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344
J . Org. Chem. 1996, 61, 8344-8346
Ester Am in olysis Ca ta lyzed by Nu cleosid es
in a Non p ola r Med iu m
Christian Melander and David A. Horne*
Department of Chemistry, Columbia University,
New York, New York 10027
Received J uly 12, 1996
Since the discovery of catalytic RNA, a number of
examples have emerged illustrating the ever increasing
1
diversity of RNA catalysis. This diversity ranges from
phosphoryl transfer reactions as seen in group I and
group II introns, RNase P, hammerheads, and snRNPs
to evidence of amide bond catalysis by rRNA during
protein synthesis.2 Moreover, the advent of polymerase
chain reaction technology has led to the evolution and
selection of both ribo- and deoxyribozymes with impres-
F igu r e 1. tert-Butyldimethylsilyl protected nucleosides A, C,
G, U, and Ψ and 2-pyridone.
3
sive catalytic abilities that include aminoacyl esterase,
4
5
6
7
amidase, DNA and RNA ligase, and biphenyl isomerase
activities. Virtually all of the examples of RNA or DNA
catalysis to date have dealt with relatively complicated
three-dimensional nucleic acid structures, and thus, the
various components contributing to the catalysis have
been difficult to sort. Moreover, the focus of the catalysis
has been attributed to the RNA in terms of template
effects, effective molarities, binding of substrates and
metal ions, and orbital steering of functional groups for
optimal reactivity. In this communication, we report that
the functional groups of certain nucleoside bases of RNA
are capable of catalyzing amide bond formation and do
so without the aid of metal ions. This bond is the key
bond formed during protein synthesis, and its formation
is catalyzed by the ribosome.
The role of the functional groups that comprise each
nucleotide base offers a multitude of donor-acceptor
possibilities when arranged in 3-dimensional space.
Unlike their protein counterparts, these functional groups
lack the chemical diversity found in the side chains of
the 20 different amino acids. Despite this apparent
shortcoming, there are unique chemical features of the
nucleic acid bases that are not found in the amino acid
side chain functionality. Such features range from the
varying degree of bifunctionality seen in the relatively
acidic imide moiety of uracil and Ψ to the weakly basic
amidine group in cytosine.
F igu r e 2. Aminolysis reaction of pentafluorophenyl benzoate
by propylamine catalyzed by various catalysts.
active site of a protein enzyme.8 To test this notion, the
effect of each protected ribose nucleoside A, C, G, U, and
Ψ was examined for its ability to catalyze amide bond
formation in a nonpolar medium, such as deuterochlo-
roform (Figure 2). A nonpolar medium was chosen for
several reasons; most importantly, it would enable an
optimal enthalpic contribution to catalysis due to any
hydrogen bonding stabilization of the presumed ionic
transition state. In addition, many active sites in
enzymes are hydrophobic in nature, and these conditions
may very well model the hydrophobic environs in pro-
8
9
teins, nucleic acids, and protein-nucleic acid complexes.
Figure 3 shows the effects of the various bases as
catalysts for the aminolysis reaction of pentafluorophenyl
benzoate by propylamine at 23 °C in deuterochloroform.
These results are summarized in Table 1. The bases A
and U showed less than 10% catalysis over the uncata-
lyzed rate, which is consistent with recent reports of
10
similar systems. G and Ψ showed rate enhancements
of 24% and 29%, respectively, while C produced a
In order to investigate the inherent catalytic abilities
of the functional groups contained within the nucleic acid
bases, each nucleoside was examined individually for its
ability to catalyze amide bond formation (Figure 1). The
experiment was designed to examine the relative contri-
butions of each base toward stabilizing the transition
state of the aminolysis reaction by hydrogen bonding. It
was hypothesized that under appropriate conditions,
individual base functionalities could operate as bifunc-
tional catalysts in much the same way as two separate
histidine and aspartate residues act in concert within the
relatively high rate increase of 210%. For comparison,
11
2
-pyridone, a well-known bifunctional catalyst, showed
a rate increase of 110% under the same conditions.
Imidazole, which constitutes the heterocyclic base in
histidine, is critical to a number of enzymatic proton
transfer processes and showed a rate increase of less than
1
0%. These results indicate that the functional groups
contained in C, G, and Ψ are not only capable of
catalyzing amide bond formation but do so more ef-
fectively than imidazole. The relatively high value for
C, as compared to the bifunctional catalyst 2-pyridone,
suggests that C might be operating in a similar manner
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T. R. Science 1992, 256, 1420.
(
(
(
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3
64.
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(
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