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8/8/2019 Diels-Alderase
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Gabriel FriedmanOctober 28, 2010
The search for a Diels-Alderase
Investigations into the origin of life have centered on the ³RNA World´
hypothesis, which suggests that ribonucleic acids were the precursor to the DNA that
enables our existence. In order to substantiate this claim, it is important to show that
RNA is capable of catalyzing a wide variety of reactions, including the crucial formation
of carbon-carbon bonds. This operation, known as the Diels-Alder cycloaddition, is
crucial to anabolic processes. In a recent paper titled, ³A small catalytic RNA motif withDiels-Alderase activity,´ Burckhard Seelig and Andres Jäschke, from the Institute for
Biochemistry at Freie University in Berlin, have characterized a ribozyme that vastly
accelerates the formation of carbon-carbon bonds.
Since the 1980s, researchers have known that RNA can act as a catalyst in
biological reactions. In 1997, two years before this paper was published, a team at
NeXstar Pharmaceuticals in Colorado was able to catalyze a Diels-Alder reaction using a
ribozyme, although the RNA had to be modified. Led by Theodore Tarasow, the
researchers substituted 5-pyridylmethylcarboxamid-UTP 13 in placed of the unmodified
nucleotide uridine triphosphate. The purpose of this alteration was to increase the amount
of hydrogen bonding, provide additional hydrophobic and dipolar interactions, and to
supply metal coordination sites that could not exist with natural RNA. The group ended
up finding a reaction acceleration rate of 800 for a Diels-Alder reaction between an
acyclic diene and a maleimide dienophile. While this finding was notable, it still was
insufficient to support the ³RNA world´ hypothesis because of the substituted nucleotide.
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The authors of this present paper first created a library of randomized 120-
nucleotide RNA conjugates which were then connected to anthracene via a polyethylene
glycol (PEG) unit. For the reaction between biotin maleimide and they first measured the
uncatalyzed rate constant and then added the antracene-PEG-RNA. This can be
visualized in the following reaction scheme. After an hour they were able to isolate the
Diels-Alder products by immobilizing them on streptavidin agarose.
The elegant methodology of the researchers must be noted. By including so many
RNA variants, they ensured to find a possible Diels-Alderase if one existed. And by
immobilizing the reacted cycloaddition products, they were able to efficiently determine
which RNA variants showed promise and which ones didn¶t. After each round, they RNA
conjugates from the reacted products were reverse-transcribed and amplified via
polymerase chain reaction (PCR) and added to the next reaction cycle. As one can see
from the following diagram, after round 5 it was clear that dramatic reaction acceleration
rates were taking place.
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From rounds 6-10, the amount of substrate and reaction time was diminished in order to
increase the selection pressure and find the motifs that were truly acting as catalysts. All
in all, the researchers found 42 different catalytic motifs, with 13 sequences that gave
acceleration rates of at least 15,000-fold.
They then examined the motifs and found that 90% of them shared a
pentanucleotide region with the sequence UGCCA and a hexanucleotide region with the
sequence AAUACU. Based on structural analysis, they proposed that the catalytic motif
contained a ³bulge´ that acted as the active site:
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To bolster this claim, they found when there was a non-complementary
³mismatch´ at the top of the bulge, which would effectively increase the size of it, they
found an increased reaction rate. The researchers also examined whether the Diels-
Alderase could act as a true catalyst in a cleavage reaction and found that it was capable
of an uninspiring rate of 1.9 turnovers per hour, but it is still notable that such a turnover
could take place with a ribozyme. Overall, the researchers devised a clever experimental
scheme and undertook a rigorous analysis of their results, resulting in the fascinating
conclusion that ribozymes are capable of catalyzing a Diels-Alder reaction.In the future, there are several steps the researchers could take to learn more about
Diels-Alder ribozymes. For example, they could alter the dienes and dienophiles used in
order to better understand the structural conformation of the active site. They could also
use selective mutations and compensatory double mutations in order to see which
nucleotides or pairs of nucleotides are truly integral to the functioning of the ribozyme.
Lastly, they could begin looking for a natural Diels-Alderase to see how such a ribozyme
would function in nature and how it compares to the catalytic motif that has now been
characterized.
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References
Seelig, Burckhard, and Andres Jäschke. "A Small Catalytic RNA Motif with Diels-
Alderase Activity." Chemistry & Biology 6.3 (1999): 167-76.
Tarasow, T.M., S.L. Tarasow, & B.E. Eaton (1997). RNA-catalysed carbon-carbon bond
formation. Nature , 389: 54-57.