Actinomycin D Binding to Single-stranded DNA: Sequence Specificity and Hemi-intercalation Model from Fluorescence and1H NMR Spectroscopy

Wadkins, Randy M.; Jares‐Erijman, Elizabeth A.; Klement, Reinhard; Rüdiger, Angelika; Jovin, Thomas M.

doi:10.1006/jmbi.1996.0498

Cited by 77 publications

(69 citation statements)

References 43 publications

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“…The current model differs from our previously proposed hemi-intercalation in which the AMD chromophore was stacked between the 5 H -ApG-3 H step (Wadkins et al, 1996) Figure 3 Crystal packing of the molecules in (a) the orthorhombic form (two types of layer) and (b) the trigonal form (three layers). Table 3 Comparison of key mean interproton distances from the orthorhombic crystal structure and molecular-dynamics simulations of the 1:1 complex corresponding to observed NOEs in the NMR spectra.…”

Section: Analysis Of the Nmr Data In The Light Of The Crystal Structurecontrasting

confidence: 70%

“…In a previous study, we proposed a model for the recognition of ssDNA sequences by actinomycin featuring the hemiintercalation of the chromophore between the two purine residues (Wadkins et al, 1996). These and subsequent not entirely consistent studies prompted the present investigation of the interactions of 7-AAMD with non-complementary 5 H -T n TAGTT n -3 H (n = 2,3) by X-ray crystallography, augmented by NMR data and molecular modelling.…”

Section: Introductionmentioning

confidence: 91%

“…AMD has also been shown to bind tightly and speci®cally to single-stranded DNA sequences (Wadkins & Jovin, 1991;Wadkins et al, 1996Wadkins et al, , 2000Yoo & Rill, 2001;Chen et al, , 2004. Fluorescence studies of 7-amino-actinomycin D (7-AAMD; a¯uorescent derivative of AMD shown to bind dsDNA by Graves & Wadkins, 1989) with ssDNA indicate a high sequence-dependence of the binding.…”

Section: Introductionmentioning

confidence: 99%

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Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

Alexopoulos

Jares‐Erijman

Jovin

et al. 2005

Acta Crystallogr D Biol Crystallogr

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The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5 H -TTAG[Br 5 U]T-3 H provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modi®cations both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the ®rst drug intercalates between a BrU±G (analogous to T±G) wobble pair and a G±T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU±G and G±BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A*T)*T triplets and Watson± Crick A±T pairs and leads to similar complex threedimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insuf®cient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines¯anking the d(AGT) core are rather exible and the G±T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.

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Section: Analysis Of the Nmr Data In The Light Of The Crystal Structurecontrasting

confidence: 70%

Section: Introductionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

Alexopoulos

Jares‐Erijman

Jovin

et al. 2005

Acta Crystallogr D Biol Crystallogr

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“…To discriminate between these possibilities, we measured the effect of vitamin E on gene expression in the presence of a actinomycin D, a selective inhibitor of DNAdirected RNA synthesis (41). Cells were treated with 1 μM actinomycin D together with 100 μM αTOH (or ethanol), and the levels of mRNAs encoding HMG-CoA reductase and the LDLreceptor were measured using real-time RT-PCR.…”

Section: Resultsmentioning

confidence: 99%

Novel Transcriptional Activities of Vitamin E: Inhibition of Cholesterol Biosynthesis

et al. 2007

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Vitamin E is a dietary lipid that is essential for vertebrate health and fertility. The biological activity of vitamin E is thought to reflect its ability to quench oxygen-and carbon-based free radicals, and thus to protect the organism from oxidative damage. However, recent reports suggest that vitamin E may also display other biological activities. Here, to examine possible mechanisms that may underlie such non-classical activities of vitamin E, we investigated the possibility that it functions as a specific modulator of gene expression. We show that treatment of cultured hepatocytes with RRR-α-tocopherol alters the expression of multiple genes and that these effects are distinct from those elicited by another antioxidant. Genes modulated by vitamin E include those that encode key enzymes in the cholesterol biosynthetic pathway. Correspondingly, vitamin E caused a pronounced inhibition of de novo cholesterol biosynthesis. The transcriptional activities of vitamin E were mediated by attenuating the post-translational processing of the transcription factor SREBP-2 that, in turn, led to a decreased transcriptional activity of sterol responsive elements in the promoters of target genes. These observations indicate that vitamin E possesses novel transcriptional activities that affect fundamental biological processes. Cross talk between tocopherol levels and cholesterol status may be an important facet of the biological activities of vitamin E.The term vitamin E refers to a family of structurally related neutral plant lipids that are critical for vertebrate health and fertility. Numerous studies established that members of the vitamin E family are efficient chain-breaking radical scavengers both in vitro and in vivo, and led to the definition of vitamin E as the most important lipid-soluble antioxidant (1). While all isoforms of vitamin E possess comparable radical trapping activity in vitro (2), RRR-α-tocopherol (denoted herein as αTOH) exhibits the highest potency in biological assays (3). This vitamer preference stems from the combined activities of the hepatic α-tocopherol transfer protein (TTP) that selectively retains αTOH (3-5), and the catabolic actions of hepatic enzymes that degrade other forms of vitamin E to water-soluble products (6).The selectivity for αTOH raises the possibility that this vitamer has unique biological roles, in addition to its anti-oxidant function. Indeed, novel regulatory properties have been ascribed in recent years to αTOH, including the modulation of apoptosis, cell adhesion, and specific enzymatic activities (cf. 7, 8). Moreover, αTOH was shown to regulate the expression levels of several mRNAs and proteins, such as collagen α1 (9), the scavenger receptors SR-BI (10) and CD36 (11,12), α-tropomyosin (13), the nuclear receptor PPARγ (14), and the adhesion molecule VCAM-I (15). These anecdotal observations were further supported by several studies that documented genomic responses to vitamin E using expression-profiling § To whom correspondence should be addressed at: Schoo...

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“…The values of ƘW nf and ƘW' also are in good accordance (see Table 1). In the work (Wadkins et al, 1996) is shown that actinomycin D (AMD) interacts with ss-polynucleotides. Moreover, aromatic ring of AMD is partially inserted in a plane between the neighbor bases, i.e.…”

Section: Discussionmentioning

confidence: 99%

The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures

Vardevanyan

Antonyan²,

Parsadanyan³

et al. 2003

Exp Mol Med

112

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A bstractThe pH-induced helix-coil transition of DNA and its com plexes w ith EtB r is carried out at acidic pH in a wide interval of change of concentration ratio of EtBr/DNA. The binding isotherm s of EtBr on double and single-stranded DNA at pH = 7.0 and pH = 3.0 (t = 25 o C) are obtained by absorption and fluorim etric m ethods. Binding constants (K) and num ber of bases (n), corresponding to one binding site were determ ined. Non fluorescent "strong" com plex w ith ds-DNA at pH = 7.0 and t = 25 o C as well as "strong" and "weak" complexes with ss-DNA at pH = 3.0 and t = 25 o C are revealed.

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Actinomycin D Binding to Single-stranded DNA: Sequence Specificity and Hemi-intercalation Model from Fluorescence and1H NMR Spectroscopy

Cited by 77 publications

References 43 publications

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

Novel Transcriptional Activities of Vitamin E: Inhibition of Cholesterol Biosynthesis

The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures

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