| 1. |
- Beke-Somfai, Tamas, 1977, et al.
(författare)
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Energy phase shift as mechanism for catalysis
- 2012
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 535, s. 169-172
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Tidskriftsartikel (refereegranskat)abstract
- Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal 'energy recycling', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F-1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex.
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| 2. |
- Feng, Bobo, 1987
(författare)
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DNA strand exchange and hydrophobic interactions between biomolecules
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The role of hydrophobic interactions in DNA strand exchange has been studied using fluorescence-labeled DNA oligomers in a FRET assay. Strand exchange was found to be accelerated in the presence of polyethylene glycol, which provides a crowded and hydrophobic environment possibly mimicking that of the catalytically active recombinase-DNA complexes. Circular dichroism spectroscopy shows that B-DNA conformation is conserved, so the increased rate of exchange is not simply caused by melting of DNA duplexes. A hydrophobic environment increases the base pairing accuracy of DNA strand exchange, which causes mismatched duplexes to quickly be replaced in the presence of matching strands. It is inferred that these effects are caused by a decrease in water activity which weakens the DNA stacking forces, and by favorable hydrophobic interactions between PEG and DNA chains, with the result that DNA breathing and subsequent strand invasion is facilitated. Linear dichroism and dynamic light scattering were also used to study some other biomolecular systems where hydrophobic interactions are important: lipid membranes, DNA-protein complex, DNA nanoconstructs anchored to membrane surface, and to study fusion of liposomes induced by shearing forces. A DNA hexagon construct was found to adopt different orientations at the membrane surface depending on the number of attached anchors, but the construct itself was inferred to have a metastable shape due to internal flexibility. Finally, an example of assembly of protein subunits to a membrane surface was considered in shape of the ATP synthase system for which we propose that the activation energy of ATP synthesis may be reduced through coupled reactions between three active sites. The results are interesting in more general contexts of methodological improvements for studying biomolecular assembly, including linear dichroism spectroscopy of transmembrane proteins.
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| 3. |
- Feng, Bobo, 1987, et al.
(författare)
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DNA strand exchange catalyzed by molecular crowding in PEG solutions
- 2010
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; 46:43, s. 8231-8233
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Tidskriftsartikel (refereegranskat)abstract
- DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology.
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| 4. |
- Feng, Bobo, 1987, et al.
(författare)
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Evidence for hydrophobic catalysis of DNA strand exchange
- 2015
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; 51:34, s. 7390-7392
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Tidskriftsartikel (refereegranskat)abstract
- The catalytic role of hydrophobic co-solutes in DNA strand exchange is demonstrated by FRET kinetics. Two mechanisms that contribute to this are base stacking destabilisation and nucleation-promoted DNA strand invasion. We propose that hydrophobic catalysis is involved in the strand-exchange activity of recombination enzymes.
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| 5. |
- Feng, Bobo, 1987, et al.
(författare)
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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects
- 2019
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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. ; 116:35, s. 17169-17174
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Tidskriftsartikel (refereegranskat)abstract
- 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 by mechanisms 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.
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| 6. |
- Fornander, Louise, 1984, et al.
(författare)
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UV Transition Moments of Tyrosine
- 2014
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:31, s. 9247-9257
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Tidskriftsartikel (refereegranskat)abstract
- To assist polarized-light spectroscopy for protein-structure analysis, the UV spectrum of p-cresol, the chromophore of tyrosine, was studied with respect to transition moment directions and perturbation by solvent environment. From linear dichroism (LD) spectra of p-cresol aligned in stretched matrices of poly(vinyl alcohol) and polyethylene, the lowest pi-pi* transition (L-b) is found to have pure polarization over its entire absorption (250-300 nm) with a transition moment perpendicular to the symmetry axis (C-1-C-4), both in polar and nonpolar environments. For the second transition (L-a), polarized parallel with the symmetry axis, a certain admixture of intensity with orthogonal polarization is noticed, depending on the environment. While the L-b spectrum in cydohexane shows a pronounced vibrational structure, it is blurred in methanol, which can be modeled as due to many microscopic polar environments. With the use of quantum mechanical (QM) calculations, the transition moments and solvent effects were analyzed with the B3LYP and omega B97X-D functionals in cyclohexane, water, and methanol using a combination of implicit and explicit solvent models. The blurred L-b band is explained by solvent hydrogen bonds, where both accepting and donating a hydrogen causes energy shifts. The inhomogeneous solvent-shift sensitivity in combination with robust polarization can be exploited for analyzing tyrosine orientation distributions in protein complexes using LD spectroscopy.
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| 7. |
- Hanczyc, Piotr, 1985, et al.
(författare)
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Identification of Thioflavin T Binding Modes to DNA: A Structure-Specific Molecular Probe for Lasing Applications
- 2021
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 12:22, s. 5436-5442
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Tidskriftsartikel (refereegranskat)abstract
- The binding mechanism of thioflavin T (ThT) to DNA was studied using polarized light spectroscopy and fluorescence-based techniques in solutions and in solid films. Linear dichroism measurements showed that ThT binds to DNA duplex by intercalation. Time-resolved fluorescence studies revealed a second binding mode which is the external binding to the DNA phosphate groups. Both binding modes represent the nonspecific type of interactions. The studies were complemented with the analysis of short oligonucleotides having DNA cavities. The results indicate that the interplay between three binding modes-intercalation, external binding, and binding inside DNA cavities-determines the effective fluorescence quantum yield of the dye in the DNA structures. External binding was found to be responsible for fluorescence quenching because of energy transfer between intercalated and externally bound molecules. Finally, amplified spontaneous emission (ASE) was successfully generated in the ThT-stained films and used for detecting different DNA structures. ASE measurements show that ThT-stained DNA structures can be used for designing bioderived microlasers.
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| 8. |
- Kogan, Maxim, 1977, et al.
(författare)
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Shear-Induced Membrane Fusion in Viscous Solutions
- 2014
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 30:17, s. 4875-4878
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Tidskriftsartikel (refereegranskat)abstract
- Large unilamellar lipid vesicles do not normally fuse under fluid shear stress. They might deform and open pores to relax the tension to which they are exposed, but membrane fusion occurring solely due to shear stress has not yet been reported. We present evidence that shear forces in a viscous solution can induce lipid bilayer fusion. The fusion of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes is observed in Couette flow with shear rates above 3000 s(-1) provided that Couette Cell the medium is viscous enough. Liposome samples, prepared at different viscosities using a 0-50 wt % range of sucrose concentration, were studied by dynamic light scattering, lipid fusion assays using Forster resonance energy transfer (FRET), and linear dichroism (LD) spectroscopy. Liposomes in solutions with 40 wt % (or more) sucrose showed lipid fusion under shear forces. These results support the hypothesis that under suitable conditions lipid membranes may fuse in response to mechanical-force-induced stress.
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| 9. |
- Lundberg, Erik, 1981, et al.
(författare)
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Controlling and Monitoring Orientation of DNA Nanoconstructs on Lipid Surfaces
- 2013
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 29:1, s. 285-293
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Tidskriftsartikel (refereegranskat)abstract
- Its extraordinary self-assembly property, with potential to form nonperiodic structures with unique addressability, makes DNA ideal for fabrication of advanced nanostructures. We here demonstrate the controllable tethering of a hexagonal DNA nanostructure in two distinct orientations at the lipid bilayer of a liposome functioning as a soft-matter support. With polarized light (linear dichroism) applied to the flow-aligned liposomes, we show that the construct is preferentially in a parallel alignment with the lipid surface when two anchors are attached while with one anchor only a perpendicular orientation is observed.
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| 10. |
- Nordén, Bengt, 1945, et al.
(författare)
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Mismatch detection in homologous strand exchange amplified by hydrophobic effects
- 2021
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 112:4
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to DNA replication and transcription where nucleotides are added and matched one by one, homologous recombination by DNA strand exchange tests whole sequences for complementarity, which requires elimination of mismatched yet thermodynamically stable intermediates. To understand the remarkable sequence specificity of homologous recombination, we have studied strand exchange between a 20-mer duplex containing one single mismatch (placed at varied positions) with the matching single strand in presence of poly(ethylene glycol) representing a semi-hydrophobic environment. A FRET-based assay shows that rates and yields of strand exchange from mismatched to matched strands rapidly increase with semi-hydrophobic co-solute concentration, contrasting previously observed general strand exchange accelerating effect of ethyl glycol ethers. We argue that this effect is not caused simply by DNA melting or solvent-induced changes of DNA conformation but is more complex involving several mechanisms. The catalytic effects, we propose, involve strand invasion facilitated by reduced duplex stability due to weakened base stacking (“longitudinal breathing”). Secondly, decreased water activity makes base-pair hydrogen bonds stronger, increasing the relative energy penalty per mismatch. Finally, unstacked mismatched bases (gaps) are stabilized through partly intercalated hydrophobic co-solvent molecules, assisting nucleation of strand invasion at the point of mismatch. We speculate that nature long ago discovered, and now exploits in various enzymes, that sequence recognition power of nucleic acids may be modulated in a hydrophobic environment.
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