The pistol RNA motif represents a new class of self-cleaving ribozymes of yet unknown biological function. Our recent crystal structure of a pre-catalytic state of this RNA shows guanosine G40 and adenosine A32 close to the G53-U54 cleavage site. While the N1 of G40 is within 3.4 Å of the modeled G53 2'-OH group that attacks the scissile phosphate, thus suggesting a direct role in general acid-base catalysis, the function of A32 is less clear. We present evidence from atom-specific mutagenesis that neither the N1 nor N3 base positions of A32 are involved in catalysis. By contrast, the ribose 2'-OH of A32 seems crucial for the proper positioning of G40 through a H-bond network that involves G42 as a bridging unit between A32 and G40. We also found that disruption of the inner-sphere coordination of the active-site Mg cation to N7 of G33 makes the ribozyme drastically slower. A mechanistic proposal is suggested, with A32 playing a structural role and hydrated Mg playing a catalytic role in cleavage.

Pistol ribozymes constitute anew class of small selfcleaving RNAs.Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage,c orresponding to the precatalytic state,avanadate mimic of the transition state,a nd the product. The results led to the proposed underlying chemical mechanism. Importantly,ahydrated Mg 2+ ion remains innersphere-coordinated to N7 of G33 in all three states,a nd is consistent with its likely role as acid in general acid base catalysis (d and b catalysis). Strikingly,t he new structures shed light on as econd hydrated Mg 2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reacho ut for water-mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg 2+ ion appears to be the stabilization of product conformation. This study delivers amechanistic understanding of ribozyme-catalyzed backbone cleavage.

Reverse transcription (RT) of RNA templates containing RNA modifications leads to synthesis of cDNA containing information on the modification in the form of misincorporation, arrest, or nucleotide skipping events. A compilation of such events from multiple cDNAs represents an RT-signature that is typical for a given modification, but, as we show here, depends also on the reverse transcriptase enzyme. A comparison of 13 different enzymes revealed a range of RT-signatures, with individual enzymes exhibiting average arrest rates between 20 and 75%, as well as average misincorporation rates between 30 and 75% in the read-through cDNA. Using RT-signatures from individual enzymes to train a random forest model as a machine learning regimen for prediction of modifications, we found strongly variegated success rates for the prediction of methylated purines, as exemplified with N1-methyladenosine (m1A). Among the 13 enzymes, a correlation was found between read length, misincorporation, and prediction success. Inversely, low average read length was correlated to high arrest rate and lower prediction success. The three most successful polymerases were then applied to the characterization of RT-signatures of other methylated purines. Guanosines featuring methyl groups on the Watson-Crick face were identified with high confidence, but discrimination between m1G and m22G was only partially successful. In summary, the results suggest that, given sufficient coverage and a set of specifically optimized reaction conditions for reverse transcription, all RNA modifications that impede Watson-Crick bonds can be distinguished by their RT-signature.

The pistol RNAmotif represents anew class of selfcleaving ribozymes of yet unknown biological function. Our recent crystal structure of ap re-catalytic state of this RNA shows guanosine G40 and adenosine A32 close to the G53-U54 cleavage site.W hile the N1 of G40 is within 3.4 of the modeled G53 2'-OH group that attacks the scissile phosphate, thus suggesting adirect role in general acid-base catalysis,the function of A32 is less clear.W ep resent evidence from atomspecific mutagenesis that neither the N1 nor N3 base positions of A32 are involved in catalysis.Bycontrast, the ribose 2'-OH of A32 seems crucial for the proper positioning of G40 through aH-bond network that involves G42 as abridging unit between A32 and G40. We also found that disruption of the innersphere coordination of the active-site Mg 2+ cation to N7 of G33 makes the ribozyme drastically slower.Amechanistic proposal is suggested, with A32 playing as tructural role and hydrated Mg 2+ playing ac atalytic role in cleavage.

Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5′ nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.

The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5′-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.

The trinucleotide repeat expansion disorders (TREDs) constitute of a group of >40 hereditary neurodegenerative human diseases associated with abnormal expansion of repeated sequences, such as CAG repeats. The pathogenic factor is a transcribed RNA or protein whose function in the cell is compromised. The disorders are progressive and incurable. Consequently, many ongoing studies are oriented at developing therapies. We have analyzed crystal structures of RNA containing CAG repeats in complex with synthetic cyclic mismatch-binding ligands (CMBLs). The models show well-defined interactions between the molecules in which the CMBLs mimic nucleobases as they form pseudo-canonical base pairs with adenosine residues and engage in extensive stacking interactions with neighboring nucleotides. The binding of ligands is associated with major structural changes of the CAG repeats, which is consistent with results of biochemical studies. The results constitute an early characterization of the first lead compounds in the search for therapy against TREDs. The crystallographic data indicate how the compounds could be further refined in future biomedical studies.

The reaction of [IrIII{C(dppm)2-κ3 P,C,P′}ClH(NH3C2)]Cl with ethyl diazo­acetate, a well known C=C coupling reagent, leads to the formation of a C=C unit, accompanied by N2 abstraction, and reorganization of a dppm subunit and, considered as a whole, to the transformation of the PCP pincer carbodi­phospho­rane system to a phospho­rus ylide ligand. After removal of the halogenides, the iridium center is stabilized by the carbonyl O atom through the formation of a five-membered chelate ring. A PCO pincer ligand system is thereby generated, which coordinates the iridium(III) atom threefold in a facial manner. The addition of carbon monoxide causes a replacement of the carbonyl O atom of the acetate subunit by a carbonyl ligand.