No Arabic abstract
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond resolution to support a characterization of single bond forces attending to its electrical origin. This fundamental issue has eluded a physical description so far. Our method is applied to describe hydrogen bonds (HB) in DNA base pairs. Numerical results reveal that base pairs in DNA could be equivalent considering HB strength contributions, which challenges previous interpretations of thermodynamic properties of DNA based on the assumption that Adenine/Thymine pairs are weaker than Guanine/Cytosine pairs due to the sole difference in the number of HB. Thus, our methodology provides solid foundations to support the development of extended models intended to go deeper into the molecular mechanisms of DNA functioning.
We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein jumps between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite frozen DNA limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in islands within random DNA configurations in solution.
The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used in the self-assembly of DNA polyhedra and periodic structures. The motif is formed through the interaction of a bulge loop in one duplex and a sticky end of another. The polarity of the sticky end has significant consequences for the thermodynamic and geometrical properties of the T-motif: different polarities create junctions spanning different grooves of the duplex. We compare experimental binding strengths with predictions of oxDNA, a coarse-grained model of DNA, for various loop sizes. We find that, although both sticky-end polarities can create stable junctions, junctions resulting from 5$$ sticky ends are stable over a wider range of bulge loop sizes. We highlight the importance of possible coaxial stacking interactions within the motif and investigate how each coaxial stacking interaction stabilises the structure and favours a particular geometry.
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative characteristics of protein-DNA interactions, no such principles are known for the cooperative interactions between DNA-binding proteins. We consider a simple theoretical model for two interacting transcription factor (TF) species, searching for and binding to two adjacent target sites hidden in the genomic background. We study the kinetic competition of a dimer search pathway and a monomer search pathway, as well as the steady-state regulation function mediated by the two TFs over a broad range of TF-TF interaction strengths. Using a transcriptional AND-logic as exemplary functional context, we identify the functionally desirable regime for the interaction. We find that both weak and very strong TF-TF interactions are favorable, albeit with different characteristics. However, there is also an unfavorable regime of intermediate interactions where the genetic response is prohibitively slow.
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecules reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput read-outs, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base-paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecules contact map. Here, we give our in-house protocol for this mutate-and-map strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other biological molecules are poorly understood. In the present work the competitive binding of the hydrogen peroxide and water molecules with the DNA double helix backbone has been studied using the molecular dynamics method. The simulations have been carried out for the DNA double helix in a water solution with hydrogen peroxide molecules and Na$^{+}$ counterions. The obtained radial distribution functions of counterions, H$_2$O$_2$ and H$_2$O molecules with respect to the oxygen atoms of DNA phosphate groups have been used for the analysis of the formation of different complexes. The calculated mean residence times show that a hydrogen peroxide molecule stays at least twice as long near the phosphate group (up to 7 ps) than a water molecule (about 3 ps). The hydrogen peroxide molecules form more stable complexes with the phosphate groups of the DNA backbone than water molecules do.