Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A·T)-rich DNA segments

Reinert, K.E.; Stutter, E.; Schweiss, H.

doi:10.1093/nar/7.5.1375

Cited by 40 publications

(23 citation statements)

References 40 publications

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“…Viscosity measurements were performed by means of an advanced titration version of the Zimm-Crothers rotational ~scometer as previously described (25). DNA for viscosity experiments was dissolved in SSC buffer (0.15 M NaCI, O.oi5 M Na citrate).…”

Section: Methodsmentioning

confidence: 99%

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Interaction of the Nonintercalative Antitumour Drugs SN-6999 and SN-18071 with DNA: Influence of Ligand Structure on the Binding Specificity

Luck¹,

Reinert²,

Baguley

et al. 1987

Journal of Biomolecular Structure and Dynamics

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Binding to DNA's of the non-intercalative ligands SN-6999 and SN-18071 has been studied by means of circular dichroism, UV absorption, thermal melting and for SN-6999 by viscosity measurements. Both antitumour drugs show a preference for dA.dT rich DNA's, but the base pair selectivity of SN-18071 is lower as indicated by some affinity to dG.dC containing duplex DNA. The dA.dT base pair specificity of SN-6999 is comparable to that of netropsin. It forms very stable complexes with dA.dT containing duplex DNA and competes with netropsin binding on DNA. The ligands SN-18071 and pentamidine are totally released from their complexes with poly(dA-dT).poly(dA-dT) by competitive netropsin binding. The results demonstrate that hydrogen bonding capacity of the ligand in addition to other factors strongly contribute to the base sequence specificity in the recognition process of the ligand with DNA. A binding model of SN-6999 with five dA.dT pairs in the minor groove of B-DNA is suggested.

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Section: Methodsmentioning

confidence: 99%

“…B: Netropsin, at 20°C, SSC buffer. Curves of the main part are least-squares lines from previous data(25).…”

mentioning

confidence: 99%

Interaction of the Nonintercalative Antitumour Drugs SN-6999 and SN-18071 with DNA: Influence of Ligand Structure on the Binding Specificity

Luck¹,

Reinert²,

Baguley

et al. 1987

Journal of Biomolecular Structure and Dynamics

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“…The most essential contributions to Lly are represented by the two linear terms. From the conformational statistical reasons described in the Introduction and elsewhere (6,4), ~is very small for very short DNA double helices and increases many times over to 1.5 for long, coiled DNA molecules. ( a'l + l) exhibits the opposite tendency.…”

Section: Changes Of Dna Conformation and Viscositymentioning

confidence: 98%

“…dlog[T]]/dlogM. For semirigid DNA molecules in the transition range between very short and almost rigid rods ( ~; 1.8) and Gau~ian coils ( ~ =0.5), and continuously drops with rising Mr [above Mr=0.2Xl0 6 (5,15)]. The required values of Ka and (a'l + 1), as also those of Qaa' QLL and QaL' are plotted in paper (5) physiological salt conditions as a function ofMr (cf.…”

Section: Changes Of Dna Conformation and Viscositymentioning

confidence: 99%

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DNA-Helix Bending, Stiffening and Elongation on Ligand Binding; Analysis for Serveral DNA-Drug Systems, General Viscometric DNA Response and Stereochemical Implications

Reinert¹

1991

Journal of Biomolecular Structure and Dynamics

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For several DNA-ligand systems the DNA helix bending, stiffening and elongation behaviour is treated quantitatively. The experimental basis are viscosity data from literature as a function of r, the ratio of drug molecules bound per DNA monomer unit. If the relative viscosity changes delta y1(r) and delta yh(r) for DNA of low and high molar mass, respectively, are known, the relative changes of contour length, delta L/L degrees, and of persistence length, delta a/a degrees, can be evaluated as a function of r, as repeatedly demonstrated. For random sequence-independent interactions, helix-bending is reflected by a helix-typical increment of delta a/a degrees (r), being zero at r = 0 and also at DNA saturation by bound ligand molecules [Reinert, Biophysical Chemistry 13, 1-14 (1981)]. This characteristic DNA behaviour often enables us to separate the bending and the stiffening increment of delta a/a degrees. The theoretical treatment of this problem (Schütz and Reinert, J. Biomolec. Struct. & Dynam. 9, 315-329, 1991) now permits a more detailed study of the ligand-induced DNA bending. The ligand-DNA systems treated here concern the following drugs (in parentheses DNA bending angle at low r-values): proflavin (8 degrees), daunomycin (11 degrees), aclacinomycin A (9.7 degrees, on cooperative interaction), actinomycin D (16 degrees), mitomycin C (16 degrees), a double intercalating bisphenantridine (12 degrees), 9-deacetyl-daunomycin (8 degrees) and 9-epi-deacetyl-daunomycin (12-18 degrees). We also demonstrate that the consideration of the DNA flexibility and its change on interaction of short DNA molecules with intercalating drugs delivers helix elongation values in better accord with the theoretical value. In the Appendix, a catalogue of simulated delta y(r)-dependences is given for both short and long DNA molecules. It systematically describes the DNA viscosity response upon typical DNA stiffening, elongation, and helix-bending effects.

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Long‐range interactions between DNA‐bound ligands

Samuelson

Jansen

Kubista

1994

J of Molecular Recognition

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We have studied the interaction of the A:T specific minor-groove binding ligand 4',6-diamidino-2-phenylindole (DAPI) with synthetic DNA oligomers containing specific binding sites in order to investigate possible long-range interactions between bound ligands. We find that DAPI binds cooperatively to the oligomers. The degree of cooperativity increases with increasing number of binding sites and decreases with the separation between them. This dependence is paralleled by changes in the induced circular dichroism spectrum of DAPI, which decreases in intensity at 335 nm and increases at 365 nm. These results are consistent with an allosteric interaction of DAPI with DNA, where bound ligands cooperatively alter the structure of the DNA molecule. This structural change seems possible to induce under various conditions, including physiological. One consequence of allosteric binding is that ligands bound at a distance from each other sense each other's presence and influence each others' properties. If some regulatory proteins induce the same conformational change as DAPI, novel mechanisms for controlling gene expression can be anticipated.

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Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A·T)-rich DNA segments

Cited by 40 publications

References 40 publications

Interaction of the Nonintercalative Antitumour Drugs SN-6999 and SN-18071 with DNA: Influence of Ligand Structure on the Binding Specificity

Interaction of the Nonintercalative Antitumour Drugs SN-6999 and SN-18071 with DNA: Influence of Ligand Structure on the Binding Specificity

DNA-Helix Bending, Stiffening and Elongation on Ligand Binding; Analysis for Serveral DNA-Drug Systems, General Viscometric DNA Response and Stereochemical Implications

Long‐range interactions between DNA‐bound ligands

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