Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

Base pair fluctuations in helical models for nucleic acids

A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, bending, and slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with ∼10.5 base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff increases. The cutoff is found to increase also in the presence of a sliding motion, which shortens the helix contour length, a situation peculiar of dsRNA molecules.

Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.

Deciphering Parameter Sensitivity in the BvgAS Signal Transduction

To understand the switching of different phenotypic phases of Bordetella pertussis, we propose an optimized mathematical framework for signal transduction through BvgAS two-component system. The response of the network output to the sensory input has been demonstrated in steady state. An analysis in terms of local sensitivity amplification characterizes the nature of the molecular switch. The sensitivity analysis of the model parameters within the framework of various correlation coefficients helps to decipher the contribution of the modular structure in signal propagation. Once classified, the model parameters are tuned to generate the behavior of some novel strains using simulated annealing, a stochastic optimization technique.

Flexibility of short DNA helices under mechanical stretching

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair.

Enhancing the branching ratios in the dissociation channels for O(16)O(16)O(18) molecule by designing optimum laser pulses: A study using stochastic optimization

We propose a strategy of using a stochastic optimization technique, namely, simulated annealing to design optimum laser pulses (both IR and UV) to achieve greater fluxes along the two dissociating channels (O(18) + O(16)O(16) and O(16) + O(16)O(18)) in O(16)O(16)O(18) molecule. We show that the integrated fluxes obtained along the targeted dissociating channel is larger with the optimized pulse than with the unoptimized one. The flux ratios are also more impressive with the optimized pulse than with the unoptimized one. We also look at the evolution contours of the wavefunctions along the two channels with time after the actions of both the IR and UV pulses and compare the profiles for unoptimized (initial) and optimized fields for better understanding the results that we achieve. We also report the pulse parameters obtained as well as the final shapes they take.

Unfolding kinetics of periodic DNA hairpins

DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as a function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyze for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterizing the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε(hb)(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics

Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.

Cellular transcription factors (TFs) are proteins that regulate gene expression, and thereby cellular activity and fate, by binding to specific DNA segments. The physicochemical determinants of protein-DNA binding specificity are not completely understood. Here, we report that the propensity of transient opening and re-closing of the double helix, resulting from thermal fluctuations, aka “DNA breathing” or “DNA bubbles,” can be associated with binding affinity in the case of Fis, a well-studied nucleoid-associated protein in Escherichia coli. We found that a particular breathing profile is characteristic of high-affinity Fis binding sites and that DNA fragments known to bind Fis in vivo are statistically enriched for this profile. Furthermore, we used simulations of DNA breathing dynamics to guide design of gel-shift experiments aimed at testing the idea that local breathing influences Fis binding. As a result, we show that via nucleotide modifications but without modifying nucleotides that directly contact Fis, we were able to transform a low-affinity Fis binding site into a high-affinity site and vice versa. The nucleotide modifications were designed only based on DNA breathing simulations. Our study suggests that strong Fis-DNA binding depends on DNA breathing - a novel physicochemical characteristic that could be used for prediction and rational design of TF binding sites.