally affected, the reaction-intermediate conformation indicated a severe electrostatic clash between the Gua38 keto oxygen and the pro-Rp oxygen of the scissile bond. Overall, position 38 modifications solved in the presence of 29-OMe Ade-1 deviated from in-line geometry, whereas variants with a 29,59 linkage exhibited S-turn destabilization, as well as base conformational changes from syn to anti. These findings demonstrate the importance of the Ade38 Watson-Crick face in attaining a reaction-intermediate state and the sensitivity of the RNA fold to restructuring when electrostatic and shape features fail to complement.

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RNA catalytic properties of the minimum (-)sTRSV sequence

Cited by 378 publications

References 11 publications

Ligation of the hairpin ribozyme in cis induced by freezing and dehydration

Ligation of the hairpin ribozyme in cis induced by freezing and dehydration

The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme

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