Interaction of aromatic residues of proteins with nucleic acids. Binding of oligopeptides to copolynucleotides of adenine and cytosine

Maurizot, Jean‐Claude; Boubault, G.; Hélène, Claude

doi:10.1021/bi00604a012

Cited by 29 publications

(12 citation statements)

References 24 publications

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“…As previously reported (Brun et al, 1975;Maurizot et al, 1978), the stacking of tryptophyl residues of peptides with bases in single-stranded polynucleotides depends of the base stacking properties of the polynucleotide. The order of decreasing K2 values (Table II) correlates with the amplitude of the positive absorption band around 300 nm (Figure 2).…”

Section: Discussionsupporting

confidence: 59%

Does tryptophan intercalate in DNA? A comparative study of peptide binding to alternating and non-alternating A.cntdot.T sequences

Rajeswari¹,

Montenay-Garestier²,

Hélène³

1987

Biochemistry

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The interactions of a tetrapeptide, lysyltryptophylglycyllysine tert-butyl ester (KWGK), with synthetic double-stranded polynucleotides [poly(dA).poly(dT), poly[d(A-T)], poly(rA).poly(dT), and poly(rA).poly(rU)], Escherichia coli DNA, and single-stranded polynucleotides [poly(rA), poly(rU), poly(dA), and poly(dT)] were studied in a low-salt buffer by absorption and fluorescence spectroscopy. From fluorescence quenching data, we determined the two binding constants K1 and K2 of the two-step mechanism previously proposed for lysyltryptophyllysine binding to polynucleotides [Brun, F., Toulmé, J.J., & Hélène, C. (1975) Biochemistry 14, 558-563]. The first complex (PN)1 is purely due to electrostatic interactions between the lysyl residues and the phosphate groups. The second complex (PN)2 involves an additional stacking of the indole moiety of the tryptophyl residue with the bases (or base pairs) of the polynucleotide and is in equilibrium with (PN)1. K2 measures the ratio of the concentrations of stacked and unstacked complexes. The fluorescence decay of the tryptophyl residue in KWGK was not significantly different in the presence and in the absence of double-stranded polynucleotides in agreement with the previous model, which assumes total quenching of tryptophan fluorescence in complex (PN)2 and identical fluorescence characteristics for free KWGK and complex (PN)1. The stacking of the tryptophyl residue with A.T base pairs in alternating poly[d(A-T)] was found to be 10 times more efficient than that with nonalternating poly(dA).poly(dT). Among A-T-containing double-stranded polynucleotides, poly(rA).poly(dT) was found to be the most favorable for tryptophan stacking. A similar behavior was previously demonstrated for several intercalating agents such as ethidium bromide, propidium iodide, and daunomycin.(ABSTRACT TRUNCATED AT 250 WORDS)

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Section: Discussionsupporting

confidence: 59%

Does tryptophan intercalate in DNA? A comparative study of peptide binding to alternating and non-alternating A.cntdot.T sequences

Rajeswari¹,

Montenay-Garestier²,

Hélène³

1987

Biochemistry

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“…Most of the hydrophobic contribution to the binding free energy is thought to originate from the occurrence of stacking interactions between the aromatic amino acid side chains (including Trp) in NCp8 and the nucleic acid bases. Intercalated Trp structures are known to present near null quantum yield (33)(34)(35); thus, the correlation between quenching and hydrophobic stabilization found in our study may point to a more intimate or more frequent Trp stacking (or both) with certain oligo sequences, leading to a more complete extinction of NCp8 Trp fluorescence.…”

Section: Resultssupporting

confidence: 49%

Nucleic Acid Binding Properties of the Simian Immunodeficiency Virus Nucleocapsid Protein NCp8

Urbaneja

McGrath

Kane

et al. 2000

Journal of Biological Chemistry

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The nucleocapsid protein of simian immunodeficiency virus (SIV) NCp8 has two copies of conserved sequences (termed zinc fingers, ZF) of 14 amino acids with 4 invariant residues (CCHC) that coordinate Zn(II). Each of its two ZFs has a Trp residue. A significant quenching of NCp8 Trp fluorescence was seen in nucleic acid complexes, suggesting stacking of the indole ring with nucleobases and the simultaneous involvement of both ZFs in the binding process. Both ZFs contribute to the nucleic acid binding free energy of NCp8, albeit in a not additive manner. NCp8 exhibited a base preference analogous to that of NCp7: G ϳ I > T > U > C > A. Alternating base sequences that bind HIV-1 NCp7 in a sequence-specific manner were also bound selectively by NCp8. Specific sequence recognition required at least five bases and the presence of bound Zn(II). The two ZFs account for the net displacement of 3 out of 4 sodium ions upon binding (2 by the first and one by the second finger), and for most (85%) of the hydrophobic stabilization in complex formation. Based on the sequence and functional similarity of SIV NCp8 and HIV-1 NCp7, and using available structural information for free and oligonucleotide bound NCp7, we propose a structural model for NCp8-oligonucleotide complexes.

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“…Previously, using circular dichroism and fluorescence, Maurizot et al explained that KWK exhibited a binding affinity to DNA with the order of AA>CC owing to the aromaticity of tryptophan. 26 This result was confirmed by Mascotti and Lohman who characterized the association constant of peptides containing lysine and tryptophan and poly A, poly C, and poly T. 27 They reported that the association constants of oligolysine containing tryptophan decreased in the following order: poly T > poly A > poly C. However, in contrast to previous hypothesis, Figure 2d~2f suggests that this sequence selectivity may not originate from the aromaticity of tryptophan. Instead, this selective preference for DNA sequences may come from lysine residues because KKKKKK shows similar sequence specificity like KWKWKK.…”

mentioning

confidence: 55%

MALDI-TOF Analysis of Binding between DNA and Peptides Containing Lysine and Tryptophan

Lee¹,

Choe²,

Oh³

et al. 2015

Mass Spectrometry Letters

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Here, we demonstrate the use of MALDI-TOF as a fast and simple analytical approach to evaluate the DNA-binding capability of various peptides. Specifically, by varying the amino acid sequence of the peptides consisting of lysine (K) and tryptophan (W), we identified peptides with strong DNA-binding capabilities using MALDI-TOF. Mass spectrometric analysis reveals an interesting novel finding that lysine residues show sequence selective preference, which used to be considered as mediator of electrostatic interactions with DNA phosphate backbones. Moreover, tryptophan residues show higher affinity to DNA than lysine residues. Since there are numerous possible combinations to make peptide oligomers, it is valuable to introduce a simple and reliable analytical approach in order to quickly identify DNA-binding peptides.

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Interaction of aromatic residues of proteins with nucleic acids. Binding of oligopeptides to copolynucleotides of adenine and cytosine

Cited by 29 publications

References 24 publications

Does tryptophan intercalate in DNA? A comparative study of peptide binding to alternating and non-alternating A.cntdot.T sequences

Does tryptophan intercalate in DNA? A comparative study of peptide binding to alternating and non-alternating A.cntdot.T sequences

Nucleic Acid Binding Properties of the Simian Immunodeficiency Virus Nucleocapsid Protein NCp8

MALDI-TOF Analysis of Binding between DNA and Peptides Containing Lysine and Tryptophan

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