Binding of netropsin to DNA and synthetic polynucleotides

Заседателев, А. С.; Gursky, G. V.; Zimmer, Ch.; Thrum, H.

doi:10.1007/bf00309567

Cited by 71 publications

(48 citation statements)

References 9 publications

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“…The IÁC base-pair resembles the major groove of the GÁ C base-pair, but due to the lack of the 2-amino group, it resembles the AÁT base-pair in the minor groove (Figure 1) with comparable electrostatic potential (Lavery & Pullman, 1981). The similarity of IÁ C base-pairs to A Á T base-pairs in minor groove drug binding was implicated in various studies (Zasedatelev et al, 1974;Bailly & Waring, 1995). The binding of distamycin to ICrich sequences and alternating AT sequence as side-by-side dimers has been reported in solution (Fagan & Wemmer, 1992).…”

Section: Introductionmentioning

confidence: 99%

Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)

Chen

Ramakrishnan

Sundaralingam

1997

Journal of Molecular Biology

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Section: Introductionmentioning

confidence: 99%

Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)

Chen

Ramakrishnan

Sundaralingam

1997

Journal of Molecular Biology

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“…The increase in the CD signal at the drug/DNA stoichiometries higher than 2 most probably re£ected non-speci¢c weak complexes with the sites containing GC pairs (Fig. 4b) [9]. The complex with stoichiometry of 2:1 does not dissociate upon increasing salt concentration up to 2 M NaCl (Fig.…”

Section: Resultsmentioning

confidence: 91%

“…As follows from the form of CD spectra, the ligand binds to DNA as a monomer [10]. These facts indicate the presence in the sample SLS31 of two duplexes containing no less than three AT pairs [9]. So, formation of duplexes III and IV as the components of SLS31 folding has been proved.…”

Section: Resultsmentioning

confidence: 92%

Slipped loop structure of DNA: a specific nucleotide sequence forms only one unique conformer

et al. 1998

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Earlier with some DNA sequences we were able to prove the existence of a new polynucleotide chain folding named slipped loop structure, or SLS [1,2]. However, the possibility of the presence of two SLS isomers in equilibrium was not excluded in the experiments. Here we are dealing with a specially designed structure formed by two short oligonucleotides intended for avoiding such a situation. To minimize the possibility of alternative structure formation and stabilize the conformation under investigation, the oligonucleotide sequences were designed in such a way that the bimolecular structure SLS31 would have two binding sites for antibiotic distamycin A. The sample was exposed to chemical probing both in the presence of distamycin A and without the ligand and the accessible nucleotides were mapped. The results do not suggest the presence in the solution of two isomers with different types of loop slippage without interloop interactions and strongly support the formation of a unique slipped loop conformation stabilized by an additional interloop helix, or slipped loop structure.z 1998 Federation of European Biochemical Societies.

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“…1) are related oligopeptide antibiotics that bind tightly to A-T-rich regions of duplex DNA. Many investigations (1)(2)(3)(4)(5)(6) have yielded information about the mode of binding of these drugs to DNA. Solution studies show that these drugs do not unwind DNA upon binding (2,7).…”

mentioning

confidence: 99%

“…Several (ii) Adenine nitrogens in the minor groove of DNA are shielded from methylation by the binding of both drugs, while guanine nitrogens in the major groove remain unshielded (9). Estimates of the number of base pairs covered per drug molecule range from three to five (2,5,10) for netropsin. These drugs are of interest because of their ability to recognize and bind to a specific feature of DNA. In this case the recognition feature consists of a region of high A-T composition.…”

mentioning

confidence: 99%

Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy.

Martin¹,

Wartell²,

O’Shea³

1978

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

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The binding of distamycin and netropsin to duplex DNA has been studied by Raman spectroscopy. Several changes occur in the Raman spectra of these drugs upon binding DNA. These changes were analyzed by assigning specific motions to the observed Raman bands through the use of molecular subunits of the drugs and normal mode calculations. Our Fig. 1.) Netropsin samples, available in both sulfate and hydrochloride forms, were purified by repeated recrystallization into the sulfate form. Various concentrations of the drug were used up to its solubility limit. At room temperature this was about 0.7 mg/ml. The distamycin A samples required no purification to obtain high-quality spectra. Because the solubility of distamycin A is much greater than that of netropsin, concentrations up to 2.5 mg/ml could be used. Spectra were obtained from 100 to 2000 cm-l. Care was taken to minimize the length of time the samples were irradiated by the laser. Raman spectra obtained at 250 and 10C were not significantly different. Laser irradiation had no effect on the ultraviolet absorbance spectra of the samples. The drugs were dissolved in a 3-4 mM NaCl solution at pH 6.0-7.0. Calf thymus DNA, obtained from Sigma, was extracted with chloroform and sonicated, then extensively dialyzed with 1.0 mM NaCI. It was rotoevaporated to dryness and redissolved with double-distilled water to a final concentration of 6.0 mg/ml. The

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Binding of netropsin to DNA and synthetic polynucleotides

Cited by 71 publications

References 9 publications

Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)

Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)

Slipped loop structure of DNA: a specific nucleotide sequence forms only one unique conformer

Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy.

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