@article {2635,
	title = {Probing General Acid Catalysis in the Hammerhead Ribozyme},
	journal = {Journal of the American Chemical Society},
	volume = {131},
	number = {3},
	year = {2009},
	note = {ISI Document Delivery No.: 427PQTimes Cited: 5Cited Reference Count: 58Thomas, Jason M. Perrin, David M.},
	month = {Jan},
	pages = {1135-1143},
	type = {Article},
	abstract = {Recent crystallographic and computational studies have provided fresh insights into the catalytic mechanism of the RNA-cleaving hammerhead ribozyme. Based on these findings, specific ribozyme functional groups have been hypothesized to act directly as the general acid and base catalysts, although the catalytic role of divalent metal cations (M2+) remains uncertain: We now report a functional characterization of the general acid catalysis mechanism and the role of an M2+ cofactor therein, for the S. mansoni hammerhead (an "extended" hammerhead ribozyme). We have compared hammerhead cleavage of substrates with natural (ribo-phosphodiester) versus bridging-5{\textquoteright}-phosphorothioate scissile linkages, in the contexts of active site mutations and M2+ substitution. Cleavage of the natural substrate is inhibited by modification of the G8 2{\textquoteright}-OH ribozyme residue and depends strongly upon the presence and identity of an M2+ cofactor; in contrast, cleavage of the bridging-phosphorothioate substrate is conspicuously insensitive to any of these factors. These results imply that (1) both an M2+ cofactor and the G8 2{\textquoteright}-OH play crucial roles in hammerhead general acid catalysis and (2) the M2+ cofactor does not contribute to general acid catalysis via Lewis acid stabilization of the leaving group. General acid pK(a) perturbation was also demonstrated for both M2+ substitution and G8 2{\textquoteright}-OH modification, which suggests transition state M2+ coordination of the G8 2{\textquoteright}-OH, to lower its pK(a) and improve its ability to transfer a proton to the leaving group. We also report a simple method for synthesizing radiolabeled bridging-5{\textquoteright}-phosphorothioate substrates.},
	keywords = {2{\textquoteright}-HYDROXYL GROUP, ACTIVE-SITE, BASE CATALYSIS, CATIONS, MEDIATED CLEAVAGE, METAL-ION, MONOVALENT, P-31 NMR, PHOSPHOLIPASE-C, RIBONUCLEASE-A, SUBSTRATE-ANALOG},
	isbn = {0002-7863},
	url = {<Go to ISI>://000264791600054},
	author = {Thomas, J. M. and Perrin,David M.}
}
@article {2285,
	title = {Probing General Base Catalysis in the Hammerhead Ribozyme},
	journal = {Journal of the American Chemical Society},
	volume = {130},
	number = {46},
	year = {2008},
	note = {ISI Document Delivery No.: 406QZTimes Cited: 8Cited Reference Count: 53Thomas, Jason M. Perrin, David M.},
	month = {Nov},
	pages = {15467-15475},
	type = {Article},
	abstract = {Recent structural and computational studies have shed new light on the catalytic mechanism and active site structure of the RNA cleaving hammerhead ribozyme. Consequently, specific ribozyme functional groups have been hypothesized to be directly involved in general/acid base catalysis. In order to test this hypothesis, we have developed an affinity label to identify the functional general base in the S. mansoni hammerhead ribozyme. The ribozyme was reacted with a substrate analogue bearing a 2{\textquoteright}-bromoacetamide group in place of the nucleophilic 2{\textquoteright}-hydroxyl group which would normally be deprotonated by a general base. The electrophilic 2{\textquoteright}-bromoacetamide group is poised to alkylate the general base, which is subsequently identified by footprinting analysis. Herein, we demonstrate alkylation of N1 of G12 in the hammerhead ribozyme in a pH and [Mg2+] dependent manner that is consistent with the native cleavage reaction. These results provide substantial evidence that deprotonated N1 of G12 functions directly as a general base in the hammerhead ribozyme; moreover, our experiments provide evidence that the pK(a) of G12 is perturbed downward in the context of the active site structure. We also observed other pH-independent alkylations, which do not appear to reflect the catalytic mechanism, but offer further insight into ribozyme conformation and structure.},
	keywords = {ACTIVE-SITE, CLEAVAGE, CRYSTAL-STRUCTURE, DELTA VIRUS RIBOZYME, HAIRPIN RIBOZYME, MECHANISM, METAL-ION, MONOVALENT CATIONS, NUCLEOBASE CATALYSIS, RNA},
	isbn = {0002-7863},
	url = {<Go to ISI>://000263311300051},
	author = {Thomas, J. M. and Perrin,David M.}
}
@article {4874,
	title = {Template effects in the formation of a tetramethylene-bridged hemicarceplex},
	journal = {Journal of the American Chemical Society},
	volume = {122},
	number = {7},
	year = {2000},
	note = {ISI Document Delivery No.: 289TZTimes Cited: 20Cited Reference Count: 57},
	month = {Feb},
	pages = {1337-1342},
	type = {Article},
	abstract = {We report a study of the template effect in the formation of tetramethylene-bridged hemicarceplex 7.guest. Two tetrol cavitands were bridged with 1,4-dibromobutane in the presence of suitable template (guest) molecules in N-formylpiperidine as solvent. Selectivity was observed when competing templates were present during the reaction: the relative templating abilities (template ratios) of 30 different guest molecules range by 3600-fold, and manifest a significant preference for para-disubstituted benzenes. Twenty-one of the 30 hemicarceplexes used in this templation study are new. The trend in guest selectivity is markedly different from previous studies in which smaller cavities (e.g., carceplex 2.guest) are formed. In such studies, capsule 3.guest was a good transition state model, whereas this is not the case in the present work.},
	keywords = {2 BOWLS, BINDING-PROPERTIES, CARCEPLEXES, CONTAINER, CRYSTAL-STRUCTURE, ENCAPSULATION, METAL-ION, O-BENZYNE, REVERSIBLE MOLECULAR CAPSULES, zeolites},
	isbn = {0002-7863},
	url = {<Go to ISI>://000085639200011},
	author = {Makeiff, D. A. and Pope, D. J. and Sherman, J. C.}
}
