Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies

Haq, Ihtshamul; Ladbury, John E.; Chowdhry, Babur Z.; Jenkins, Terence C.; Chaires, Jonathan B.

doi:10.1006/jmbi.1997.1170

Cited by 300 publications

(342 citation statements)

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“…51 Displacement of bound water from the minor groove in AT sequences provides a general favorable contribution to the binding entropy. 49,[52][53][54] The netropsin structure led the Lown 48,55 and Dickerson 49 groups to propose an extension of the model in which GC base pair specificity could be designed into minor groove binding polyamides by replacing some of the hydrogen bond donating groups on the concave face of the compounds with hydrogen bond acceptors. Such acceptors would be sterically able to accommodate the extra size of the G-NH 2 group, which hydrogen bonds with C in the minor groove, and could form an extra hydrogen bond with the -NH 2 group.…”

Section: Discussionmentioning

confidence: 99%

Design of DNA Minor Groove Binding Diamidines That Recognize GC Base Pair Sequences: A Dimeric-Hinge Interaction Motif

et al. 2007

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The classical model of DNA minor groove binding compounds is that they should have a crescent shape that closely fits the helical twist of the groove. Several compounds with relatively linear shape and large dihedral twist, however, have been found recently to bind strongly to the minor groove. These observations raise the question of how far the curvature requirement could be relaxed. As an initial step in experimental analysis of this question, a linear triphenyl diamidine, DB1111 and a series of nitrogen tricyclic analogues were prepared. The goal with the heterocycles is to design GC binding selectivity into heterocyclic compounds that can get into cells and exert biological effects. The compounds have a zero radius of curvature from amidine carbon to amidine carbon but a significant dihedral twist across the tricyclic and amidine-ring junctions. They would not be expected to bind well to the DNA minor groove by shape-matching criteria. Detailed DNaseI footprinting studies of the sequence specificity of this set of diamidines indicated that a pyrimidine heterocyclic derivative, DB1242, has remarkable binding specificity for a GC rich sequence, -GCTCG-. It binds to the GC sequence more strongly than to the usual AT recognition sequences for curved minor groove agents. Other similar derivatives did not exhibit the GC specificity. Biosensor-surface plasmon resonance and isothermal titration calorimetry experiments indicate that DB1242 binds to the GC sequence as a highly cooperative stacked dimer. Circular dichroism results indicate that the compound binds in the minor groove. Molecular modeling studies support a minor groove complex and provide an inter-compound and compound-DNA hydrogen bonding rational for the unusual GC binding specificity and the requirement for a pyrimidine heterocycle. This compound represents a new direction in development of DNA sequence specific agents and it is the first non-polyamide, synthetic compound to specifically recognize a DNA sequence with a majority of GC base pairs.

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Section: Discussionmentioning

confidence: 99%

Design of DNA Minor Groove Binding Diamidines That Recognize GC Base Pair Sequences: A Dimeric-Hinge Interaction Motif

et al. 2007

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“…The eIF4E cap binding affinity differences observed using ITC and fluorescence titration (Fig. 1D and Table 2) is likely due to methodological differences (63).…”

Section: Isothermal Titration Calorimetry (Itc) Characterization Of Smentioning

confidence: 99%

Structural Insights into Parasite eIF4E Binding Specificity for m7G and m2,2,7G mRNA Caps

Liu

Zhao

McFarland

et al. 2009

Journal of Biological Chemistry

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The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m 7 G) or a trimethylguanosine (m 2,2,7 G) cap derived from spliced leader trans-splicing. Quantitative fluorescence titration analyses demonstrated that schistosome eIF4E has similar binding specificity for both caps. We present the first crystal structure of an eIF4E with similar binding specificity for m 7 G and m 2,2,7 G caps. The eIF4E⅐m 7 GpppG structure demonstrates that the schistosome protein binds monomethyl cap in a manner similar to that of single specificity eIF4Es and exhibits a structure similar to other known eIF4Es. The structure suggests an alternate orientation of a conserved, key Glu-90 in the capbinding pocket that may contribute to dual binding specificity and a position for mRNA bound to eIF4E consistent with biochemical data. Comparison of NMR chemical shift perturbations in schistosome eIF4E on binding m 7 GpppG and m 2,2,7 GpppG identified key differences between the two complexes. Isothermal titration calorimetry demonstrated significant thermodynamics differences for the binding process with the two caps (m 7 G versus m 2,2,7 G). Overall the NMR and isothermal titration calorimetry data suggest the importance of intrinsic conformational flexibility in the schistosome eIF4E that enables binding to m 2,2,7 G cap. Eukaryotic initiation protein eIF4E2 is an essential translation factor that recognizes the mRNA cap (1-3). Recognition of the mRNA cap by eIF4E is the key and rate-limiting step in mRNA translation. The majority of translation in eukaryotic cells is cap-dependent; that is recruitment of mRNAs to the ribosome for translation is dependent on the interaction between eIF4E and the mRNA cap. eIF4E directly binds to the mRNA cap. However, for productive translation initiation to occur, eIF4E must interact with eIF4G. eIF4G acts as a bridge protein interacting with factors in the 40 S ribosomal subunit that facilitate ribosome recruitment to the mRNA. Increased expression of eIF4E is associated with a variety of cancers and cancer progression (4). Efforts in a number of laboratories are directed toward therapies against eIF4E in cancer, including the development of cap analogs (5-9).The mRNA cap in most eukaryotes is m 7 GpppN (where N is A, C, G, or U). The cap contains a 5Ј-5Ј triphosphate bridge with the first guanosine methylated at the N-7 position. However, spliced leader trans-splicing in metazoa adds a different cap to recipient mRNAs, a trimethylguanosine cap, m 2,2,7 GpppN (see Fig. 1A) (10 -14). trans-splicing is present in a variety of parasitic nematodes and flatworms, and these organisms remain a significant health problem in many parts of the world, infecting upward of 2 billion people (15-17). Translation of these trans-spliced mRNAs is thought to require eIF4E recognition of the m 2,2,7 G cap to facilitate ribosomal ...

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“…Viscosity experiments were carried out in an Ostwald-type capillary viscometer maintained at 25.0 ± 0.1°C by immersion in a circulating water bath (Pilch et al, 1993;Suh and Chaires, 1995 (Loontiens et al, 1990;Quintana et al, 1991;Haq et al, 1997).…”

Section: Dna Binding -Viscometric Studiesmentioning

confidence: 99%

“…These values were selected on the basis of the binding isotherms obtained from the optical titration experiments. Control experiments were performed with Hoechst 33258 dye, an established DNA minor groove-binding ligand (Loontiens et al, 1990;Quintana et al, 1991;Haq et al, 1997).…”

Section: Dna Binding -Viscometric Studiesmentioning

confidence: 99%

Cellular uptake, cytotoxicity and DNA-binding studies of the novel imidazoacridinone antineoplastic agent C1311

et al. 1999

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Summary C1311 is a novel therapeutic agent with potent activity against experimental colorectal cancer that has been selected for entry into clinical trial. The compound has previously been shown to have DNA-binding properties and to inhibit the catalytic activity of topoisomerase II. In this study, cellular uptake and mechanisms by which C1311 interacts with DNA and exerts cytotoxic effects in intact colon carcinoma cells were investigated. The HT29 colon cancer cell line was chosen to follow cellular distribution of C1311 over a time course of 24 h at drug concentrations that just inhibited cell proliferation by 50% or 100%. Nuclear uptake of C1311 and co-localization with lysosomal or mitochondrial dyes was examined by fluorescence microscopy and effects on these cellular compartments were determined by measurement of acid phosphatase levels, rhodamine 123 release or DNA-binding behaviour. The strength and mode of DNA binding was established by thermal melting stabilization, direct titration and viscometric studies of host duplex length. The onset of apoptosis was followed using a TUNEL assay and DNA-fragmentation to determine a causal relationship of cell death. Growth inhibition of HT29 cells by C1311 was concomitant with rapid drug accumulation in nuclei and in this context we showed that the compound binds to duplex DNA by intercalation, with likely A/T sequence-preferential binding. Drug uptake was also seen in lysosomes, leading to lysosomal rupture and a marked increase of acid phosphatase activity 8 h after exposure to C1311 concentrations that effect total growth inhibition. Moreover, at these concentrations lysosomal swelling and breakdown preceded apoptosis, which was not evident up to 24 h after exposure to drug. Thus, the lysosomotropic effect of C1311 appears to be a novel feature of this anticancer agent. As it is unlikely that C1311-induced DNA damage alone would be sufficient for cytotoxic activity, lysosomal rupture may be a critical component for therapeutic efficacy.Keywords: C1311; HT29 cells; colorectal cancer; cytotoxicity; DNA intercalation; lysosomes 367British Journal of Cancer (1999) 81(2), 367-375 © 1999 Cancer Research Campaign Article no. bjoc.1999 Received MATERIALS AND METHODS Materials/DrugsThe 5-(ω-aminoalkyl)amino-8-hydroxyimidazoacridinone C1311 (Figure 1) was synthesized at the Technical University of Gdansk, as described elsewhere (Cholody et al, 1990(Cholody et al, , 1992. Stock solutions were prepared in dimethyl sulphoxide (DMSO) or normal saline. Aqueous solutions were prepared in polystyrene tubes to minimize adsorption effects and quantified by spectrophotometry. Hoechst 33258 dye (Sigma-Aldrich Ltd) was used as a control ligand for viscometric studies and quantified using ε 338 = 42 000 M -1 cm -1 (Loontiens et al, 1990). All DNA binding experiments were performed in aqueous phosphate buffer (10 mM NaH 2 PO 4 /Na 2 HPO 4 , 1 mM Na 2 EDTA, pH 7.00 ± 0.01). Doublestranded calf thymus DNA (CT-DNA, type-I [Sigma-Aldrich Ltd.]) was sonicated and purified using a publ...

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Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies

Cited by 300 publications

References 50 publications

Design of DNA Minor Groove Binding Diamidines That Recognize GC Base Pair Sequences: A Dimeric-Hinge Interaction Motif

Design of DNA Minor Groove Binding Diamidines That Recognize GC Base Pair Sequences: A Dimeric-Hinge Interaction Motif

Structural Insights into Parasite eIF4E Binding Specificity for m7G and m2,2,7G mRNA Caps

Cellular uptake, cytotoxicity and DNA-binding studies of the novel imidazoacridinone antineoplastic agent C1311

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