Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II).

Dyke, Michael W. Van; Hertzberg, Robert; Dervan, Peter B.

doi:10.1073/pnas.79.18.5470

Cited by 325 publications

(150 citation statements)

References 28 publications

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“…Therefore, we employed an indirect method to test if UBF interacts with the minor groove. Specifically, we tested whether UBF could bind enhancer DNA in the presence of the minor groove binding drugs chromomycin A3, distamycin A, or actinomycin D (39,40). In preliminary titration experiments, all three drugs were found to produce discrete DNase I footprints on the enhancer probe (Putnam and Pikaard, unpublished).…”

Section: Methodsmentioning

confidence: 99%

The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids

Copenhaver¹,

Putnam²,

Denton³

et al. 1994

Nucl Acids Res

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Section: Methodsmentioning

confidence: 99%

The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids

Copenhaver¹,

Putnam²,

Denton³

et al. 1994

Nucl Acids Res

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“…Footprinting, which involves examining drug-induced inhibition of cleavage of definedsequence DNA fragments by either enzymatic [13] or chemical [ 141 agents has been shown to be an effective technique for addressing these questions. Structurally 'complex' intercalators such as actinomycin [ 15,161, the quinoxaline antibiotics [ 13,141, and the anthracycline nogalamycin [ 171 all induce large changes in the cleavage pattern, consistent with the existence of definite nucleotide sequence preferences. 'Simple' intercalators do not generally produce clear footprinting patterns, presumably because they lack selectivity.…”

Section: Introductionmentioning

confidence: 96%

DNA sequence preferences for the anti‐cancer drug mitoxanthrone and related anthraquinones revealed by DNase I footprinting

et al. 1986

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The interaction has been studied of several anthraquinone-based intercalating drugs, including the anti-cancer agent mitoxantrone, with defined sites of DNA. A 160 base pair DNA sequence from tyrT was employed for footprinting with DNase I. The anthraquinones had aminoalkylamino substituents in various positions of the ring system. Inhibition of enzymatic cutting of the DNA was observed at various positions on the sequence, mostly around some of the pyrimidine-3',5'-purine sites. Enhancements to cutting were observed clustered around AT-rich regions. The compounds showed differences in detailed footprinting behaviour, which have been related to differences in their mode of interaction with DNA as found in earlier computer modelling studies.Anthraquinone Mitoxanthrone Intercalator Footprinting

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“…Footprinting, i.e., protection against chemical or enzymatic attack, has been used to determine the DNA-binding sites of many drugs and proteins (18)(19)(20). The use of hydroxyl radical as the cleavage agent in footprinting experiments can reveal structural features of protein-DNA complexes that other probes do not detect (15,21,22).…”

mentioning

confidence: 99%

“…Both these features are characteristic of a situation where a (right-handed) double helix is protected on one face, so that access is permitted only on the other face (26). This offset is also the signature of a minor groove interaction (20,25,27) and reflects the fact that hydroxyl radical is most sensitive to protection or distortion of the minor groove of the DNA. To see the offset better the plots have been overlaid and offset by 3 nucleotides in the lower portion of Fig.…”

mentioning

confidence: 99%

Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus.

Churchill

Tullius

Klug

1990

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

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The zinc finger protein TFHIA, a positive transcription factor of the SS RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex-for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide ofDNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.Transcription factor IIIA (TFIIIA) is the archetype of a class of proteins that use the zinc finger motif for DNA binding (1)(2)(3). No complexes of zinc finger proteins with DNA have so far yielded to structural analysis, so we must rely on mutagenesis (4-6), chemical and nuclease probing in solution (7-9), and model building (10, 11) to suggest how binding might occur. The nine zinc fingers ofTFIIIA bind to -"50 base pairs (bp) of the internal control region of the 5S ribosomal RNA gene of . DNase I (6,15) and hydroxyl radical (15) footprints of TFIIIA deletion mutants on the 5S RNA gene show that TFIIIA protects the internal control region in a collinear fashion. Two models for the TFIIIA-DNA interaction have been considered (9): (i) the "wrapping around" model, where successive zinc fingers make structurally equivalent contacts in the major groove without crossing over the minor groove (10), and (ii) the "alternating" model, where alternate fingers bind on one face of the DNA in an equivalent manner to the major groove, so that successive minor grooves must be crossed (9). Protection experiments that use DNase I and DNase II (8), micrococcal nuclease, and dimethyl sulfate (9) suggest that TFIIIA binds in the major groove, mainly to one face ofthe DNA helix and, therefore, support model ii. However, a model of the zinc finger polypeptide proposed by Berg (10), which agrees in its essentials with recent two-dimensional NMR structure determination (16, 17), has been considered to favor the "wrapping around" mode of binding to DNA. To help settle this question we have analyzed quantitatively hydroxyl radical footprints of the intact TFIIIA-DNA complex. We discuss the feasibility of the two models and propose a mode of binding consistent with the results from all of the studies on the TFIIIA-DNA complex.Quantitative Hydroxyl Radical Footprinting. Footprinting, i.e., protection against chemical or enzymatic attack, has been used to determine the DNA-binding sites of many drugs and proteins (18)(19)(20). The use of hydroxyl radical as the cleavage age...

show abstract

Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II).

Cited by 325 publications

References 28 publications

The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids

The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids

DNA sequence preferences for the anti‐cancer drug mitoxanthrone and related anthraquinones revealed by DNase I footprinting

Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus.

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