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| 2. |
- Almaqwashi, A. A., et al.
(författare)
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Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex
- 2014
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 42:18, s. 11634-11641
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Tidskriftsartikel (refereegranskat)abstract
- DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Delta, Delta-[mu-bidppz-(phen)(4)Ru-2]4(+) (Delta, Delta-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Delta, Delta-P intercalation K-d is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Delta-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Delta, Delta-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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| 3. |
- Andersson, Johanna, 1983, et al.
(författare)
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AT-Specific DNA Binding of Binuclear Ruthenium Complexes at the Border of Threading Intercalation
- 2010
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Ingår i: Chemistry - A European Journal. - : Wiley. - 1521-3765 .- 0947-6539. ; 16:36, s. 11037-11046
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Tidskriftsartikel (refereegranskat)abstract
- The binuclear ruthenium complex [mu-bidppz(phen)(4)Ru-2](4+) has been extensively studied since the discover}, of its unusual threading intercalation interaction with DNA, a binding mode with extremely slow binding and dissociation kinetics. The complex has been shown to be selective towards long stretches of alternating AT base pairs, which makes it interesting, for example, as a model compound for anti-malaria drugs due to the high AT content of the genome of the malaria parasite P falciparum. We have investigated the effect of bridging ligand structure on threading intercalation ability and found that length and rigidity as well as the size of the intercalated ring system are all factors that affect the rate and selectivity of the threading intercalation. In particular, we discovered a new DNA-threading compound, [mu-dppzip(phen)(4)Ru-2](4+) which appears to be just at the border of being capable of threading intercalation and displays even greater selectivity for AT-DNA than the parent compound, [mu-bidppz(phen)(4)Ru-2](4+).
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| 4. |
- Andersson, Johanna, 1983, et al.
(författare)
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Lifetime Heterogeneity of DNA-Bound dppz Complexes Originates from Distinct Intercalation Geometries Determined by Complex-Complex Interactions
- 2013
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 52:2, s. 1151-1159
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Tidskriftsartikel (refereegranskat)abstract
- Despite the extensive interest in structurally explaining the photophysics of DNA-bound [Ru(phen)(2)dppz](2+) and [Ru(bpy)(2)dppz](2+), the origin of the two distinct emission lifetimes of the pure enantiomers when intercalated into DNA has remained elusive. In this report, we have combined a photophysical characterization with a detailed isothermal titration calorimetry study to investigate the binding of the pure Delta and Lambda enantiomers of both complexes with [poly(dAdT)](2). We find that a binding model with two different binding geometries, proposed to be symmetric and canted intercalation from the minor groove, as recently reported in high-resolution X-ray structures, is required to appropriately explain the data. By assigning the long emission lifetime to the canted binding geometry, we can simultaneously fit both calorimetric data and the binding-density-dependent changes in the relative abundance of the two emission lifetimes using the same binding model. We find that all complex complex interactions are slightly unfavorable for Delta-[Ru(bpy)(2)dppz](2+), whereas interactions involving a complex canted away from a neighbor are favorable for the other three complexes. We also conclude that Delta-[Ru(bpy)(2)dppz](2+) preferably binds isolated, Delta-[Ru(phen)(2)dppz](2+) preferably binds as duplets of canted complexes, and that all complexes are reluctant to form longer consecutive sequences than triplets. We propose that this is due to an interplay of repulsive complex complex and attractive complex-DNA interactions modulated by allosteric DNA conformation changes that are largely affected by the nature of the ancillary ligands.
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| 5. |
- Andersson, Johanna, 1983, et al.
(författare)
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Stereoselectivity for DNA Threading Intercalation of Short Binuclear Ruthenium Complexes
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:49, s. 14768-14775
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Tidskriftsartikel (refereegranskat)abstract
- Threading intercalation is an unusual DNA binding mode with significantly slower association and dissociation rates compared with classical intercalation. The latter has been shown to correlate well with cytotoxicity, and therefore, threading intercalating compounds are of great interest in the search for new DNA binding drugs. Thus, there is a need for better understanding of the mechanisms behind this type of binding. In this work, we have investigated the threading intercalation ability, of the four stereoisomers of the AT-specific binuclear ruthenium complex [mu-dppzip(phen)(4)Ru(2)](4+) using different spectroscopic techniques. This complex contains an unsymmetrical bridging ligand consisting of a dipyridophenazine and an imidazophenanthroline ring system, in which the photophysical properties of the Ru-dipyridophenazine complex moiety make it possible to distinguish the intercalating part from the nonintercalating part We have found that Delta geometry around the ruthenium on the intercalating dipyridophenazine moiety and Lambda geometry on the nonintercalating imidazophenanthroline moiety is the optimal configuration for threading intercalation Of this complex and that the chirality on the ruthenium of the nonintercalating half dominates the stereospecificity in the threaded state. This is the cause of the reversed enantioselectivity compared with the parent threading intercalating complex [mu-bidppz(phen)(4)Ru(2)](4+), in which the enantioselectivity is controlled by the chirality on the intercalating half. The differences in the interactions with DNA between the two, complexes are most likely due to the fact that [mu-dppzip(phen)(4)Ru(2)](4+) has a slightly shorter bridging ligand than the parent complex.
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| 6. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Double-lock ratchet mechanism revealing the role of alpha SER-344 in FoF1 ATP synthase
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:12, s. 4828-4833
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Tidskriftsartikel (refereegranskat)abstract
- In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP + Pi. ATP + H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the gamma P-O-ADP bond-forming step via a double-proton transfer. At this step, the highly conserved alpha S344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar PO3- ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.
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| 7. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites
- 2010
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 49:3, s. 401-403
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Tidskriftsartikel (refereegranskat)abstract
- Despite exhaustive chemical and crystal structure studies, the mechanistic details of how F o F 1 -ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO 3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in β TP and, thus, promote ATP. © 2009 American Chemical Society.
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| 8. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Rate of hydrolysis in ATP synthase is fine-tuned by alpha-subunit motif controlling active site conformation
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:6, s. 2117-2122
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Tidskriftsartikel (refereegranskat)abstract
- Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. FoF1 ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F-1 performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central gamma-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-angstrom-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to.-subunit position, the active site conformation is fine-tuned mainly by small alpha-subunit changes. Quantum mechanics-based results confirm that the sub-Angstrom gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.
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| 9. |
- Dehkordi, Maryarn Nejat, et al.
(författare)
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Comprehensive Study on the Binding of Iron Schiff Base Complex with DNA and Determining the Binding Mode
- 2013
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Ingår i: Journal of Fluorescence. - : Springer Science and Business Media LLC. - 1573-4994 .- 1053-0509. ; 23:4, s. 813-821
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Tidskriftsartikel (refereegranskat)abstract
- The iron (III) [N, N' Bis (5-(triphenyl phosphonium methyl) salicylidene)-1, 2 ethanediamine] chloride [Fe Salen]Cl, has been synthesized and characterized as described previously. The interaction of iron complex with calf thymus (CT) DNA has been studied extensively by experimental techniques. Absorption spectra showed both hypochromism and hyperchromism. Thermal denaturation study of DNA with complex revealed the Delta T-m of 5 A degrees C. Competitive binding study shows that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding of the iron complex indicating that it displaces EB from its binding site in DNA and the apparent binding constant has been estimated to be 5 x 10(6) mu M-1. Fluorescence Scatchard plot revealed type B behavior for interaction of complex to DNA. Circular dichroism (CD) spectra measurements showed that the complex interacts with DNA via surface and groove bindings. Linear dichroism (LD) measurements confirmed the bending of DNA in the presence of complex. Furthermore, Isothermal titration calorimetry (ITC) experiments approved that the binding of complex is based on both electrostatic and hydrophobic interactions. More, ITC profile exhibits the existence of two binding phases for the complex.
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| 10. |
- Dehkordi, Maryarn Nejat, et al.
(författare)
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Spectroscopic study on the interaction of ct-DNA with manganese Salen complex containing triphenyl phosphonium groups
- 2012
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Ingår i: Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425. ; 90, s. 50-54
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Tidskriftsartikel (refereegranskat)abstract
- The DNA binding properties of a bulky and hydrophobic Schiff base complex of manganese(III) [N,N'-bis(5-(triphenyl phosphonium methyl)salicylidene)-1,2-ethylene diamine chloride Mn(III) acetate] was examined by spectroscopic techniques. UV-vis titration data indicate both hypo and hyperchromic effect with addition of DNA to complex. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding Mn Salen complex. This finding indicates that Mn Salen complex displaces EB from its binding site in DNA. Helix melting studies indicate improvement in the helix stability, and an increase in the melting temperature. The analysis of CD spectra represents the structural changes in DNA due to the binding of Mn Salen complex. The binding constant has been calculated using absorbance and fluorescence data. The results also represent that the binding process proceeds by strong electrostatic and hydrophobic interactions.
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