Krzysztof Bielec's research while affiliated with University of Zurich and other places

Publications (12)

Article
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The reaction kinetics between like-charged compounds in water is extremely slow due to Coulomb repulsions. Here, we demonstrate that by screening these interactions and, in consequence, increasing the local concentration of reactants, we boost the reactions by many orders of magnitude. The reaction between negatively charged Coenzyme A molecules ac...
Article
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The equilibrium constant (K) of biochemical complex formation in aqueous buffers with high concentration (>20 wt %) of nonionic compounds can vary by orders of magnitude in comparison with the K in a pure buffer. The precise molecular mechanisms of these profound changes are not known. Herein, we show up to a 1000-fold decrease of the K value of DN...
Article
We simulated Brownian diffusion and reaction-diffusion processes to study the influence of molecular rebinding on the reaction rates of bimolecular reactions. We found that the number of rebinding events, Nreb, is proportional to the target's size and inversely proportional to the diffusion coefficient D and simulation time-step Δt. We found the pr...
Article
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The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation...
Article
Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure-function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) w...
Article
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Bacteriophages (phages for short) are viruses, which have bacteria as hosts. The single phage body virion, is a colloidal particle, often possessing a dipole moment. As such, phages were used as perfectly monodisperse systems to study various physicochemical phenomena (e.g., transport or sedimentation in complex fluids), or in the material science...
Article
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Anthracyclines are one of the most studied anticancer drugs approved for medical treatment. The equilibrium constant (K) of reaction between those drugs with DNA in both in-vitro and in-vivo experiments is a lack of consensus. The K values vary from 10⁴ up to 10⁸ M⁻¹, which suggests a 1000-fold error in determining the effective concentration neede...
Article
Full-text available
Intrinsic molecular brightness (MB) is a number of emitted photons per second per molecule. When a substrate labeled by a fluorophore and a second unlabeled substrate form a complex in solution, the MB of the fluorophore changes. Here we use this change to determine the equilibrium constant (K) for the formation of the complex at pM concentrations....
Article
Although DNA hybridization/melting is one of the most important biochemical reactions, the non-trivial kinetics of the process is not yet fully understood. In this work, we use Forster resonance energy transfer (FRET) to investigate the influence of temperature, ionic strength, and oligonucleotide length on the kinetic and equilibrium constants of...
Article
Faster and more sensitive environmental monitoring should be developed to face the worldwide problem of bacterial infections. To remedy this issue we demonstrate bacteria sensing element, which utilizes dense and ordered layers of bacteriophages specific for given bacteria strain. We combine 1) chemical modification of the surface to increase the s...

Citations

... To establish generality and validate whether the proposed acceleration method works for like-charged compounds in other systems, we introduced a second experimental model. We chose DNA hybridization because it is a well-known ion-sensitive process that occurs between two negatively charged reactants at neutral pH (Fig. 5a) 14 . This example also introduces broader generality since the product of CoA with CoA-M reaction is formed via covalent bonds, whereas DNA duplex assembles via non-covalent interactions. ...
... FCS allowed measurements of single molecules and provided delivery effectiveness at a single-cell level (intracellular concentration measurement). The diffusion coefficient calculations enabled the precise identification of the biomacromolecules introduced into the cell [22][23][24][25]. FCS was supported with confocal imaging. ...
... In the first decades, the main focus was on the search for specific binding peptides for medical and pharmaceutical applications, such as antibody development [15], epitope mapping [16,17], drug discovery [18][19][20], investigation of protein-protein interactions [21][22][23], and nanotechnological applications [24][25][26][27]. New fields of application are increasingly emerging, such as the search for binding peptides for inorganic surfaces [28][29][30], sensor development [31][32][33][34], or the removal of toxic or economically significant metal ions from complexly composed aqueous streams [35][36][37][38]. ...
... 27 The formation of PEG−sodium complexes was also used in cation template-assisted cyclopolymerization. 28 In this Letter, we revise molecular crowding's effect on biochemical reactions at the nanomolar concentration range using a previously validated brightness-based method. 18,19 Figure 1 presents the schematic concept workflow. We studied DNA hybridization in standard molecular crowder systems (i.e., PEG, EG, glycerol, Ficoll, and dextrans) as a noncovalent complex formation model. ...
... The average value is log(K h /M − 1 ) = 8.0 ± 0.3, in agreement with literature values for similar strands and hybridization conditions [22][23][24]. ...
... In the case of the oligonucleotides, we used Milli-Q ultrapure water as the medium or 1 mM phosphate buffer (PB). Since the strands' concentrations were kept at a nanomolar scale, we added 0.002% Tween 20 to prevent their accumulation on the glass and air surfaces 17 . The temperature during all measurements was 25°C. ...
... They also suggested that the Debye length (L D ) between the sample solution and the sensor's surface is crucial for the successful alignment of bacteriophages. A 33-fold rise in the density of phages on the surface compared to the chemical modification of the surface with dithiobis succinimidyl propionate (DTSP) and the sensitivity of the sensor increased by 64-fold in comparison to the physical adsorption immobilization method [107]. A typical phage-based electrochemical sensor consists of potentiometric and amperometric measurements [108]. ...