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A ribozyme composed of only two different nucleotides


RNA molecules are thought to have been prominent in the early history of life on Earth because of their ability both to encode genetic information and to exhibit catalytic function1. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, owing to the chemical instability of cytosine, which readily deaminates to uracil2, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unit3,4,5,6,7. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyse the template-directed joining of two RNA molecules, one bearing a 5′-triphosphate and the other a 3′-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalysed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3′,5′-phosphodiester linkages.

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Figure 1: Sequence and secondary structure of ligase ribozymes containing either three or two different nucleotide subunits.
Figure 2: Time course of the cyclization reaction involving the final selected ribozyme, which contained only D and U residues.
Figure 3: Saturation plot for the bimolecular reaction involving the final selected ribozyme and an RNA substrate, both of which contained only D and U residues.


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We thank J. Rogers for many discussions during the initial stages of this project. We also thank the members of the Joyce laboratory for their advice and E. Tzima for assistance in preparation of the manuscript. This work was supported by a grant from the National Aeronautics and Space Administration and the Skaggs Institute for Chemical Biology. J.S.R. was supported by a postdoctoral fellowship from the NASA Specialized Center for Research and Training (NSCORT) in Exobiology.

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Correspondence to Gerald F. Joyce.

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Reader, J., Joyce, G. A ribozyme composed of only two different nucleotides. Nature 420, 841–844 (2002).

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