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cat varies logarithmically with pH (4); and phosphorothioate substitution results in apparent rate effects of a magnitude typical for chemically limited reactions (7)
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19
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0025048746
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The 41-nt D5, containing seven flanking nucleotides, was synthesized in two pieces on an ABI 392 DNA/ RNA synthesizer and worked up according to standard procedures [S. A. Scannge, C Francklyn, N. Usman, Nucleic Acids Res. 18, 5433 (1990)]. Oligonacleotides were punfied on a Waters high-performance liquid chromatography (HPLC) system with a Machery-Nagel Nucleogen DEAE 60-7 column. Oligonucleotides were then desalted with ABI Oligonucleotide Purification Cartridges following the manufacturer's instructions.
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2, 500 mM KCl, and 40 mM MOPS (pH 7.5) at 45°C as described (4).
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22
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4243173283
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note
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In predominantly RNA duplexes, a single deoxynbonucleotide is expected to exist primarily in the C3′-endo conformation of its neighbors, resulting in minimal perturbations of the structure. Although twofold effects on binding constants of oligonucleotide strands have been observed (6), these would be invisible here because each D5 chimera was preincubated before reaction to ensure full annealing of the strands. Aside from effects on D5 duplex stability, single deoxynucleotides may affect electrostatics and local water structure However, if water organization is important to catalytic activity and such activrty is mediated by a 2′-OH group, we consider such effects to represent important contributions to the catalytic process.
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23
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0029258956
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32P-exD123), which are the most sensitive for measurement of competitor effects [J. A. Doudna and T. R. Cech, RNA 1, 36 (1995)] WT D5 was in one piece, whereas competitor chimeric D5 molecules were provided in excess as two-piece annealed strands (3 μM) Competitor D5 derivatives containing both single- and double-deoxynucleotide substitutions were tested, and for substitutions at similar positions the same results were obtained. Kinetics were measured under standard conditions (70).
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There were no lags during initial portions of the the first-order plots, which were linear for all chimeras described in this study (data not shown)
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We thank B. Honig and M Akke for helpful discussion of the D5 model, S Strobel for discussion of the data and help with ligations, and Z Qin and B. Konforti for critical review of the manuscript. We also thank F. Major for use of, and help with, MC-SYM; D McKay for the coordinates of the GAAA tetraloop in the hammerhead ribozyme; and C Bingman for advice on HPLC Supported by grants GM50313 to A.M.P. and GM41371 to B. Honig from the National Institutes of Health.
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