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At least 127 records · Page 7Linked to original sources
PubMed1979

The role of tyrosine in the association of proteins and nucleic acids. Specific recognition of single-stranded nucleic acids by tyrosine-containing peptides.

Oligopeptides containing tyrosyl, lysyl, and alanyl residues bind to polynucleotides and nucleic acids as shown by proton magnetic resonance, fluorescence spectroscopy, and difference absorption spectroscopy. Proton magnetic resonance data indicate that stacking of tyrosyl residues with nucleic acid bases takes place only in single-stranded structures (such as poly(A) or denatured DNA). Stacking interactions lead to a quenching of tyrosine fluorescence. However, the tyrosyl fluorescence of the peptides is quenched in their complexes with both single-stranded and double-stranded nucleic acids. A comparison of the behavior of homologous peptides containing Tyr, methoxytyrosine, and Phe leads to the conclusion that hydrogen bonding of tyrosine with bases or phosphates is not involved in the investigated complexes. An energy transfer mechanism from tyrosine to nucleic acid bases is proposed to account for fluorescence quenching in oligopeptide complexes with double-stranded DNAs. Due to the specificity of its stacking interaction for single-stranded nucleic acid structures, tyrosine might be involved through such interactions in the selective recognition of single strands by proteins.

Alanine↗
PubMed1988

The inhibition of glucosylceramide beta-glucosidase and other acid hydrolases by nucleic acids.

During the isolation of the activator protein for glucosylceramide beta-glucosidase, we found that certain column fractions contained an inhibitor of the enzyme. After separation from the activator protein by a DEAE-Sephacel column, the inhibitor was purified further with a Spehadex G-75 column. The u.v. absorption spectrum of the purified material was similar to that of nucleic acids and the protein content of the purified material was negligible. Furthermore the purified inhibitor reacted with orcinol but not with diphenylamine, and its inhibitory activity was completely destroyed by treatment with RNAases. It seems likely that the purified inhibitor was tRNA. Authentic RNA, tRNA and DNA had similar inhibitory effects on beta-glucosidase (Ki 17 micrograms/ml for tRNA, noncompetitive toward the substrate). The inhibitory effect of nucleic acids was not fully overcome by an excess amount of the activator protein, but phosphatidylserine could restore the activity to normal. Tests with several other hydrolases revealed that the inhibitory effect of nucleic acids was fairly general.

DNA↗
PubMed1993

Laser cross-linking of proteins to nucleic acids. I. Examining physical parameters of protein-nucleic acid complexes.

Pulsed laser cross-linking results in efficient and rapid formation of covalent bonds between proteins and the nucleic acids to which they are bound, creating a "snapshot" of the protein-nucleic acid equilibrium existing at the moment of irradiation. The "frozen" equilibrium allows the determination of protein-nucleic acid binding constants, confirming both theoretical predictions and experimental determinations by standard physical chemical methods. Laser cross-linking results accurately reflect the alteration of protein-nucleic acid interactions induced by traditional methods such as increasing the salt concentration or by the addition of a nucleic acid that competes for binding of the protein. Thus this technique is very useful for the study of the association of proteins and protein complexes with nucleic acids under environmental conditions at which the reactions are not amenable to study by traditional physical chemical methods. In this paper we continue our calibration of the method, focusing primarily on interactions with single-stranded DNA-binding proteins and describe techniques for measuring quantitative interactions between nucleic acid constructs and single-protein or multiprotein complexes. Laser cross-linking can also provide direct evidence that binding correlates with functional activity.

Bacterial Proteins↗
PubMed1979

Model studies of interactions between nucleic acids and proteins: hydrogen bonding of amides with nucleic acid bases.

The formation of hydrogen bonded complexes between nucleic acid bases and acetamide has been studied by nuclear magnetic resonance in CDC13 at different temperatures. Pairs of hydrogen bonds are formed when acetamide binds to nucleic acid bases. Thermodynamic parameters have been computed and compared to those obtained for the association of carboxylic acids with nucleic acid bases. The role of hydrogen bonded complexes in the association of proteins with nucleic acids is discussed.

Acetamides↗
PubMed1996

Nucleic acid crystallography: a view from the nucleic acid database.

What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB.

Base Sequence↗
PubMed1972

Uptake of amino acids and nucleic acid precursors by regenerating rat liver.

1. At 0.5-1.0h after partial hepatectomy the intracellular acid-soluble fraction of rat liver took up twice as much radioactivity from [(3)H]orotic acid, [(3)H]uridine and [(3)H]thymidine as did similar fractions from sham-operated animals. This increase in penetration was not prevented by adrenalectomy or actinomycin, both of which decreased precursor uptake into nuclear RNA at this time. The increase in entry was still shown by thymidine at 22h after operation, at the height of the S period. Adenine penetration was not increased 1h after partial hepatectomy. 2. Plasma concentrations of ornithine and possibly methionine, tyrosine and lysine were raised 1.5h after partial hepatectomy. [(3)H]Lysine entry into regenerating liver at this time was increased by 60%; [(3)H]valine uptake was unaffected. Intracellular amounts of tyrosine, phenylalanine and ornithine in the liver were also increased. 3. The relation of these events to the start of liver regeneration is discussed.

Adenine↗
PubMed1970

Regulation of Bud Rest in Tubers of Potato, Solanum tuberosum L: VII. Effect of Abscisic and Gibberellic Acids on Nucleic Acid Synthesis in Excised Buds.

The effect of gibberellin A(3) (10(-4)m) and abscisic acid (10(-4)m), applied separately and together, on incorporation of (3)H-thymidine and (3)H-uridine into DNA and RNA of buds from freshly harvested potatoes was investigated. In some treatments apical buds in intact tubers were treated three times daily for 3 days with test solution before the buds were excised and treated an additional 12 hours in Petri dishes. In other treatments, untreated buds were excised and treated 12 hours. Irrespective of length of treatment, gibberellin A(3) slightly promoted synthesis of DNA and RNA, and abscisic acid essentially blocked such synthesis, in both the presence and absence of gibberellin A(3).

Journal Article↗