Study of DNA accessibility in the condensed chromatin structures by resonance energy transfer

The linker DNA accessibility of chicken erythrocyte chromatin was studied by diffusion-enhanced resonance energy transfer (DERET). The 4″-{9?-[((4-carboxy-3-hydroxyphenyl)-acetatamido)-3?,6?,9?-(triacetyl)-3″,6?,9?-triazanonamido]-2″,6″-diazanonyl}-4,5′,8-trimethyl psoralen-terbium complex was photocovalently bound to linker DNA and transferred its energy to fluorescein free in solution or bound on proteins of different sizes. We observed a diminution of linker DNA accessibility in chromatin as the protein size increased. Free fluorescein and proteins (up to a molecular weight of 24,000) labeled with fluorescein isothiocyanate (FITC) showed no variation in linker accessibility as chromatin condensation from 10- to 30-nm fibers was induced by an increase in ionic strength. We can conclude from these observations that linker DNA is located on the outside of the condensed chromatin fiber or, alternatively, that small proteins are free to diffuse toward an inside-located linker DNA, even in the condensed state of chromatin, possibly through the central cavity of the solenoïd model.     

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.     

Force-extension behavior of folding polymers

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy ε associated with maintaining the folded state is comparable to k _B T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA. Received 7 August 2002 and Received in final form 7 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: jmarko@uic.edu     

Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder

The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start reviewing recent results obtained when exploring the scaling properties of eucaryotic, eubacterial and archaeal genomic sequences using the space-scale decomposition provided by the wavelet transform (WT). These results suggest that the existence of LRC up to distances ∼ 20-30kbp is the signature of the nucleosomal structure and dynamics of the chromatin fiber. Actually the LRC are mainly observed in the DNA bending profiles obtained when using some structural coding of the DNA sequences that accounts for the fluctuations of the local double-helix curvature within the nucleosome complex. Because of the approximate planarity of nucleosomal DNA loops, we then study the influence of the LRC structural disorder on the thermodynamical properties of 2D elastic chains submitted locally to mechanical/topological constraint as loops. The equilibrium properties of the one-loop system are derived numerically and analytically in the quite realistic weak-disorder limit. The LRC are shown to favor the spontaneous formation of small loops, the larger the LRC, the smaller the size of the loop. We further investigate the dynamical behavior of such a loop using the mean first passage time (MFPT) formalism. We show that the typical short-time loop dynamics is superdiffusive in the presence of LRC. For displacements larger than the loop size, we use large-deviation theory to derive a LRC-dependent anomalous-diffusion rule that accounts for the lack of disorder self-averaging. Potential biological implications on DNA loops involved in nucleosome positioning and dynamics in eucaryotic chromatin are discussed.     

DNA spools under tension

DNA spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core, are ubiquitous in nature. We develop a general theory describing the nonequilibrium behavior of DNA spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension, are theoretically explained and shown to be of the same origin. The study provides new insights into nucleosome and chromatin fiber stability and dynamics.     

Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure

Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures (Felsenfeld and Groudine in Nature 421:448, 2003). Each nucleosome, the fundamental unit of chromatin, has 147 base pairs (bp) of DNA wrapped around a histone octamer (Richmond and Davey in Nature 423:145, 2003). In order to describe how chromatin fiber formation affects nucleosome positioning and energetics, we have developed a thermodynamic model of finite-size particles with effective nearest-neighbor interactions and arbitrary DNA-binding energies. We show that both one- and two-body interactions can be extracted from one-particle density profiles based on high-throughput maps of in vitro or in vivo nucleosome positions. Although a simpler approach that neglects two-body interactions (even if they are in fact present in the system) can be used to predict sequence determinants of nucleosome positions, the full theory is required to disentangle one- and two-body effects. Finally, we construct a minimal model in which nucleosomes are positioned primarily by steric exclusion and two-body interactions rather than intrinsic histone-DNA sequence preferences. The model reproduces nucleosome occupancy patterns observed over transcribed regions in living cells.     

Salt-modulated structure of polyelectrolyte-macroion complex fibers

The structure and stability of strongly charged complex fibers, formed by complexation of a single long semi-flexible polyelectrolyte chain and many oppositely charged spherical macroions, are investigated numerically at the ground-state level using a chain-sphere cell model. The model takes into account chain elasticity as well as electrostatic interactions between charged spheres and chain segments. Using a numerical optimization method based on a periodically repeated unit cell, we obtain fiber configurations that minimize the total energy. The optimal fiber configurations exhibit a variety of helical structures for the arrangement of macroions including zig-zag, solenoidal and beads-on-a-string patterns. These structures result from the competition between attraction between spheres and the polyelectrolyte chain (which favors chain wrapping around the spheres), chain bending rigidity and electrostatic repulsion between chain segments (which favor unwrapping of the chain), and the interactions between neighboring sphere-chain complexes which can be attractive or repulsive depending on the system parameters such as salt concentration, macroion charge and chain length per macroion (linker size). At about physiological salt concentration, dense zig-zag patterns are found to be energetically most stable when parameters appropriate for the DNA-histone system in the chromatin fiber are adopted. In fact, the predicted fiber diameter in this regime is found to be around 30 nanometers, which roughly agrees with the thickness observed in in vitro experiments on chromatin. We also find a macroion (histone) density of 5–6 per 11nm which agrees with results from the zig-zag or cross-linker models of chromatin. Since our study deals primarily with a generic chain-sphere model, these findings suggest that structures similar to those found for chromatin should also be observable for polyelectrolyte-macroion complexes formed in solutions of DNA and synthetic nano-colloids of opposite charge. In the ensemble where the mean linear density of spheres on the chain is fixed, the present model predicts a phase separation at intermediate salt concentrations into a densely packed complex phase and a dilute phase.     

Diffusion-enhanced resonance energy transfer shows that linker-DNA accessibility decreases during salt-induced chromatin condensation

Accessibility of linker-DNA chromatin during salt-induced condensation of chicken erythrocytes chromatin was studied by diffusion-enhanced resonance energy transfer. A terbium complex was covalently bound to linker-DNA and fluorescein molecules bound to latex particles with diameters ranging from 14 to 2470 nm were used as acceptor. The accessibility of linker-DNA to molecules with a diameter superior to 14 nm diminished during condensation, but for an acceptor diameter of 14 nm or less, no accessibility variation was observed. It can be concluded that (1) linker-DNA is located inside the fiber when chromatin is in the condensed state, (2) chromatin condensation can prevent the approach to DNA due to steric hindrance, (3) salt-induced chromatin condensation is a gradual process, and (4) condensed chromatin models containing a central cavity are more likely.Abbreviations DTPA diethylene tetramine pentacetic acid - FDL-DERET fast diffusion limit of diffusion-enhanced resonance energy transfer - Pso-Tb psoralen-terbium complex - PAS paraamino salicylic acid - TREF time-resolved emission of fluorescence     

Non-equilibrium physical systems approach to modeling evolution of optical fiber reliability

We propose a new approach, based on physics of non-equilibrium systems, to modeling optical fiber reliability. Unlike the traditional approach to statistical modeling of fracture, the presented one describes the phenomenon in terms of its dynamics and links the thermal-fluctuation damage events with the corresponding strength deterioration, thereby establishing an evolution equation of the time-dependent strength distribution. The developed model is validated by both simulations and experimental data.     

用单分子技术研究Sso7d与DNA的相互作用

为了维持基因的稳定性,每种生物体都含有一套独特的染色质蛋白来保护脱氧核糖核酸(DNA)的结构,观察染色质蛋白对DNA结构的作用过程和结果,可以帮助人们了解这些蛋白的具体功能和作用机理.硫化叶菌是一种能在高温下存活的古细菌,Sso7d是硫化叶菌的一种染色质蛋白.深入地了解Sso7d和DNA链的相互作用,有助于解释硫化叶菌的DNA为何能在高温环境下保持活性,本文通过原子力显微镜(AFM)和磁镊两种单分子操作手段,研究了Sso7d与DNA的相互作用.AFM的实验结果给出了Sso7d与DNA的作用过程:结合Sso7d后,DNA首先发生弯折,然后出现loop结构,最终DNA会团聚为致密的核结构.利用磁镊装置测量了Sso7d的结合对打开DNA双链的影响,实验结果表明Sso7d的结合导致打开DNA双链的力的增大,经过数据分析,计算出Sso7d与DNA结合的结合能?G=3.1k_BT,平均每5.5个碱基对(bp)结合一个Sso7d,较高的结合密度和较大的结合能,两方面的作用结果,解释了Sso7d能够稳定DNA结构的原因.     

Chromatin condensation and sensitivity of DNA in situ to denaturation during cell cycle and apoptosis--a confocal microscopy study

The goal of this study was to construct high resolution 3D confocal images of regions of condensed and extended chromatin in cell nuclei and individual chromosomes. It has been shown previously that sensitivity of DNA in situ to denaturation correlates with chromatin condensation and varies during cell cycle and apoptosis. Thus, detection of DNA which was partially denatured in situ provided a means to image areas of condensed chromatin. DNA denaturation was detected using a metachromatic dye acridine orange (AO) which differentially stains single stranded (ss) and double-stranded (ds) DNA sections. Early studies of denaturability of cellular DNA utilized flow cytometry and standard fluorescence microscopy. These techniques could not reveal small local differences in DNA denaturability within cell nucleus or in individual chromosomes. For instance, it was not possible to detect the initial points of chromosome condensation in G2-phase of the division cycle or in apoptosis. In order to achieve this goal we have recently extended these studies by applying confocal microscopy. We investigated DNA denaturability in normal human fibroblasts and HL-60 leukemic cells, at different stages of cell cycle and apoptosis. Following removal of RNA and partial denaturation of DNA with acid cells were stained with AO. Green (530 nm) and red (640 nm) fluorescence (exc. 457 nm) of non-denatured and denatured DNA was imaged by confocal microscopy. Blind deconvolution was used to further improve the quality of 3D images. Photobleaching of AO fluorescence was minimized and a correction for chromatic aberration and register shift was implemented. Nuclei of interphase cells exhibited predominantly green fluorescence representing AO binding to ds DNA. Punctuate areas of red fluorescence representing AO binding to denatured DNA and most likely associated with local regions of condensed chromatin were also present in all interphase nuclei. The proportion of denatured DNA increased in cells entering mitosis. In prophase individual condensing chromosomes exhibited varied proportions of green and red fluorescence indicating different content of denatured chromatin. In some chromosomes bands of denatured and denaturation-resistant chromatin were clearly resolved. In metaphase and anaphase chromosomes exhibited red fluorescence along all length of their arms indicating the highest and uniform susceptibility to denaturation. In telophase chromosomes contained predominantly denaturation-resistant DNA again and denaturated regions were significantly less abundant. At cytokinesis some decondensing chromosomes were still resolved. At this stage almost all regions of denatured DNA were located close to nuclear envelope. These regions may correspond to pockets of heterochromatin reforming at nuclear periphery. In early apoptosis condensation of chromatin appeared to commence in several distinct regions within nucleus. Some apoptotic bodies contained condensed chromatin surrounding central regions of extended chromatin. At late stages of apoptosis the whole volume of apoptotic bodies was occupied by condensed chromatin.     

Modeling and optimizing of high-concentration erbium-doped fiber amplifiers with consideration of ion-clusters

Starting from the modeling of isolated ions and ion-clusters, a closed form rate and power evolution equations for high-concentration erbium-doped fiber amplifiers are constructed. Based on the equations, the effects of the fraction of ion-clusters in total ions and the number of ions per cluster on the performance of high-concentration erbium-doped fiber amplifiers are analyzed numerically. The results show that the presence of the ion-clusters deteriorates amplifier performance, such as the signal power, signal gain, the threshold pump power for zero gain, saturated signal gain, and the maximum gain efficiency, etc. The optimum fiber length or other parameters should be modified with the ion-clusters being taken into account for the amplifiers to achieve a better performance.     

Self-stabilizing additive-pulse mode-locking due to thermo-optical non-linearity in an optical fiber

16 , 1671 (1991)] described a Nd:YLF APM laser which somehow automatically adjusted the relative resonator phase. We reproduce this behavior and analyse its origin. Thermal effects due to the light power guided in the fiber affect the effective fiber length, which in turn influences the phase and thus the power level; hence a closed servo loop results. We demonstrate this explanation to be correct in quantitative terms. Consequences arise for other systems involving fiber-optic loops or interferometers. Received: 7 April 1997/Revised version: 15 July 1997     

Polymer optical fiber SERS sensor with gold nanorods

A surface-enhanced Raman scattering sensor is developed by etching polymer optical fiber and coating with gold nanorods. The SERS sensing experiments are demonstrated with the analyte molecules of rhodamine 6G (R6G) at 514.5 nm laser excitation. The results show that a strong fiber Raman background scattering overwhelm the R6G molecule Raman signal in common optrod configuration, but a distinct R6G SERS spectrum with 9 order magnitude enhancement can be observed while directly focusing light on the probe. Further modeling indicates the enhancement is attributed to both nanorods local field and their coupling.     

On the behaviour of dispersion-managed soliton from the perspective of its energy components

We investigate the behaviour of dispersion-managed (DM) soliton from its energy. Using the variational analysis, it is possible to represent the energy of the DM soliton as a combination of three components, respectively, one component for the average dispersion of the optical fiber, second component for the local dispersion of the dispersion map and the third component for the Hamiltonian of the anomalous fiber section. From the results of the numerical simulations, we show that the Hamiltonian component of the DM soliton energy plays a vital role in the determination of its stability.     

The moment method for fiber Raman amplifier gain ripple minimization

We aim to propose a novel fiber Raman amplifier modeling based on the moment method, which is previously introduced for modeling the inhomogeneous Erbium doped fiber amplifiers and recently employed to analyze the fiber Raman amplifier with continuous pump spectrum. In this model, the number of governing equations is independent of the number of signals and according to the degree of accuracy it is proportional to the number of pumps. This method is employed to analyze the Raman fiber amplifiers with an arbitrary input signal line shape and to minimize the gain ripple of the fiber Raman amplifier with respect to the pump powers and pump frequencies.