Synthetic Polynucleotides and the Amino Acid Code, Iii

Lengyel, Péter; Speyer, Joseph F.; Basilio, C.; Ochoa, Severo

doi:10.1073/pnas.48.2.282

Cited by 48 publications

(6 citation statements)

References 3 publications

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“…The relative amounts of the four amino acids incorporated with any particular polymer are clearly related to the proportion of U and G. The data show that efficient incorporation of tryptophan requires a greater proportion of G in the polymer than is necessary for incorporation of valine or leucine. These data, therefore, confirm the earlier assignment of codewords UUG, UUG, and UGG to valine, leucine, and tryptophan, respectively.11' 12,14 It is evident that the efficiency of a polymer as template RNA ( Table 1) for any of the amino acids shown decreases sharply when the U/G ratio becomes less than 1. For example, the incorporation of phenylalanine with the polymer of U/G ratio 6.7/1 is about 60-fold greater than that obtained with the polymer of U/G ratio, 0.58/1.…”

supporting

confidence: 85%

“…Using this system and randomly mixed polyribonucleotides composed of various combinations of the four common ribonucleotides, nucleotide codewords corresponding to almost all of the protein amino acids have been determined. [10][11][12][13][14][15] Observations made with this system suggested that the secondary structure of polymers influenced template efficiency. For example, the ability of poly U to direct polyphenylalanine synthesis is lost when poly A-poly U double or triple helices are formed.9' 10 The present report describes certain physical properties of a series of poly UG preparations as well as the efficiency of these polymers in directing amino acid incorporation in the cell-free system.…”

mentioning

confidence: 99%

“…12,14 However, several properties of the poly UG preparations used indicate that meaningful comparisons between theoretical frequencies of doublets or triplets and relative amino acid incorporations cannot be made. One such factor is the secondary structure of the polymers and is discussed in detail below.…”

mentioning

confidence: 99%

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The Effect of Secondary Structure on the Template Activity of Polyribonucleotides

Singer¹,

Jones²,

Nirenberg³

1963

Proc. Natl. Acad. Sci. U.S.A.

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6Other workers have also observed satellite bands in studying DNA from a variety of sources. Ephrussi-Taylor (J. de Chim. Phys., 58, 1090) working with synchronized D. pneumoniae, and Lark, Cavalieri, and Rosenberg (unpublished observations, 1962) studying synchronized A. faecali8, have observed satellite bands of increased buoyant density. With animal cell DNA, satellite bands both of increased and of decreased density have been reported (Kit, S., J. Mol. Biol., 3, 711 (1961); Sueoka, N., J. Mol. Biol., 3, 31 (1961); Schildkraut, C., J. Marmur, and P. Doty, J. Mol. Biol., 4, 430 (1962)). Bands of decreased density were also reported by Marmur, Rownd, Falkow, Baron, Schildkraut, and Doty (these PROCEEDINGS, 47, 972 (1961)) with purified DNA from A. faecalis and S. marcesens following preparative CsCl-density-gradient fractionation.7When bacterial DNA is isolated by other standard procedures (e.g., Marmur, J., J. Mol. Biol., 3, 208 (1961)) or by density-gradient centrifugation of bacterial lysates2 the satellite band is not observed. Our isolation procedure utilizes deproteinization with phenol (Kirby, K. S., Biochem. J., 66, 495 (1957)) and ammonium sulfate-isopropanol precipitation of the nucleic acids. It will be described in detail elsewhere. The heavy satellite band is not an artifact of preparation, as it hbis been verified experimentally that native DNA is not denatured by our isolation procedure.> 8 With saturated cultures, or cultures in which DNA synthesis has run to completion after a shift to & medium lacking an essential amino acid (or after a shift from a medium containing amino-aids to a minimal medium),9 the satellite band is absent or greatly reduced in amount.

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confidence: 85%

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confidence: 99%

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The Effect of Secondary Structure on the Template Activity of Polyribonucleotides

Singer¹,

Jones²,

Nirenberg³

1963

Proc. Natl. Acad. Sci. U.S.A.

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“…Contradicting Brenner, he concluded that these frequencies 54 For example, if UUU coded for the amino acid phenylalanine, as Nirenberg and Matthaei had established, and phenylalanine was replaced by another amino acid in a mutant, one could deduce that this amino acid was coded by one of only nine different codons (all including two Us), and thus excluding 44 other possible combination. 55 Lengyel et al, 1961Lengyel et al, , 1962Speyer et al, 1962a, b;Basilio et al, 1962. 56 Smith, 1962a, b.…”

Section: Comparing Sequences To Crack the Genetic Codementioning

confidence: 99%

Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965

Strasser

2009

J Hist Biol

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Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While these practices are generally associated with the rise of molecular evolution in the 1960s, this paper shows that they grew out of research agendas from the previous decade, including the biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. It also shows how computers became essential for the handling and analysis of sequence data. Finally, this paper reflects on the relationships between experimenting and collecting as two distinct "ways of knowing" that were essential for the transformation of the life sciences in the twentieth century.

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“…Except for L-isoleucine, L-lysine, and L-tyrosine, which were uniformly labeled with C14 and of high specific radioactivity (1 mc/mg), obtained from the Schwarz Laboratories, Orangeburg, New York, the remaining C'4-labeled amino acids and other preparations were as previously noted.6 9 Methods: The incubations were conducted in general as previously described6 with use of the improved conditions noted in more recent publications of this series.' 9 Departures from these conditions not indicated in Table 1 were as follows: The samples with isoleucine-C'4 had 5 umoles of cold, highly purified L-leucine10 and 0.14 umole of cold L-tyrosine in addition to the usual mixture of 19 cold amino acids. The samples with tyrosine-C14 had 5 ,umoles of each cold Lleucine and L-isoleucine'°besides the amino acid mixture.…”

mentioning

confidence: 99%

Synthetic Polynucleotides and the Amino Acid Code. Vi

Wahba¹,

Basilio²,

Speyer³

et al. 1962

Proc. Natl. Acad. Sci. U.S.A.

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Previous experiments with synthetic polynucleotides of random nucleotide distribution have provided information about the base composition of the triplet code letters for 19 amino acids.1 These results were confirmed by other investigators.2 However, the sequence of bases in the code triplets is known only in the case of phenylalanine (UUU).3 Through the use of nonrandom copolymers it should be possible to establish the base sequence of some code letters, the direction in which the code is read, and the colinearity of the synthesized polypeptides with the template polynucleotide.The simplest approach to the problem is to place one or more triplets of known sequence at one end of a poly U chain. This is made possible by the fact that short oligonucleotides prime polynucleotide phosphorylase by acting as nuclei for growth of. the polynucleotide chains.4 By priming with a mixture of ApU and ApApU5 we have obtained polymers which promoted the incorporation of small amounts of tyrosine besides phenylalanine, but not that of isoleucine, asparagine, or lysine. In contrast, random poly UA stimulated the incorporation of tyrosine and isoleucine to the same extent. This suggested that tyrosine incorporation may be caused by a beginning AUU sequence in these polymers.Preparation of oligonucleotide primers of polynucleotide phosphorylase:-Poly UA(5: 1), 16 mg, from a previously prepared batch6 (actually determined U:A ratio, 4.8:1) was dissolved in 1.6 ml of 0.02 M Tris-HCl buffer, pH 7.4, and digested for 15 hr at room temperature with 0.32 mg of crystalline pancreatic ribonuclease (Worthington) after adding a few drops of toluene. The solution was then adjusted to pH 5.6 with acetic acid and made 0.01 M with sodium acetate. Ribonuclease digestion of the above polymer yields Up, ApUp, ApApUp, and traces of higher oligonucleotides (ApApApUp, etc.). In order to remove the terminal phosphate, monoesterified at ribose carbon 3', the solution was incubated with prostatic phosphomonoesterase7 until no more orthophosphate was released. Following this treatment the solution was adjusted to pH 7.9 with NaOH and digested with 0.1 mg of crystalline trypsin (Armour) for 15 min to destroy the ribonuclease and phosphomonoesterase. The phosphomonoesterase and trypsin digestions were conducted at 37°. The solution was shaken with phenol for 1 hr at room temperature. The aqueous layer was washed with ether and acidified to pH 3.0 with HCl. The oligonucleotides (mostly ApU and ApApU) together with the uridine were then adsorbed on 100 mg of charcoal,

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Synthetic Polynucleotides and the Amino Acid Code, Iii

Cited by 48 publications

References 3 publications

The Effect of Secondary Structure on the Template Activity of Polyribonucleotides

The Effect of Secondary Structure on the Template Activity of Polyribonucleotides

Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965

Synthetic Polynucleotides and the Amino Acid Code. Vi

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