Circular dichroism and thermal melting differentiation of Hoechst 33258 binding to the curved (A4T4) and straight (T4A4) DNA sequences

Canzonetta, Claudia; Caneva, R.; Savino, M.; Scipioni, Anita; Catalanotti, Bruno; Galeone, Aldo

doi:10.1016/s0167-4781(02)00338-x

Cited by 15 publications

(13 citation statements)

References 21 publications

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“…Using isothermal titration calorimetry (ITC) and circular dichroism (CD), we find that the binding of Hoechst 33258 to A 2 T 2 and A 3 T 3 is very similar, only a single dye molecule binds into the DNA minor groove. When the AT-site is saturated, further increased concentration of Hoechst 33258 results most probably in a nonspecific electrostatic binding to the negatively charged DNA phosphate backbone. , However, in contrast to some conclusions previously published, ,,, we observe that for the oligonucleotide with the longer AT tract, A 4 T 4 , a second Hoechst 33258 molecule can also be accommodated in the minor groove.…”

Section: Introductioncontrasting

confidence: 96%

“…In crystal structures where Hoechst 33258 binds to oligonucleotides containing 5′-GAATTC-3′ in the middle, the dye has been reported to cover AATT, ATTC, or GAAT, with the phenyl group usually facing the narrow AT tract. ,− , Also, a high-resolution NMR structure has shown that Hoechst 33258 behaves similarly in solution: it covers exactly the AATT in such an oligonucleotide . Crystal structures of oligomers containing a longer AT sequence, 5′-CAAATTTG-3′, show that the dye covers ATTTG or AATTT, again with the phenyl group pointing toward the middle of the AT sequence. , When the AT region is expanded even further, to 5′-CAAAATTTTG-3′, two spectroscopic studies suggest that only one dye binds in the middle of the oligomer, , while yet another suggests that Hoechst 33258 can bind as a monomer, dimer, or tetramer to 5′-CAAAATTTTG-3′ . Loontiens et al suggest that the drug may even form larger aggregate complexes, up to six dye molecules per five base pairs, when the AT sequence is expanded to a [poly(dAdT)] 2 duplex.…”

Section: Introductionmentioning

confidence: 99%

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Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

Fornander

Billeter

et al. 2013

J. Phys. Chem. B

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Hoechst 33258 binds with high affinity into the minor groove of AT-rich sequences of double-helical DNA. Despite extensive studies of this and analogous DNA binding molecules, there still remains uncertainty concerning the interactions when multiple ligand molecules are accommodated within close distance. Albeit not of direct concern for most biomedical applications, which are at low drug concentrations, interaction studies for higher drug binding are important as they can give fundamental insight into binding mechanisms and specificity, including drug self-stacking interactions that can provide base-sequence specificity. Using circular dichroism (CD), isothermal titration calorimetry (ITC), and proton nuclear magnetic resonance ((1)H NMR), we examine the binding of Hoechst 33258 to three oligonucleotide duplexes containing AT regions of different lengths: [d(CGCGAATTCGCG)]2 (A2T2), [d(CGCAAATTTGCG)]2 (A3T3), and [d(CGAAAATTTTCG)]2 (A4T4). We find similar binding geometries in the minor groove for all oligonucleotides when the ligand-to-duplex ratio is less than 1:1. At higher ratios, a second ligand can be accommodated in the minor groove of A4T4 but not A2T2 or A3T3. We conclude that the binding of the second Hoechst to A4T4 is not cooperative and that the molecules are sitting with a small separation apart, one after the other, and not in a sandwich structure as previously proposed.

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Section: Introductioncontrasting

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

Fornander

Billeter

et al. 2013

J. Phys. Chem. B

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“…The continuum GB/SA model of water, as implemented in MacroModel, was used in all calculations. Five of the six amines in neomycin were protonated, in agreement with NMR studies of neomycin ( , ), as well as the terminal amine in the piperazine ring of the Hoechst moiety.…”

Section: Methodssupporting

confidence: 73%

Recognition of B-DNA by Neomycin−Hoechst 33258 Conjugates

Willis

Arya

2006

Biochemistry

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Recent developments have indicated that aminoglycoside binding is limited not to RNA but to nucleic acids that, like RNA, adopt conformations similar to the A-form. We have further sought to expand the utility of aminoglycoside binding to B-DNA structures by conjugating neomycin, an aminoglycoside antibiotic, with the B-DNA minor groove binding ligand Hoechst 33258. Described herein are novel neomycin-Hoechst 33258 conjugates developed for exploring B-DNA groove recognition. We have varied the two reported conjugates in linker length and composition in an effort to improve our understanding of the spatial differences that define B-DNA binding. Spectroscopic studies such as ultraviolet (UV) melting, isothermal fluorescence titrations, differential scanning calorimetry (DSC), and circular dichroism (CD) together illustrate the mode of binding by such conjugates. Both conjugates exhibit enhanced thermal stabilization of A.T rich duplexes when compared to Hoechst 33258.

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“…IIT Delhi for docking. The docked structures were closely analyzed in Viewer Lite and UCSF-Chimera 27,28 and the CURVES programme was used for helicoidal parameter generations. Molecular modeling & simulation.…”

Section: Molecular Biosystems Papermentioning

confidence: 99%

“…23 It was earlier reported that Hoechst and other minor groove ligands bind to AT/GC specific sequences, specifically, the hexadecamers d(GCGCGCGCGCGCGCGC) 2 and d(ATATATATATATAT) 2 were chosen for their G-C or A-T rich tracts that make the interior of the constructed dsDNA very similar to previously studied polyamine-binding sites. [24][25][26][27][28] Therefore, systematic studies by designing analogues with improved sequence selectivity would facilitate a comprehensive understanding of ligand-DNA interaction leading to the development of better fluorescent probes and drug designing. The decamers d(GAAAATTTTC) 2 and d(GTTTTAAAAC) 2 are two chemically equivalent DNA duplex, yet one d(GAAAATTTTC) 2 , exhibits properties that are distinctive of curved DNA, while the other d(GTTTTAAAAC) 2 , manifests the feature of normal DNA, that is why we have chosen those particular sequences.…”

Section: Introductionmentioning

confidence: 99%

Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study

et al. 2013

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Recently synthesis of programmable DNA ligands which can regulate transcription factors have increased the interest of researchers on the functional ability of DNA interacting compounds. A series of DNA interacting compounds are being designed which can differentiate between GC and AT rich DNA. In this study, we have studied the specificity of a few novel bisbenzimidazoles having different bi/tri-substituted phenyl rings, with DNA duplexes using spectroscopic methods. This study entails an integrative approach where we combine biophysical methods and molecular dynamics simulation studies to establish suitable scaffolds to target A/T DNA. We have designed a few analogues of Hoechst 33342 viz.; dimethoxy (DMA), trimethoxy (TMA), dichloro (DCA) and difluoro (DFA) functionalities and performed molecular docking of newly designed analogues with biologically relevant AT and GC rich DNA sequences. The docking studies, along with molecular dynamics (MD) simulations of d(ATATATATATATATAT)2, d(GA4T4C)2, d(GT4A4C)2 and GC rich sequence: d(GCGCGCGCGCGCGCGC)2 complexed with DMA, TMA and DFA, showed that these molecules have higher binding affinity towards AT rich DNA. None of these compounds exhibited an affinity to GC rich DNA rather we observed that these compounds destabilize GC rich DNA. The binding was characterized by strong stabilization of the polynucleotides against thermal strand separation in thermal melting experiments. New insights into the molecules binding to DNA have emerged from these studies. All the DNA binding ligands stabilized d(GA4T4C)2 and d(GT4A4C)2 more out of the five oligomers used for the study, suggesting that these ligands bind 'A4T4' and 'T4A4' strongly as compared to 'ATAT' base pairs.

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Circular dichroism and thermal melting differentiation of Hoechst 33258 binding to the curved (A4T4) and straight (T4A4) DNA sequences

Cited by 15 publications

References 21 publications

Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

Recognition of B-DNA by Neomycin−Hoechst 33258 Conjugates

Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study

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