Biomedical subjects

Zhi-Jie Tan

Publications and source records attributed to Zhi-Jie Tan.

11 recordsLinked to original sources

PubMed2026

Multivalent cations stabilize DNA duplexes beyond charge neutralization.

Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA-protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 k B T/bp for Na+ and increased to 3.98 k B T/bp for protamine, which is a small arginine-rich protein with a highly positive charge (≈21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.

Journal Article↗

PubMed2006

Electrostatic free energy landscapes for nucleic acid helix assembly.

Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na+ and Mg2+ play distinctive roles in helix-helix assembly. High [Na+] (>0.3 M) causes a reduced helix-helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix-helix attraction and results in a more compact and ordered helix-helix packing. Mg2+ is much more efficient in causing nucleic acid compaction. In addition, the free energy landscape shows that the tethering loops between the helices also play a significant role. A flexible loop, such as a neutral loop or a polynucleotide loop in high salt concentration, enhances the close approach of the helices in order to gain the loop entropy. On the other hand, a rigid loop, such as a polynucleotide loop in low salt concentration, tends to de-compact the helices. Therefore, a polynucleotide loop significantly enhances the sharpness of the ion-induced compaction transition. Moreover, we find that a larger number of helices in the system or a smaller radius of the divalent ions can cause a more abrupt compaction transition and a more compact state at high ion concentration, and the ion size effect becomes more pronounced as the number of helices is increased.

DNA↗

PubMed2006

Ion-mediated nucleic acid helix-helix interactions.

Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an interhelix distance approximately 26-36 A, and the strength of the attractive force can reach -0.37 k(B)T/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.

Computer Simulation↗

PubMed2005

Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length.

Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg2+) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.

DNA↗

PubMed2005

Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte.

A statistical mechanical model is presented which explicitly accounts for the fluctuations, the electrostatic, and the excluded volume correlations for ions bound to a polyelectrolyte such as DNA. The method can be employed to treat a wide range of ionic conditions including multivalent ions. The microscopic framework of the theory permits the use of realistic finite length and grooved structural model for the polyelectrolyte and modeling of the finite size of the bound ions. Test against Monte Carlo simulations suggests that the theory can give accurate predictions for the ion distribution and the thermodynamic properties. For multivalent ions, the theory makes improved predictions as compared with the mean-field approach. Moreover, for long polyelectrolyte and dilute salt concentration, the theory predicts ion binding properties that agree with the counterion condensation theory.

Biophysics↗

PubMed2004

Particle-cluster aggregation on a small-world network.

To describe the aggregation behaviors on substrates with long-range jump paths, a model of particle-cluster aggregation on a two-dimensional small-world network is presented. This model is characterized by two parameters: the clustering exponent alpha and the long-range connection rate phi. The results show that there exists an asymptotic fractal dimension D(max)(f) that depends upon alpha. With decrement of alpha, D(max)(f) varies from 1.7 to 2.0, which corresponds to a crossover from diffusion-limited-aggregation-like to dense growth. The change of the aggregation pattern results from the long-range connection in the network, which reduces the effect of screening during the aggregation. When the system size is not large enough, the effective fractal dimension D(f) depends upon phi because of the finite-size effect. With primitive analysis, we obtain the expression of the effective fractal dimension D(f) with the network parameters alpha and phi.

Journal Article↗

PubMed2003

Critical behavior of efficiency dynamics in small-world networks.

Some dynamical processes in a small-world network shows a critical transition at a finite disorder phi(c) of the network, in contrast with the geometrical properties that exhibit the critical behavior at phi(c)=0. Although it has been pointed out in previous works that the transition is related to the structural properties of the network, it is still not very clear why the transition occurs at phi(c) not equal 0. In this paper we present a simple social model of efficiency dynamics in small-world networks, which also shows a transition at phi(c)>0. We obtain the critical point with phi(c) approximately equal 0.098 from the finite-size analysis. It is found that both the geometrical properties of the network and the specific dynamical characters of the model contribute to the critical transition. This work is useful for understanding this kind of transition occurring in many dynamical processes in small-world networks.

Journal Article↗

PubMed2003

Network-induced nonequilibrium phase transition in the "game of Life".

A cellular automation model of the "game of Life" on a two-dimensional small-world network is presented in order to count in long-range interactions among living individuals in social or biological systems. The density of the life and its fluctuation are calculated, respectively. The present model exhibits a nonequilibrium phase transition from an "inactive-sparse" state to an "active-dense" one at a certain intermediate value of the network disorder. Employing finite-size scaling analysis, we estimate the location of the critical point with p(c)( infinity ) approximately 0.3685. The transition is of the "second-order" type with power-law diverging length. We obtain the critical exponents 1/nu approximately 1.70, beta approximately 0.50, and beta/nu approximately 0.85. The calculated results indicate that the present model may belong to the universality class of directed percolation.

Journal Article↗

PubMed2002

Patterns of particle distribution in multiparticle systems by random walks with memory enhancement and decay.

We investigate the pattern of particle distribution and its evolution with time in multiparticle systems using the model of random walks with memory enhancement and decay. This model describes some biological intelligent walks. With decrease in the memory decay exponent alpha, the distribution of particles changes from a random dispersive pattern to a locally dense one, and then returns to the random one. Correspondingly, the fractal dimension D(f,p) characterizing the distribution of particle positions increases from a low value to a maximum and then decreases to the low one again. This is determined by the degree of overlap of regions consisting of sites with remanent information. The second moment of the density rho(2) was introduced to investigate the inhomogeneity of the particle distribution. The dependence of rho(2) on alpha is similar to that of D(f,p) on alpha. rho(2) increases with time as a power law in the process of adjusting the particle distribution, and then rho(2) tends to a stable equilibrium value.

Journal Article↗

PubMed2002

Pattern formation on nonuniform surfaces by correlated random sequential absorptions.

The pattern formation on nonuniform surfaces by correlated-random sequential absorption (CRSA) process has been investigated by computer simulations. The nonuniform surfaces are represented by percolation clusters with probabilities p(s) and p(s) stands for the nonuniform degree of surfaces. The interactions between the particles and the defects in surfaces are involved by introducing a sticking coefficient s. When s-->0, the CRSA process is controlled by the absorption of surfaces and the correlation between particles. With the correlation increasing from a weak limit to a strong one, the cluster consisting of absorbed particles changes from the dispersed pattern of site percolation to correlated percolation, and then to Leath percolation clusters. When s-->1 and p(s)-->p(c), the CRSA process is dominated by the absorption of the defects, where p(c) is the threshold of percolations. The patterns appear randomly dispersed in spite of the correlation. With the decrease of s and increase of p(s), the interaction controlling the CRSA process changes from the absorption of defects to that of surface and the correlation between particles gradually. For the system s-->0, the transition correlation exponent alpha(c)=d(s), where d(s) is the fractal dimension of the percolation surfaces.

Journal Article↗

PubMed2002

Random walk with memory enhancement and decay.

A model of random walk with memory enhancement and decay was presented on the basis of the characteristics of the biological intelligent walks. In this model, the movement of the walker is determined by the difference between the remaining information at the jumping-out site and jumping-in site. The amount of the memory information s(i)(t) at a site i is enhanced with the increment of visiting times to that site, and decays with time t by the rate e(-beta(t)), where beta is the memory decay exponent. When beta=0, there exists a transition from Brownian motion (BM) to the compact growth of walking trajectory with the density of information energy u increasing. But for beta>0, this transition does not appear and the walk with memory enhancement and decay can be considered as the BM of the mass center of the cluster composed of remembered sites in the late stage.

Animals↗