Base-sequence specificity of Hoechst 33258 and DAPI binding to five (A/T)4 DNA sites with kinetic evidence for more than one high-affinity Hoechst 33258-AATT complex

Breusegem, Sophia Y.; Clegg, Robert M.; Loontiens, Frank G.

doi:10.1006/jmbi.2001.5301

Cited by 113 publications

(114 citation statements)

References 42 publications

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“…This result is in good agreement with the experimental observation of Breusegem et al (2002), who reported a 30-fold (by $2 kcal/mol) stronger binding of DAPI to AATT vs TTAA. In contrast, the GB model predicts a reversed relative binding affinity of DAPI to these two target sequences (due to a smaller calculated desolvation penalty difference for complex formation, see below).…”

Section: Discussionsupporting

confidence: 93%

DAPI binding to the DNA minor groove: a continuum solvent analysis

Castro¹,

Zacharias²

2002

J of Molecular Recognition

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A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.

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Section: Discussionsupporting

confidence: 93%

DAPI binding to the DNA minor groove: a continuum solvent analysis

Castro¹,

Zacharias²

2002

J of Molecular Recognition

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“…42 Both dyes display a strong preference for binding to the relatively narrow minor groove of AT rich sequences, with DAPI spanning 3-4 and HOC 4-6 base pairs. 33,42 As indicated in Table 1, both dyes possess similar macroscopic affinity constants for DNA but differ somewhat in stoichiometries. Several previous studies have demonstrated that the sequence specific microscopic affinity constants can vary by 200-fold for HOC and 30-fold for DAPI for five possible combinations of tetrameric A/T base pairs.…”

Section: Displacement Of Minor Groove Binding Dyes From Dnamentioning

confidence: 96%

“…Several previous studies have demonstrated that the sequence specific microscopic affinity constants can vary by 200-fold for HOC and 30-fold for DAPI for five possible combinations of tetrameric A/T base pairs. 33,42 Additional differences between the interaction of DAPI and HOC include the observation that HOC is more likely to interact with G/C sequences directly up and downstream from the AT binding sites 42 and apparent differences in sensitivity to the width of the minor groove. 42 Given the similarities in the relative affinities of DAPI and HOC for plasmid DNA, the significant differences in displacement of these dyes by cationic lipids and PEI is unexpected.…”

Section: Displacement Of Minor Groove Binding Dyes From Dnamentioning

confidence: 96%

A Fluorescence Study of the Structure and Accessibility of Plasmid DNA Condensed with Cationic Gene Delivery Vehicles

Wiethoff

Gill

Koe³

et al. 2003

Journal of Pharmaceutical Sciences

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“…Breusegem et al [14], by using fluorescence changes on binding, found a 200 fold better affinity for Hoechst 33258 binding to AATT versus TTAA in DNA oligomers while a 30 fold difference was observed for the heterocyclic diamidine, DAPI, with the same sequences. It has been suggested that the difference among these sites is at least partly due to differences in groove width [15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Liu

Kumar

Boykin

et al. 2007

Biophysical Chemistry

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With the goal of developing a better understanding of the antiparasitic biological action of DB75, we have evaluated its interaction with duplex alternating and nonalternating sequence AT polymers and oligomers. These DNAs provide an important pair of sequences in a detailed thermodynamic analysis of variations in interaction of DB75 with AT sites. The results for DB75 binding to the alternating and nonalternating AT sequences are quite different at the fundamental thermodynamic level. Although the Gibbs energies are similar, the enthalpies for DB75 binding with poly(dA)·poly (dT) and poly(dA-dT)·poly(dA-dT) are +3.1 and −4.5 kcal/mole, respectively, while the binding entropies are 41.7 and 15.2 cal/mol·K, respectively. The underlying thermodynamics of binding to AT sites in the minor groove plays a key role in the recognition process. It was also observed that DB75 binding with poly(dA)·poly(dT) can induce T·A·T triplet formation and the compound binds strongly to the dT·dA·dT triplex.

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Base-sequence specificity of Hoechst 33258 and DAPI binding to five (A/T)4 DNA sites with kinetic evidence for more than one high-affinity Hoechst 33258-AATT complex

Cited by 113 publications

References 42 publications

DAPI binding to the DNA minor groove: a continuum solvent analysis

DAPI binding to the DNA minor groove: a continuum solvent analysis

A Fluorescence Study of the Structure and Accessibility of Plasmid DNA Condensed with Cationic Gene Delivery Vehicles

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

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