The kinetics of J-aggregate formation has been studied for two chromophores, tetrakis-4-sulfonatophenylporphine in an acid medium and pseudoisocyanine on a polyvinylsulfonate template. The assembly processes differ both in their sensitivity to initiation protocols and in the reaction profiles they produce. The porphyrin's assembly kinetics, for example, displays an induction period unlike that of the cyanine dye. Two kinetic models are presented. For the porphyrin, an autocatalytic pathway in which the formation of an aggregation nucleus is rate-determining appears to be applicable; for the pseudoisocyanine dye, an equation derived for diffusion-limited aggregation of a fractal object satisfactorily fits the data. These models are shown to be useful for the analysis of kinetic data obtained for several biologically important aggregation processes.

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In certain methanogenic archaea a new amino acid, pyrrolysine (Pyl), is inserted at in-frame UAG codons in the mRNAs of some methyltransferases. Pyl is directly acylated onto a suppressor tRNA Pyl by pyrrolysyl-tRNA synthetase (PylRS). Due to the lack of a readily available Pyl source, we looked for structural analogues that could be aminoacylated by PylRS onto tRNA Pyl . We report here the in vitro aminoacylation of tRNA Pyl by PylRS with two Pyl analogues: -prolyl-lysine) and N-e-cyclopentyloxycarbonyl-L L-lysine (Cyc). Escherichia coli, transformed with the tRNA Pyl and PylRS genes, suppressed a lacZ amber mutant dependent on the presence of D D-prolyl-lysine or Cyc in the medium, implying that the E. coli translation machinery is able to use Cyc-tRNA Pyl and D D-prolyl-lysine-tRNA Pyl as substrates during protein synthesis. Furthermore, the formation of active b-galactosidase shows that a specialized mRNA motif is not essential for stop-codon recoding, unlike for selenocysteine incorporation.

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Pyrrolysine (Pyl), the 22nd naturally encoded amino acid, gets acylated to its distinctive UAG suppressor tRNA Pyl by the cognate pyrrolysyl-tRNA synthetase (PylRS). Here we determine the RNA elements required for recognition and aminoacylation of tRNA Pyl in vivo by using the Pyl analog N--cyclopentyloxycarbonyl-L-lysine. Forty-two Methanosarcina barkeri tRNA Pyl variants were tested in Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA Pyl mutants were selected to determine in vivo binding to M. barkeri PylRS in a yeast three-hybrid system and to measure in vitro tRNA Pyl aminoacylation. tRNA Pyl identity elements include the discriminator base, the first base pair of the acceptor stem, the T-stem base pair G51:C63, and the anticodon flanking nucleotides U33 and A37. Transplantation of the tRNA Pyl identity elements into the mitochondrial bovine tRNA Ser scaffold yielded chimeric tRNAs active both in vitro and in vivo. Because the anticodon is not important for PylRS recognition, a tRNA Pyl variant could be constructed that efficiently suppressed the lac opal U4 mutation in E. coli. These data suggest that tRNA Pyl variants may decode numerous codons and that tRNA Pyl :PylRS is a fine orthogonal tRNA:synthetase pair that facilitated the late addition of Pyl to the genetic code.orthogonal tRNA ͉ suppression ͉ tRNA identity ͉ pyrrolysyl-tRNA synthetase ͉ aminoacyl-tRNA synthetase

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