Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene ...glycol ethers are found to modify structure, dynamics, and reactivity of DNA bymechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
The biexponential excited-state emission decay characteristic of DNA intercalated tris-bidentate dppz-based ruthenium complexes of the general form Ru(L)2dppz2+ has previously been explained by a ...binding model with two distinct geometry orientations of the bound ligands, with a distinct lifetime associated with each orientation. However, it has been found that upon DNA binding of Ru(phen)2dppz2+ the fractions of short and long lifetimes are strongly dependent on environmental factors such as salt concentration and, in particular, temperature. Analyzing isothermal titration calorimetry for competitive binding of Ru(phen)2dppz2+ enantiomers to poly(dAdT)2, we find that a consistent binding model must assume that the short and long lifetimes states of intercalated complexes are in equilibrium and that this equilibrium is altered when neighboring bound ligands affect each other. The degree of intercomplex binding is found to be a subtle manifestation of several attractive and repulsive factors that are highly likely to directly reflect the strong diastereomeric difference in the binding enthalpy and entropy values. In addition, as the titration progresses and the binding sites on the DNA lattice become increasingly occupied, a general resistance for the saturation of the binding sites is observed, suggesting diastereomeric crowding of the neighboring bound ligands.
Linear and circular dichroism (LD and CD) spectroscopy as well as isothermal titration calorimetry (ITC) have been used to investigate the interaction of Ru(tpy)(py)dppz(2+) (tpy = ...2,2':6',2''-terpyridyl; py = pyridine; dppz = dipyrido3,2-a:2'3'-cphenazine) with DNA, providing detailed information about the DNA binding thermodynamics and binding geometry of the metal complex. Flow LD, CD and isotropic absorption indicate that Ru(tpy)(py)dppz(2+) bind to DNA from the minor groove with the dppz ligand intercalated between base pairs, very similar to its chiral structural isomers Δ- and Λ-Ru(bpy)2dppz(2+) (bpy = 2,2'-bipyridine). A simple cooperative binding model with one binding geometry provide an excellent fit for calorimetric and absorption titration data. The values of the neighbor interaction thermodynamic parameters for Ru(tpy)(py)dppz(2+) suggest that complexes bound contiguously prefer to have their tpy ligands oriented towards the same strand.
Isothermal titration calorimetry (ITC) has been utilized to investigate the effect of methyl substituents on the intercalating dppz ligand of the enantiomers of the parent complex Ru(phen)2dppz2+ ...(phen = 1,10-phenanthroline; dppz = dipyrido3,2-a:2′,3′-cphenazine) on DNA binding thermodynamics. The methylated complexes (10-methyl-dppz and 11,12-dimethyl-dppz) have large, concentration-dependent, positive heats of dilution, and a strong endothermic background is also apparent in the ITC-profiles from titration of methylated complexes into poly(dAdT)2, which make direct comparison between complexes difficult. By augmenting a simple cooperative binding model with one equilibrium for complex self-aggregation in solution and one equilibrium for complex aggregation on saturated DNA, it was possible to find an excellent global fit to the experimental data with DNA affinity parameters restricted to be equal for all Δ-enantiomers as well as for all Λ-enantiomers. In general, enthalpic differences, compared to the unsubstituted complex, were small and less than 4 kJ mol−1, except for the heat of intercalation of Δ-10-methyl-dppz (−11,6 kJ mol−1) and Λ-11,12-dimethyl-dppz (+4.3 kJ mol−1).
While isothermal titration calorimetry (ITC) is widely used and sometimes referred to as the “gold standard” for quantitative measurements of biomolecular interactions, its usage has so far been ...limited to the analysis of the binding to isolated, non-cooperative binding sites. Studies on more complicated systems, where the binding sites interact, causing either cooperativity or anti-cooperativity between neighboring bound ligands, are rare, probably due to the complexity of the methods currently available. Here we have developed a simple algorithm not limited by the complexity of a binding system, meaning that it can be implemented by anyone, from analyzing systems of simple, isolated binding sites to complicated interactive multiple-site systems. We demonstrate here that even complicated competitive binding calorimetric isotherms can be properly analyzed, provided that ligand–ligand interactions are taken into account. As a practical example, the competitive binding interactions between the two enantiomers of Ru(bpy)2dppz2+ (Ru-bpy) and poly(dAdT)2 (AT-DNA) are analyzed using our new algorithm, which provided an excellent global fit for the ITC experimental data.
The enantiomers of a novel mononuclear ruthenium(ii) complex Ru(phen)2bidppz2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an ...aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
The enantiomers of a novel mononuclear ruthenium(
ii
) complex Ru(phen)
2
bidppz
2+
with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in ...an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(
ii
) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
Using water-miscible PEG, the association rate of thread-intercalating Ru(
ii
) complexes is increased, enabling a more effective evaluation of DNA-binding properties.
Isothermal titration calorimetry (ITC) has been utilized to investigate the effect of methyl substituents on the intercalating dppz ligand of the enantiomers of the parent complex Ru(phen)2dppz2+ ...(phen = 1,10-phenanthroline; dppz = dipyrido3,2-a:2',3'-cphenazine) on DNA binding thermodynamics. The methylated complexes (10-methyl-dppz and 11,12-dimethyl-dppz) have large, concentration-dependent, positive heats of dilution, and a strong endothermic background is also apparent in the ITC-profiles from titration of methylated complexes into poly(dAdT)2, which make direct comparison between complexes difficult. By augmenting a simple cooperative binding model with one equilibrium for complex self-aggregation in solution and one equilibrium for complex aggregation on saturated DNA, it was possible to find an excellent global fit to the experimental data with DNA affinity parameters restricted to be equal for all Δ-enantiomers as well as for all Λ-enantiomers. In general, enthalpic differences, compared to the unsubstituted complex, were small and less than 4 kJ mol-1, except for the heat of intercalation of Δ-10-methyl-dppz (-11,6 kJ mol-1) and Λ-11,12-dimethyl-dppz (+4.3 kJ mol-1).
While isothermal titration calorimetry (ITC) is widely used and sometimes referred to as the "gold standard" for quantitative measurements of biomolecular interactions, its usage has so far been ...limited to the analysis of the binding to isolated, non-cooperative binding sites. Studies on more complicated systems, where the binding sites interact, causing either cooperativity or anti-cooperativity between neighboring bound ligands, are rare, probably due to the complexity of the methods currently available. Here we have developed a simple algorithm not limited by the complexity of a binding system, meaning that it can be implemented by anyone, from analyzing systems of simple, isolated binding sites to complicated interactive multiple-site systems. We demonstrate here that even complicated competitive binding calorimetric isotherms can be properly analyzed, provided that ligand-ligand interactions are taken into account. As a practical example, the competitive binding interactions between the two enantiomers of Ru(bpy)
dppz
(Ru-bpy) and poly(dAdT)
(AT-DNA) are analyzed using our new algorithm, which provided an excellent global fit for the ITC experimental data.
The aim of this study is to explore whether trends in sustainability and digitalisation from the 1980s until today have left any significant practical or epistemological footprints on the quality ...management paradigm. The study design consists of a mixed-methods approach that applies a data-mining methodology and content analysis to the digital archives of eight scientific journals: six within the quality management (QM) domain and two with a focus on operations management (OM). The data set contains an unbroken time series of over 12,000 research paper abstracts, the first of them published in 1980, giving the study a coverage of almost 40 years. The findings show that sustainability came onto the scholarly scene in 1996 and has since become an increasingly popular research area. In regard to digitalisation, the story is quite different, as the concept is currently absent from the scholarly QM and OM literatures. However, a search for information technology (IT) and information systems (IS) revealed that these topics have been gaining attention since the 1980s. However, it was found that QM research only addresses one part of digitalisation, omitting several interesting dimensions. One example is that the QM and OM literatures address IS mainly in relation to standardised guidelines and business processes within organisations. At the same time, we found a handful of studies combining QM and topics related to modern digitisation, like social media.
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