Topography of nucleic acid helices in solution. XXVI. Specific interaction of peptides with nucleic acids

Ej, Gabbay; Sanford, Karl; Cs, Baxter

doi:10.1021/bi00768a016

Cited by 87 publications

(34 citation statements)

References 21 publications

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“…Proton magnetic resonance (2,4) and circular dichroism* studies have provided evidence for a stacking interaction of the tryptophyl ring with bases. A similar conclusion has also been reached by Gabbay and coworkers for different tryptophan-containing peptides (5,6). Fluorescence and phosphorescence studies at low temperature have shown that the tryptophyl ring stacked with bases acts as a trap for the triplet excitation energy (7).…”

supporting

confidence: 69%

Specific Recognition of Single-Stranded Regions in Ultraviolet-Irradiated and Heat-Denatured DNA by Tryptophan-Containing Peptides

Toulmé

Charlier

Hélène

1974

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

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We are presently investigating the origin and the nature of molecular interactions responsible for the specific recognition of nucleic acid sequences by proteins (see refs. 1-4 for previous publications). Since we are interested in the role played by aromatic amino acids, we have studied the binding of oligopeptides containing lysyl and tryptophyl residues such as Lys-Trp-Lys to different nucleic acids and polynucleotides. Proton magnetic resonance (2, 4) and circular dichroism* studies have provided evidence for a stacking interaction of the tryptophyl ring with bases. A similar conclusion has also been reached by Gabbay and coworkers for different tryptophan-containing peptides (5, 6). Fluorescence and phosphorescence studies at low temperature have shown that the tryptophyl ring stacked with bases acts as a trap for the triplet excitation energy (7). At room temperature, fluorescence spectroscopy is appropriate for study of the binding of tryptophyl-containing peptides to nucleic acids since only the tryptophyl ring emits fluorescence in fluid medium. The weak fluorescence of nucleic acid bases (8, 9) at room temperature has a quantum yield that is 3 orders of magnitude smaller than that of tryptophan.A quantitative analysis of fluorescence data is presented here which shows that two types of complexes are formed when oligopeptides such as Lys-Trp-Lys bind to nucleic acids. The role of the local structure of nucleic acids in the binding process is investigated by comparing the behavior of heatdenatured or UV-irradiated DNA with native double-stranded DNA with respect to stacking of the tryptophyl ring with bases. It is also shown that the tryptophyl ring is able to photosensitize the splitting of thymine dimers in UV-irradiated DNA. EXPERIMENTALFluorescence measurements were made with a Jobin-Yvon spectrofluorimeter that was modified to correct for lamp fluctuations by deflecting part of the incident beam onto a rhodamine B quantum counter. The sample was contained in a 5-mm quartz Suprasil thermostated cell (usually 2°).Difference absorption spectrophotometry measurements have shown that the binding of tryptophan-containing peptides to nucleic acids is accompanied by a small but reproducible absorption change. The excitation wavelength was therefore chosen at the isosbestic point of these difference spectra (292 nm).To correct fluorescence intensities for the screening effect of the nucleic acid at the excitation wavelength, peptidenucleic acid complexes were dissociated by increasing the ionic strength (2, 12). At high ionic strength (0.5 M NaCl), only the screening effect of the nucleic acid was assumed to lead to an apparent decrease of the fluorescence quantum yield of the peptide. All fluorescence quantum yields were measured with respect to that of the free peptide and corrected for the screening effect of the nucleic acid.Polynucleotides and oligopeptides were purchased from RESULTSThe binding of peptides containing lysyl and tryptophyl residues to nucleic acids is accompanied by a decrease o...

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supporting

confidence: 69%

Specific Recognition of Single-Stranded Regions in Ultraviolet-Irradiated and Heat-Denatured DNA by Tryptophan-Containing Peptides

Toulmé

Charlier

Hélène

1974

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

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“…In fact the viscosity of the complex with (DLys)3 is more affected with respect to DNA than that with other oligopeptides. The same marked effect on the specific viscosity has been reported by Gabbay's group for the case of L-Lys-LLeu-DLys and NI-~3-(CH2)-NI-~3 [1,2] bound to DNA. Using the Gabbay's reasoning one should conclude that these last compounds together with (L-Lys)3 should also partially intercalate into DNA chains.…”

Section: Resultssupporting

confidence: 84%

On the interaction of oligopeptides containing aromatic amino acids with DNA in aqueous solution

1976

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“…Such variations in the relative importance of dispersion and electrostatic interaction energies, and the low degree of overlap in the stacking geometries (Figs. [2][3][4][5][6][7][8][9] suggest that the interaction of His with the bases and the base pairs has a large Coulombic contribution.…”

Section: Partitioning Of the Stacking Energiesmentioning

confidence: 99%

Theoretical studies on protein–nucleic acid interactions. III. Stacking of aromatic amino acids with bases and base pairs of nucleic acids

Kumar

Govil

1984

Biopolymers

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SynopsisStacking of aromatic amino acids tryptophan (Trp), tyrosine (Tyr), phenylalanine (Phe), and histidine (His) with bases and base pairs of nucleic acids has been studied. Stacking energies of the amino acid-base (or base pair) complexes have been calculated by second-order perturbation theory. Our results show that, in general, the predominant contribution to the total stacking energy comes from the dispersion term. In these cases, repulsion energy is greater than the sum of electrostatic and polarization energies. In contrast to this, interaction of histidine with the bases and base pairs is largely Coulombic in nature. The complexes of guanine with aromatic amino acids are more stable than the corresponding complexes of adenine. Among pyrimidines, cytosine forms the most stable complexes with the aromatic amino acids. The G C base pair has the highest affinity with aromatic amino acids among various sets of base pairs. Optimized geometries of the stacked complexes show that the aromatic moieties overlap only partially. The heteroatom of one residue generally overlaps with the other aromatic moiety. There is a considerable degree of configurational freedom in the stacked geometries. The role of stacking in specific recognition of base sequences by proteins is discussed.

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Topography of nucleic acid helices in solution. XXVI. Specific interaction of peptides with nucleic acids

Cited by 87 publications

References 21 publications

Specific Recognition of Single-Stranded Regions in Ultraviolet-Irradiated and Heat-Denatured DNA by Tryptophan-Containing Peptides

Specific Recognition of Single-Stranded Regions in Ultraviolet-Irradiated and Heat-Denatured DNA by Tryptophan-Containing Peptides

On the interaction of oligopeptides containing aromatic amino acids with DNA in aqueous solution

Theoretical studies on protein–nucleic acid interactions. III. Stacking of aromatic amino acids with bases and base pairs of nucleic acids

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