DNA Breathing Dynamics Research Articles

Mapping of DNA base-pair sequence from breathing dynamics of hetero-polymeric DNA: A genetic algorithm-based study

Mapping of DNA base-pair sequence from breathing dynamics of hetero-polymeric DNA: A genetic algorithm-based study

Breathers-like rogue wave trains induced by nonlinear dynamics of DNA breathing

Breathers-like rogue wave trains induced by nonlinear dynamics of DNA breathing

Ancillary Ligand in Ternary CuII Complexes Guides Binding Selectivity toward Minor-Groove DNA.

Copper-containing compounds known as Casiopeínas are biologically active molecules which show promising antineoplastic effects against several cancer types. Two possible hypotheses regarding the mode of action of the Casiopeínas have emerged from the experimental evidence: the generation of reactive oxygen species or the ability of the compounds to bind and interact with nucleic acids. Using robust molecular dynamics simulations, we investigate the interaction of four different Casiopeínas with the DNA duplex d(GCACGAACGAACGAACGC). The studied copper complexes contain either 4–7- or 5–6-substituted dimethyl phenanthroline as the primary ligand and either glycinate or acetylacetonate as the secondary ligand. For statistical significance and to reduce bias in the simulations, four molecules of each copper compound were manually placed at a distance of 10 Å away from the DNA and 20 independent molecular dynamics simulations were performed, each reaching at least 30 μs. This time scale allows us to reproduce expected DNA terminal base-pair fraying and also to observe intercalation/base-pair eversion events generated by the compounds interacting with DNA. The results reveal that the secondary ligand is the guide toward the mode of binding between the copper complex and DNA in which glycinate prefers minor-groove binding and acetylacetonate produces base-pair eversion and intercalation. The CuII complexes containing glycinate interact within the DNA minor groove which are stabilized principally by the hydrogen bonds formed between the amino group of the aminoacidate moiety, whereas the compounds with the acetylacetonate do not present a stable network of hydrogen bonds and the ligand interactions enhance DNA breathing dynamics that result in base-pair eversion.

DNA breathing dynamics under periodic forcing: Study of several distribution functions of relevant Brownian functionals.

In this paper, we study DNA breathing dynamics in the presence of an external periodic force by proposing and inspecting several probability distribution functions (PDFs) of relevant Brownian functionals which specify the bubble lifetime, reactivity, and average size. We model the bubble dynamics process by an overdamped Langevin equation of broken base pairs on the Poland-Scheraga free energy landscape. Introducing an effective time-independent description for timescales larger than T[over ̃]=2π/ω (where ω is the frequency of external periodic force) and using an elegant backward Fokker-Planck method we derive closed form expressions of several PDFs associated with such stochastic processes. For instance, with an initial bubble size of x_{0}, we derive the following analytical expressions: (i) the PDF P(t_{f}|x_{0}) of the first passage time t_{f} which specifies the lifetime of the DNA breathing process, (ii) the PDF P(A|x_{0}) of the area A until the first passage time, and it provides much valuable information about the average bubble size and reactivity of the process, and (iii) the PDF P(M) associated with the maximum bubble size M of the breathing process before complete denaturation. Our analysis is limited to two limits: (a) large bubble size and (b) small bubble size. We further confirm our analytical predictions by computing the same PDFs with direct numerical simulations of the corresponding Langevin equations. We obtain very good agreement of our theoretical predictions with the numerically simulated results. Finally, several nontrivial scaling behaviors in the asymptotic limits for the above-mentioned PDFs are predicted, which can be verified further from experimental observation. Our main conclusion is that the large bubble dynamics is unaffected by the rapidly oscillating force, but the small bubble dynamics is significantly affected by the same periodic force.

Fractional nonlinear dynamics of DNA breathing

The classical Lagrangian formulation for the nonlinear dynamics of a homogeneous Peyrard–Bishop DNA molecular chain is reviewed and extended to include coordinates with time derivative of fractional order γ (0 < 2γ < 2), which can be viewed as memory effect. We obtain the equations of motion depending on γ. The analytical procedure for obtaining nonlinear waves solutions is performed through the application of a powerful fractional perturbation technique. The results show that both the amplitude and the velocity of waves increase when γ decreases. Accordingly, for low values of γ, the system exhibits highly localized waves with high amplitude and velocity. The numerical results agree with the theoretical ones and show that the system can support fractional breather-like modes.

Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies.

We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria.

BackgroundThere is a need for strong and tightly regulated promoters to construct more reliable and predictable genetic modules for synthetic biology and metabolic engineering. For this reason we have previously constructed a TetR regulated L promoter library for the cyanobacterium Synechocystis PCC 6803. In addition to the L03 promoter showing wide dynamic range of transcriptional regulation, we observed the L09 promoter as unique in high leaky gene expression under repressed conditions. In the present study, we attempted to identify the cause of L09 promoter leakage. TetR binding to the promoter was studied by theoretical simulations of DNA breathing dynamics and by surface plasmon resonance (SPR) biosensor technology to analyze the kinetics of the DNA–protein interactions.ResultsDNA breathing dynamics of a promoter was computed with the extended nonlinear Peyrard–Bishop–Dauxois mesoscopic model to yield a DNA opening probability profile at a single nucleotide resolution. The L09 promoter was compared to the L10, L11, and L12 promoters that were point-mutated and different in repressed promoter strength. The difference between DNA opening probability profiles is trivial on the TetR binding site. Furthermore, the kinetic rate constants of TetR binding, as measured by SPR biosensor technology, to the respective promoters are practically identical. This suggests that a trivial difference in probability as low as 1 × 10−4 cannot lead to detectable variations in the DNA–protein interactions. Higher probability at the downstream region of transcription start site of the L09 promoter compared to the L10, L11, and L12 promoters was observed. Having practically the same kinetics of binding to TetR, the leakage problem of the L09 promoter might be due to enhanced RNA Polymerase (RNAP)-promoter interactions in the downstream region.ConclusionsBoth theoretical and experimental analyses of the L09 promoter’s leakage problem exclude a mechanism of reduced TetR binding but instead suggest enhanced RNAP binding. These results assist in creating more tightly regulated promoters for realizing synthetic biology and metabolic engineering in biotechnological applications.

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.

Watching DNA breath one molecule at a time

As the carrier of genetic information, DNA is the template and substrate in many fundamental biological reactions, including replication, transcription, DNA repair, recombination, and remodeling. It is now well accepted that the power of DNA in controlling gene expression is not limited to the actual genetic codes contained in DNA sequence. Compared with the well-documented chemical modifications of DNA and their functions in shaping gene expression patterns (1⇓–3), the impact of physical properties of DNA is much less characterized, partially because they are relatively difficult to describe and measure directly. Nevertheless, it is now more and more appreciated that physical properties, such as DNA bending (4, 5) and DNA breathing (6⇓–8), play important roles in gene expression by affecting binding and assembly of molecular machineries on DNA. In PNAS, Phelps et al. introduce to us a unique single-molecule approach to study DNA breathing dynamics and investigate the role of DNA breathing in protein assembly on DNA (9).

Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.

Changes in global DNA linking number can be accommodated by localized changes in helical structure. We have used single-molecule torque measurements to investigate sequence-specific strand separation and Z-DNA formation. By controlling the boundary conditions at the edges of sequences of interest, we have confirmed theoretical predictions of distinctive boundary-dependent backbending patterns in torque-twist relationships. Abrupt torque jumps are associated with the formation and collapse of DNA bubbles, permitting direct observations of DNA breathing dynamics.

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.

76 Protein–DNA binding and breathing dynamics of DNA

In the living cell, the double-stranded DNA molecule experiences thermal motions that induce spontaneous openings and re-closings of the double helix known as “DNA breathing,” or “DNA transient bubbles” (Englander et al., 1980). The propensity for breathing is interconnected with DNA local stability and flexibility (Vafabakhsh & Ha, 2012), which play a key role in DNA biological function (Bishop et al., 2012). Here, we investigate the relationship between the DNA local propensity for breathing and binding of two transcription factors (TFs): (i) the human TF YY1, (see e.g. Usheva & Shenk, 1996), and (ii) the nucleoid-associated protein Fis in Escherichia coli (see e.g. Finkel & Johnson, 1992). Using a mesoscopic nonlinear model of double-stranded DNA (Peyrard & Bishop, 1989) that can be augmented for rational design of DNA breathing (Alexandrov et al., 2010), we have simulated the dynamics of known Fis- and YY1-binding sites, analyzed published in vitro and genomic data-sets, and conducted targeted experimental tests of our predictions (Alexandrov et al., 2012; Nowak-Lovato et al., in press). We found a strong correlation between the propensity for breathing (at the binding sites) and YY1/Fis binding. We identified a breathing profile that is characteristic for a strong Fis-binding site that is significantly enriched among the identified in vivo E. coli Fis-binding sites. To test our understanding of how Fis binding is influenced by the breathing, we designed base-pair substitutions, mismatch, and O6-Guanine methylation modifications of nucleotides, in sequences that are known to interact (or not interact) with Fis, seeking to make the breathing either closer to or farther from the breathing profile of a strong Fis-binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by EMSA, changed in accordance with our expectations. Further, by using site-specific chromatin immunopecipitations, BIOBASE data, and simulations, we also found a specific breathing profile at the binding cites of YY1 in vivo. Our finding suggests that the genomic-flanking sequence variations and SNPs presence may exert long-range effects on DNA breathing and predetermine YY1 binding in cells.

Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H· · ·N and N-H· · ·O hydrogen bonding, we identify a high-frequency (~96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (~300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein–DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.

Dynamics of DNA breathing in the Peyrard–Bishop model with damping and external force

The impact of the damping effect and external forces on DNA breathing is investigated within the Peyrard–Bishop model. In the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger equation and studied by means of the variational method. The analytical solutions are obtained for special cases. It is shown that the breather propagation is decelerated in the presence of a damping factor without the external force, while the envelope velocity and the amplitude increase significantly with the presence of external force. It is particularly found that the higher harmonic terms are enhanced when the periodic force is applied. It is finally argued that the external force accelerates the DNA breathing.

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

We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local denaturation zones (bubbles). On the basis of the reconstructed bubble size distribution, this is achieved through stochastic optimization of the free energies in terms of simulated annealing. In particular, it is shown that even noisy time series allow the identification of the stability parameters at remarkable accuracy. This method will be useful to obtain the DNA stacking and hydrogen bonding free energies from single bubble breathing assays rather than equilibrium data.

Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia

In a previous study, we detected a 6p25-p24 region linked to schizophrenia in families with high composite cognitive deficit (CD) scores, a quantitative trait integrating multiple cognitive measures. Association mapping of a 10 Mb interval identified a 260 kb region with a cluster of single-nucleotide polymorphisms (SNPs) significantly associated with CD scores and memory performance. The region contains two colocalising genes, LYRM4 and FARS2, both encoding mitochondrial proteins. The two tagging SNPs with strongest evidence of association were located around the overlapping putative promoters, with rs2224391 predicted to alter a transcription factor binding site (TFBS). Sequencing the promoter region identified 22 SNPs, many predicted to affect TFBSs, in a tight linkage disequilibrium block. Luciferase reporter assays confirmed promoter activity in the predicted promoter region, and demonstrated marked downregulation of expression in the LYRM4 direction under the haplotype comprising the minor alleles of promoter SNPs, which however is not driven by rs2224391. Experimental evidence from LYRM4 expression in lymphoblasts, gel-shift assays and modelling of DNA breathing dynamics pointed to two adjacent promoter SNPs, rs7752203-rs4141761, as the functional variants affecting expression. Their C-G alleles were associated with higher transcriptional activity and preferential binding of nuclear proteins, whereas the G-A combination had opposite effects and was associated with poor memory and high CD scores. LYRM4 is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters, essential cofactors in multiple processes, including oxidative phosphorylation. LYRM4 downregulation may be one of the mechanisms involved in inefficient oxidative phosphorylation and oxidative stress, increasingly recognised as contributors to schizophrenia pathogenesis.

DNA Dynamics Is Likely to Be a Factor in the Genomic Nucleotide Repeats Expansions Related to Diseases

Trinucleotide repeats sequences (TRS) represent a common type of genomic DNA motif whose expansion is associated with a large number of human diseases. The driving molecular mechanisms of the TRS ongoing dynamic expansion across generations and within tissues and its influence on genomic DNA functions are not well understood. Here we report results for a novel and notable collective breathing behavior of genomic DNA of tandem TRS, leading to propensity for large local DNA transient openings at physiological temperature. Our Langevin molecular dynamics (LMD) and Markov Chain Monte Carlo (MCMC) simulations demonstrate that the patterns of openings of various TRSs depend specifically on their length. The collective propensity for DNA strand separation of repeated sequences serves as a precursor for outsized intermediate bubble states independently of the G/C-content. We report that repeats have the potential to interfere with the binding of transcription factors to their consensus sequence by altered DNA breathing dynamics in proximity of the binding sites. These observations might influence ongoing attempts to use LMD and MCMC simulations for TRS–related modeling of genomic DNA functionality in elucidating the common denominators of the dynamic TRS expansion mutation with potential therapeutic applications.

DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals

We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landscape. We suggest several probability distribution functions that characterize the breathing process, and adopt the recently studied backward Fokker-Planck method and the path decomposition method as elegant and flexible tools for deriving these distributions. In particular, for a bubble of an initial size x₀, we derive analytical expressions for (i) the distribution P(t{f}|x₀) of the first-passage time t{f}, characterizing the bubble lifetime, (ii) the distribution P(A|x₀) of the area A until the first-passage time, providing information about the effective reactivity of the bubble to processes within the DNA, (iii) the distribution P(M) of the maximum bubble size M attained before the first-passage time, and (iv) the joint probability distribution P(M,t{m}) of the maximum bubble size M and the time t{m} of its occurrence before the first-passage time. These distributions are analyzed in the limit of small and large bubble sizes. We supplement our analytical predictions with direct numericalsimulations of the related Langevin equation, and obtain a very good agreement in the appropriate limits. The nontrivial scaling behavior of the various quantities analyzed here can, in principle, be explored experimentally.

Mammalian Stem Cells Reprogramming in Response to Terahertz Radiation

We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.