1973

DOI: 10.1021/bi00745a001

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Topography of nucleic acid helixes in solution. XXX. Specific interaction of peptides with nucleic acids. Evidence for a selective bookmark recognition hypothesis

Edmond J. Gabbay¹,

Karl Sanford²,

C. Stuart Baxter³

et al.

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Purification Of L51

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1974

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Cited by 107 publications

(59 citation statements)

References 16 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%

“…However, this does not introduce a large error in the determination of K2. The main conclusion that can be 6.0 for DNA or pH 7.0 for polynucleotides. Solutions were made in a sodium cacodylate buffer (1 mM), 0.2 mM EDTA, in the presence of 1 mM sodium chloride.…”

Section: Resultsmentioning

confidence: 97%

See 1 more Smart Citation

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

¹

,

²

,

³

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...

“…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%

“…However, this does not introduce a large error in the determination of K2. The main conclusion that can be 6.0 for DNA or pH 7.0 for polynucleotides. Solutions were made in a sodium cacodylate buffer (1 mM), 0.2 mM EDTA, in the presence of 1 mM sodium chloride.…”

Section: Resultsmentioning

confidence: 97%

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

¹

,

²

,

³

1974

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

View full text Add to dashboard Cite

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...

“…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

¹

,

²

,

³

1976

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“…Another mutation in loop C (A 42 3 C) has no impact on binding. The only mutation outside of this region that affects binding of L5 is the transversion T 76 3 G located in loop E. We have shown earlier that this substitution engenders an alternative conformation in the RNA that is in equilibrium with the wildtype structure.…”

Section: Purification Of L5mentioning

confidence: 99%

Analysis of the Binding of Xenopus Ribosomal Protein L5 to Oocyte 5 S rRNA

¹

,

²

1995

Journal of Biological Chemistry

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Xenopus ribosomal protein L5 was expressed in Escherichia coli and exhibits high affinity (K d ‫؍‬ 2 nM) and specificity for oocyte 5 S rRNA. The pH dependence of the association constant for the complex reveals an ionization with a pK a value of 10.1, indicating that tyrosine and/or lysine residues are important for specific binding of L5 to the RNA. Formation of the L5⅐5 S rRNA complex is remarkably insensitive to ionic strength, providing evidence that nonelectrostatic interactions make significant contributions to binding. Together, these results suggest that one or more tyrosine residues may form critical contacts through stacking interactions with bases in the RNA. In order to locate recognition elements within 5 S rRNA, we measured binding of L5 to a collection of site-specific mutants. Mutations in the RNA that affected the interaction are confined to the hairpin structure comprised of helix III and loop C. Earlier experiments with a rhodium structural probe had shown that the two-nucleotide bulge in helix III and the intrinsic structure of loop C create sites in the major groove that are opened and accessible to stacking interactions with the metal complex. In the present studies, we detect a correlation between the intercalative binding of the rhodium complex to mutants in the hairpin and binding of L5, supporting the proposal that binding of the protein is mediated, in some part, by stacking interactions. Furthermore, the results from mutagenesis establish that, despite overlapping binding sites on 5 S rRNA, L5 and transcription factor IIIA utilize distinct structural elements for recognition.The metabolism of Xenopus 5 S ribosomal RNA during oogenesis provides the opportunity to study the interaction of several different proteins with the same nucleic acid. Moreover, these individual ribonucleoprotein complexes appear to determine the intracellular translocation of 5 S rRNA. Initially, the primary transcripts are transiently associated with the La antigen in the nucleus (1, 2). However, the synthesis of 5 S rRNA and ribosome assembly are discontinuous in the early stages of oogenesis, so that much of the RNA is stored in the cytoplasm complexed either with transcription factor IIIA (TFIIIA) 1 or with the protein p43 as part of a large multicomponent 42 S RNP complex (3, 4). Coincident with the expression of the ribosomal proteins during vitellogenesis, an increasing amount of cytoplasmic 5 S rRNA becomes associated with ribosomal protein L5 (5). This latter complex then moves to the nucleolus, where it becomes integrated into nascent ribosomes (1, 6). Mutant forms of 5 S rRNA that are unable to bind to TFIIIA or L5 are retained in the nucleus of the oocyte, indicating that the RNA can only be exported to the cytoplasm in the form of an RNP complex (2). Likewise, the ultimate return of cytoplasmic 5 S rRNA to the nucleolus depends on the formation of the complex with L5 (6, 7). It is not known how the formation of a particular RNP particle creates a signal for nucleocytoplasmic transport.The interacti...

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