An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions. The enzyme is comprised of a catalytic domain of 15 deoxynucleotides, f lanked by two substrate-recognition domains of seven to eight deoxynucleotides each. The RNA substrate is bound through Watson-Crick base pairing and is cleaved at a particular phosphodiester located between an unpaired purine and a paired pyrimidine residue. Despite its small size, the DNA enzyme has a catalytic efficiency (k cat ͞K m ) of Ϸ10 9 M ؊1 ⅐min ؊1 under multiple turnover conditions, exceeding that of any other known nucleic acid enzyme. Its activity is dependent on the presence of Mg 2؉ ion. By changing the sequence of the substrate-recognition domains, the DNA enzyme can be made to target different RNA substrates. In this study, for example, it was directed to cleave synthetic RNAs corresponding to the start codon region of HIV-1 gag͞pol, env, vpr, tat, and nef mRNAs.DNA has long been regarded as a passive molecule, ideally suited for carrying genetic information but structurally monotonous and therefore functionally impoverished. After the discovery of catalytic RNA (1, 2), it became clear that nucleic acid molecules of a particular sequence and 3-dimensional structure are able to carry out specific chemical reactions, often with an efficiency comparable to that of protein enzymes (3). In recent years, the first examples of DNA enzymes have appeared, each having been obtained by in vitro selection methodology (4-7). Although it is remarkable that DNA can have catalytic activity, all of the DNA enzymes generated to date have little utility in a biological context. This is in contrast to some of the naturally occurring RNA enzymes, such as the ''hammerhead'' and ''hairpin'' ribozymes, which have been used to cleave and thereby inactivate target viral and messenger RNAs (reviewed in ref. 8).We sought to develop a DNA enzyme that could be made to cleave almost any RNA substrate, efficiently and specifically under physiological conditions. Such a molecule could be used to inactivate a target RNA, probe a structured RNA, or assist in the manipulation of recombinant RNA. Compared with synthetic RNA enzymes, DNA enzymes are easier to prepare and less sensitive to chemical and enzymatic degradation. In a previous study, DNA was shown to catalyze the Mg 2ϩ -dependent cleavage of an RNA phosphoester embedded within an otherwise all-DNA substrate (6). Although that DNA enzyme was unable to cleave an all-RNA substrate, its properties suggested that a DNA enzyme with general purpose RNA cleavage activity might be attainable.Using in vitro selection, we carried out an extensive search of DNA sequences, seeking molecules that best met the following criteria: (i) ability to cleave RNA with multiple turnover under simulated physiological conditions (e.g., 2 mM MgCl 2 ͞150 mM KCl, pH 7.5, 37ЊC); (ii) ability to recognize the RNA substrate through Watson-Crick base pairing; ...

We report the selection of a new orthogonal aminoacyl tRNA synthetase/tRNA pair for the in vivo incorporation of a photocrosslinker, p-azido-l-phenylalanine, into proteins in response to the amber codon, TAG. The amino acid is incorporated in good yield with high fidelity and can be used to crosslink interacting proteins.

We previously reported the in vitro selection of a general-purpose RNA-cleaving DNA enzyme that exhibits a catalytic efficiency (kcat/KM) exceeding that of any other known nucleic acid enzyme [Santoro, S. W. and Joyce, G. F. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 4262-4266]. This enzyme contains approximately 30 deoxynucleotides and can cleave almost any RNA substrate under simulated physiological conditions, recognizing the substrate through two Watson-Crick binding domains. The kinetics of cleavage under conditions of varying pH, choice of divalent metal cofactor, and divalent metal concentration are consistent with a chemical mechanism involving metal-assisted deprotonation of a 2'-hydroxyl of the substrate, leading to substrate cleavage. Kinetic measurements reveal that the enzyme strongly prefers cleavage of the substrate over ligation of the two cleavage products and that the enzyme's catalytic efficiency is limited by the rate of substrate binding. The enzyme displays a high level of substrate specificity, discriminating against RNAs that contain a single base mismatch within either of the two substrate-recognition domains. With appropriate design of the substrate-recognition domains, the enzyme exhibits a potent combination of high substrate sequence specificity and selectivity, high catalytic efficiency, and rapid catalytic turnover.

With few exceptions the genetic codes of all known organisms encode the same 20 amino acids, yet all that is required to add a new building block are a unique tRNA͞aminoacyl-tRNA synthetase pair, a source of the amino acid, and a unique codon that specifies the amino acid. For example, the amber nonsense codon, TAG, together with orthogonal Methanococcus jannaschii or Escherichia coli tRNA͞synthetase pairs have been used to genetically encode a variety of unnatural amino acids in E. coli and yeast, respectively. However, the availability of noncoding triplet codons ultimately limits the number of amino acids encoded by any organism. Here, we report the design and generation of an orthogonal synthetase͞ tRNA pair derived from archaeal tRNA Lys sequences that efficiently and selectively incorporates an unnatural amino acid into proteins in response to the quadruplet codon, AGGA. Frameshift suppression with L-homoglutamine (hGln) does not significantly affect protein yields or cell growth rates and is mutually orthogonal with amber suppression, permitting the simultaneous incorporation of two unnatural amino acids, hGln and O-methyl-L-tyrosine, at distinct positions within myoglobin. This work suggests that neither the number of available triplet codons nor the translational machinery itself represents a significant barrier to further expansion of the genetic code.