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Hypericin (Hyp) is one of the principal active constituents of a traditional folk medicine, Hypericum (Saint John’s wort), and possesses variety biological activities. The interaction of Hyp with DNA may play an important role in biological activity, however only a few investigations were reported on this issue. In this paper, we studied the interaction of Hyp with different DNA forms. Hyp was found to selectively bind parallel DNA G-Quadruplexes (G4) over other DNA forms, such as ss-/ds-DNA, antiparallel G4s and mix-type G4s. Binding studies suggest that Hyp bind on G-quartet surface of G4s through end-stacking interaction. These results provide new information for the investigation of action mechanism of Hyp. [ABSTRACT FROM AUTHOR]

Two tiny hairpin DNAs, CORE (dAGGCTTCGGCCT) and AP2 (dAGGCTXCGGCCT; X: abasic nucleotide), fold into almost the same tetraloop hairpin structure with one exception, that is, the sixth thymine (T6) of CORE is exposed to the solvent water (Kawakami, J. et al., Chem. Lett. 2001, 258-259). In the present study, we selected small peptides that bind to CORE or AP2 from a combinatorial pentapeptide library with 2.5 × 106 variants. On the basis of the structural information, the selected peptide sequences should indicate the essential qualifications for recognition of the hairpin loop DNA with and without a flipped base. In the selected DNA binding peptides, aromatic amino acids such as histidine for CORE and glutamine/aspartic acid for AP2 were found to be abundant amino acids. This amino acid preference suggests that CORE-binding peptides use π-π stacking to recognize the target while hydrogen bonding is dominant for AP2-binding peptides. To investigate the binding properties of the selected peptide to the target, surface plasmon resonance was used. The binding constant of the interaction between CORE and a CORE-binding peptide (HWHHE) was about 1.1 × 106 M-1 at 25°C and the resulting binding free energy change at 25°C (ΔG°25) was -8.2 kcal mol-1. The binding of the peptide to AP2 was also analyzed and the resulting binding constant and ΔG°25 were about 4.2 × 104 M-1 and -6.3 kcal mol-1, respectively. The difference in the binding free energy changes (ΔΔG°25) of 1.9 kcal mol-1 was comparable to the values reported in other systems and was considered a consequence of the loss of π-π stacking. Moreover, the stabilization effect by stacking affected the dissociation step as well as the association step. Our results suggest that the existence of an aromatic ring (T6 base) produces new dominant interactions between peptides and nucleic acids, although hydrogen bonding is the preferable mode of interaction in the absence of the flipping base. These findings regarding CORE and AP2 recognition are expected to give useful information in the design of novel artificial DNA binding peptides. [ABSTRACT FROM AUTHOR]

Abstract: Isothermal titration calorimetry (ITC) is a well established technique for the study of biological interactions. The strength of ITC is that it directly measures enthalpy changes associated with interactions. Experiments can also yield binding isotherms allowing quantification of equilibrium binding constants, hence an almost complete thermodynamic profile can be established. Principles and application of ITC have been well documented over recent years, experimentally the technique is simple to use and in ideal scenarios data analysis is trivial. However, ITC experiments can be designed such that previously inaccessible parameters can be evaluated. We outline some of these advances, including (1) exploiting different experimental conditions; (2) low affinity systems; (3) high affinity systems and displacement assays. In addition we ask the question: What if data cannot be fit using the fitting functions incorporated in the data-analysis software that came with your ITC? Examples where such data might be generated include systems following non 1:n binding patterns and systems where binding is coupled to other events such as ligand dissociation. Models dealing with such data are now appearing in literature and we summarise examples relevant for the study of ligand–DNA interactions. [Copyright &y& Elsevier]

Circular dichroism (CD) spectra of complexes of 4-benzylaminopyrimido[4′,5′ :4,5]selenolo(2,3-b)quinoline (BAPSQ) with octanucleotide I (d(TGACGTCA)), which is the cAMPresponsive element (CRE) in gene promoters, and its inverse d(ACTGCAGT) (octanucleotide II) have been measured over a range of drug/DNA ratios. It was demonstrated that the anticancer polyaromatic drug BAPSQ intercalates into DNA basepairs with its long direction perpendicular to both the DNA helix axis and the base pair long axis and induces larger conformational changes in CpG containing octanucleotide I CRE than in its reverse sequence, octanucleotide II. It was concluded that CD is a powerful and sensitive technique to discriminate between drug-binding modes of DNA and to define the geometry of the chromophore inserted into base pairs. [ABSTRACT FROM AUTHOR]

The interaction between double-stranded (ds) DNA and the 4-butylamino pyrimido[4′,5′:4,5]selenolo(2,3-b)quinoline (BPSQ) has been studied with spectral luminescence methods. Binding constant values determined by absorption and fluorescence titration indicated a binding constant of 4.24 × 104 and 5.9 × 104 M−1, respectively. The interaction was markedly suppressed by increasing the salt concentration. BPSQ exhibited a strong specificity for the guanine–cytosine (GC) sequence in total DNA at an ionic strength of 0.01 (5.54 × 106 M−1). BPSQ increased the viscosity of sonicated rod-like DNA fragments, producing a calculated increment in length of 2.4 Å per bound drug molecule. A circular dichroism experiment showed that BPSQ might interact with DNA according to two possible binding modes depending on its structure and concentration. The first mode concerned intercalation of BPSQ with its long axis perpendicular to the long axis of the DNA helix. The same drug was able to bind to external sites, second mode, once the intercalation sites were saturated at high concentration. The results from cytotoxicity assays indicate that BPSQ was found to be toxic to all cell lines tested with IC50 values ranging from 2.8 to ≥ 20 µM. It was concluded that the binding of BPSQ to DNA occurs by a mechanism of intercalation, which probably accounts for its reported antitumor activity. [ABSTRACT FROM AUTHOR]

Complexes of DNA with actinocin derivatives containing benzocrown groups at positions 1 and/or 9 of the chromophore were studied by spectrophotometric titration and circular dichroism. The actinocin chromophore and the crown fragments are the DNA-binding sites of the ligands. The mode of ligand–DNA binding is shown to depend on the size of the crown group, its distance to the actinocin chromophore, and the ionic strength of the medium. Na+-selective benzocrown fragments combine with DNA phosphate groups. The simultaneous interaction of the actinocin chromophore with the DNA bases is possible only at an optimal distance between the two binding sites of ligand molecule. [ABSTRACT FROM AUTHOR]