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J R Fresco

Publications and source records attributed to J R Fresco.

At least 37 records · Page 2Linked to original sources
PubMed1987

Formation of the triple-stranded polynucleotide helix, poly(A.A.U).

A polynucleotide helical structure containing two strands of poly(A) and one of poly(U) is reported. As shown by spectroscopic observations, the complex only forms when the poly(A) strands are of Mr between 9000 and 50,000 (degree of polymerization congruent to 28-150), whereas the size of the poly(U) strand has no effect. This limitation may explain why poly(A.A.U) was not seen in previous investigations. The potential of the poly(A) tails of mRNA for formation of this triple helix and of A.A.U or/and A.A.T triplet formation to contribute to the binding of specific RNA strands to gene-encoding nucleic acid double helices are noted.

Circular Dichroism↗
PubMed1986

Ultraviolet-induced 8,8-adenine dehydrodimers in oligo- and polynucleotides.

Characteristic fluorescence excitation and emission is induced by either acetone-sensitized 313 nm irradiation of mixtures of 8-bromoadenosine and adenosine or 254 nm irradiation of oligo- and polynucleotides containing adenine neighbors. The acetone-sensitized reaction involves cleavage of bromine from 8-bromoadenosine with activation of C-8, leading to formation of an 8,8-adenosine dehydrodimer. Comparable fluorescence properties arise in the unsensitized photoreaction of dApdA, pdApdA, ApA, poly(dA), poly(A), poly(dA.dT), and poly(dA.U). The previously unidentified adenine ultraviolet photoproduct described by Porschke has been isolated as several variants from solutions of pdApdA and poly(dA) irradiated at 254 nm. Based upon fluorescence spectra and mass spectra, these variants are shown to contain the 8,8-adenine dehydrodimer moiety.

Acetone↗
PubMed1983

Correlation of crystallographically determined and computationally predicted hydrogen-bonded pairing configurations of nucleic acid bases.

Crystals of pairs of H-bonded nucleic acid bases are generally grown from nonaqueous solutions. We have been able to predict the H-bonded configuration of most of the base pairs in such crystals by using an empirical-potential function we recently developed for calculating the energetics of such interactions in chloroform solution. The following configurations were computationally predicted to predominate and are those observed in crystal structures: the Watson-Crick G.C configuration instead of two competing configurations; the Hoogsteen-type configurations for A.T, A.U, and A.br5U instead of Watson-Crick-type configurations; the Watson-Crick-type configurations for 2-aminopurine.br5U instead of the purine N3-type configuration; the Watson-Crick-type configurations for 8-bromo-2,6-diaminopurine.T instead of the Hoogsteen or purine-N3-type configurations; the syn-anti configuration for br8A.br8I instead of the anti-anti configuration; the Watson-Crick-type configurations for br8A.br5U instead of the Hoogsteen-type configurations; and the Hoogsteen-type configurations for me8A.T instead of the Watson-Crick configurations. In addition, the H-bonded base triplet br5U.2,6-diaminopurine.br5U was calculated to have Hoogsteen and Watson-Crick-type configurations but not the purine N3-type configuration. Apparently, lattice forces and chance nucleation of a minor base pairing configuration are not significant when the stability difference between the preferred and alternative configurations exceeds a relatively small value. In one case, in order to correctly predict the base pairing configuration in the crystal, it was necessary to include a contribution due to a C--H...O bond, suggesting that this type of H bond can make a significant contribution to base pair stability.

Base Composition↗
PubMed1982

Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein.

The ability of a nucleic acid helix-destabilizing protein from calf thymus, UP1, to facilitate renaturation of yeast tRNALeu3 and Escherichia coli 5S RNA is shown to be a consequence of the protein's ability to bind stoichiometrically to single-stranded polynucleotide regions. A comparison of the inhibitory effect of different homopolymers on UP1-induced renaturation of tRNALeu3 does not indicate significant base specificity in UP1 binding, and a 3'-5' ribose phosphate polymer devoid of heterocyclic bases inhibits as well as the homopolynucleotides. These inhibition studies also show that UP1 requires polynucleotide segments of at least three phosphate residues to bind. Mg2+ (which is required for the stabilization of native tRNALeu3) dissociates complexes of UP1 with inactive tRNA, and since the RNAs in those complexes lack a substantial amount of secondary structure, it can upon dissociation readily refold into the native structure. A semiquantitative treatment of UP1-RNA interaction is developed that suggests that only a small number (approximately six) of protein molecules are bound to tRNALeu3 in the complex while analysis of the inhibition studies suggests that these UP1 molecules are not bound in a highly cooperative manner.

Animals↗
PubMed1980

Fluorescence of terbium ion-nucleic acid complexes: a sensitive specific probe for unpaired residues in nucleic acids.

The interaction of the lanthanide cation Tb3+ with the phosphate moieties of non-hydrogen-bonded residues of nucleic acids has been shown to result in substantial enhancement of the fluorescence of this cation. The excitation spectrum for this fluorescence is characteristic of the base moiety of the residue to which the Tb3+ is bound, while the emission spectrum is characteristic of the cation itself. The intensity of the fluorescence enhancement, however, is dependent upon the base of the ligand moiety, with G inducing the strongest enhancement, C and T rather less, and A very little. Base-paired residues of nucleic acids induce no such fluorescence enhancement, even though the cation is more tightly bound to double helical regions than to residues in single strands. The enhancement of Tb3+ fluorescence upon binding to non-hydrogen-bonded residues therefore provides a highly specific conformational probe for such residues. This probe has been exploited successfully for the purpose of analyzing the kinetics of reassociation of DNAs (C0t analysis) and as a specific stain for single-strand DNA bands on polyacrylamide gels.

DNA↗
PubMed1977

Metabolic regulation of aminoacyl-tRNA synthetase biosynthesis in bakers' yeast.

The specific activities of 15 aminoacyl-tRNA synthetases in Saccharomyces cerevisiae were measured after growth under a variety of conditions that produced a range of cell-doubling times. The specific activity of each synthetase increased as cell-doubling time decreased. Control experiments eliminate the possibility that these results are due to preferential recovery of synthetases, or to the presence of activators in the faster growing cultures or inhibitors in the slower growing ones. These observations run counter to the expectation that synthetases in bacteria and yeast are negatively regulated by free amino acids, or, more likely, by aminoacyl-tRNA. In fact, as the growth medium was enriched, generation times decreased, and synthetase and aminoacyl-tRNA levels increased. It is suggested that cytoplasmic aminoacyl-tRNA synthetases may be more or less coordinately controlled such that their response to growth follows the pattern observed for ribosome production and RNA synthesis. This suggests the possibility of coordinated response of genes for components of the protein synthetic apparatus.

Alcohol Oxidoreductases↗
PubMed1976

Complementary base pairing and the origin of substitution mutations.

On the basis of chemical considerations and model building, the Watson-Crick concept of complementary base pairing is extended to a wider range of DNA pairs that A-T and G-C (including A-C, G-T, A-A, G-G and G-A) by invoking imino or enol tautomers (or protonated species) and synisomers. The virtual absence of these additional base pairs from DNA is explained in terms of the low frequency with which these unfavoured forms occur and the two-step mechanism of DNA synthesis, whereby residues are first incorporated by the DNA polymerase and then checked. This base-pairing hypothesis is used to explain the origin, nature and level of spontaneous substitution mutations, their enhancement by base analogues, and the unique effects of certain mutator alleles.

2-Aminopurine↗
PubMed1976

Base pairing and fidelity in codon-anticodon interaction.

Base pairing in codon-anticodon interaction has been investigated in order to understand the basis on which particular base pairs have been selected for or against participation at the wobble position and the basis for codon-anticodon infidelity.

Adenine↗