Flexibility of nucleic acids: From DNA to RNA

The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid flexibility, extensive studies have been performed using various experimental methods and theoretical models. In this review, we will introduce the progress that has been made in understanding the flexibility of nucleic acids including DNAs and RNAs,and will emphasize the experimental findings and the effects of salt, temperature, and sequence. Finally, we will discuss the major unanswered questions in understanding the flexibility of nucleic acids.     

Ultrasonic wave propagation in metals in the hydrodynamic limit: Implications of including the bragg reflection force

We have included the Bragg reflection force, which is expressed in terms of the effective mass $\text{m}{}^1$ of an electron, in calculating the non-resonant changes in the velocity and attenuation of an ultrasonic wave propagating through a metal in the presence of an external magnetic field in the limit kl, ω_cτ ? 1. The results obtained show significantly different magnetic field dependence from that predicted under the free electron approximation. Our results also suggest a way of measuring the effective mass of an electron in a metal.     

Secondary structure of T2 intraphage DNA: a spectrophotometric study

Summary Relevant differences in the spectral properties (in the (230÷320) nm range) between intraphage and free T₂ DNA are reported in this work. These differences are very similar to the variation in absorption obtained for a native DNA solution when thepH is lowered starting from the neutral value. On this basis, cytosine protonation in intraphage DNA is hypothesized. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

A quantum-mechanical treatment of Szilard's engine: Implications for the entropy of information

We present a quantum-mechanical analysis of Szilard's famous single-molecule engine, showing that it is analogous to the double-slit experiment. We further show that the energy derived from the engine's operation is provided by the act of observing the molecule's location. The engine can be operated with no increase in physical entropy, and the second law of thermodynamics does not compel us to relate physical entropy to informational entropy. We conclude that information per seis a subjective, idealized, concept separated from the physical realm. Physical entropy depends on physical objects and physical interactions, and any entropy change owing to observations is entirely a result of the entropy created in the physical apparatus by the process of observation.     

强迫耗散系统的有序结构和系统的发展(Ⅰ)，最小熵产生原理和有序结构

一个系统的发展总是由不可逆热力过程和非线性动力过程所驱动.将大气动力学方程组同考虑了动能变化的Gibbs关系结合起来构建的熵平衡方程，才能更好地描述大气系统的不可逆热力过程和非线性动力过程.至今非平衡态热力学仅利用Onsager线性唯象关系证明了最小熵产生原理.利用新建立的熵平衡方程和大气动力学方程的性质证明，最小熵产生原理在热力学线性区和非线性区都是普遍成立的.且当热量输送平衡、水汽输送平衡和动量输送平衡时，系统达到不可逆过程最弱的最小熵产生热力学状态.当系统又是动力平衡且无平流时，这种最小熵产生态就是 关键词： 非线性热力学 熵产生 最小熵产生原理 有序结构     

Characterization of DNA chips on the molecular scale before and after hybridization with an atomic force microscope

Using two different 25-mer oligonucleotide probes covalently grafted on a silicon substrate, we demonstrate how efficient atomic force microscopy (AFM) can be for monitoring each step of DNA chip preparation: from probe immobilization to hybridization on the molecular scale. We observed the probe-molecule organization on the chip after immobilization, and the target molecules, which hybridized with probes could be individually identified. This article presents a method of straightforwardly identifying not only single and double DNA strands, but also, and more significantly, the hybridized part on them.     

Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules

We obtain, using transfer-matrix methods, the distribution function P(R) of the end-to-end distance, the loop formation probability, and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of "bubbles," localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in P(R) and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.     

An atomic force microscopy study of DNA hairpin probes monolabelled with gold nanoparticle: Grafting and hybridization on oxide thin films

First and original results are reported regarding the surface evolution of two kinds of oxide film after covalent grafting and hybridization of hairpin oligonucleotide probes. These hairpin probes were monolabelled with a 1.4 nm gold nanoparticle. One kind of oxide film was rough Sb doped SnO₂ oxide film and the other kind was smooth SiO₂ film. Same process of covalent grafting, involving a silanization step, was performed on both oxide surfaces. Atomic force microscopy (AFM) was used to study the evolution of each oxide surface after different steps of the process: functionalization, probe grafting and hybridization. In the case of rough SnO₂ films, a slight decrease of the roughness was observed after each step whereas in the case of smooth SiO₂ films, a maximum of roughness was obtained after probe grafting. Step height measurements of grafted probes could be performed on SiO₂ leading to an apparent thickness of around 3.7 ± 1.0 nm. After hybridization, on the granular surface of SnO₂, by coupling AFM with SEM FEG analyses, dispersed and well-resolved groups of gold nanoparticles linked to DNA duplexes could be observed. Their density varied from 6.6 ± 0.3 × 10¹⁰ to 2.3 ± 0.3 × 10¹¹ dots cm⁻². On the contrary, on smooth SiO₂ surface, the DNA duplexes behave like a dense carpet of globular structures with a density of 2.9 ± 0.5 × 10¹¹ globular structures cm⁻².     

Persistency of single-stranded DNA: The interplay between base sequences and base stacking

The chain persistency of single-stranded (ss) DNA at a high-salt limit mainly arises from the so-called base-stacking interaction between consecutive bases along the strand. Stacking is appreciable for purine–purine (e.g., A–A) and purine–pyrimidine stacks (e.g., A–T), but it is weak for pyrimidine stacks (i.e., T–T, T–C, and C–C). We study how base stacking can stiffen the strand by classifying bases into two subclasses: stacking pairs (i.e., purine–purine and purine–pyrimidine) and non-stacking (i.e., pyrimidine–pyrimidine) pairs. With this simplification, we develop an exactly solvable model for calculating the stacking-induced persistence length ${\ell }_{\mathit{stack}}$ of heterogeneous ssDNA. It is shown that ${\ell }_{\mathit{stack}}$ is mainly determined by the occurrence rate of purines; intrinsic correlations in real DNA sequences barely influence ${\ell }_{\mathit{stack}}$. Our approach leads to a reasonable estimate of ${\ell }_{\mathit{stack}}\approx 2b$–$3b$ (under typical conditions), where b is the inter-base distance.     

Counterion-hopping along the backbone of single-stranded DNA in nanometer pores: a mechanism for current conduction

Molecular dynamics calculations are performed to investigate ionic current conduction through nanopores in the presence of single-stranded DNA. We find the counterions to be strongly attracted to the phosphate groups of the DNA, with resident time on the order of nanoseconds, while coions are strongly excluded. The diffusion constant of the counterions is calculated and used to estimate the ionic current through the pore, which gives a similar magnitude as in experiment. The results suggest a counterion-hopping mechanism along the ssDNA backbone in the current conduction through nanopores.     

Accelerator irradiations of minerals: Implications for track formation mechanisms and for studies of lunar and meteoritic materials

Abstract

Natural crystals of feldspars, pyroxenes, quartz and apatite have been irradiated in the Berkeley HILAC with neon and argon ions of up to 10.2 MeV/amu with maximum doses of 1.6 × 10¹³ argon ions/cm² and 4.0 × 10¹³ neon ions/cm² respectively. The samples were thinned to thicknesses near 30 microns, stacked to form the target and then bathed completely in the ion beams. X-ray and optical observations revealed: (a) a crystal distortion and curvature with the argon irradiation similar to that produced in mica; (b) a lesser effect from neon bombardment; (c) a fracturing of the crystal samples which depended on the total dose and energy of the incident ion; (d) polygonized structures produced when either neon or argon ions (with sufficiently high concentration) were trapped within the crystals. The interpretation of the measurements, their correlation with the mechanism of track formation and implications concerning the alteration of the lunar surface due to solar particles and the exposure of lunar and meteoritic material in the ancient solar flare cosmic rays are discussed.     

Electron and atomic structure of polymers: Implication for nuclear tracks formation

A review of experimental and theoretical activities in a study of an electron and atomic structure of polymers is presented. Polymers having conjugated π-electron systems were studied experimentally in different aggregate states within the temperature interval 4.2– 300 K using spectrophotometric and spectroluminescence methods. Special attention has been paid to oxidization processes in polymers caused by ionizing radiation. The theoretical approach developed in Ukraine for electron and atomic structure calculations is based on the theory of multiple scattering of elementary excitations (electrons and phonons). This approach provides a possibility to estimate energy spectra of elementary excitations, parameters of interatomic correlations, electron density distributions, absorption and emission (photoluminescence) spectra. Study of the fluorescence spectra provides a possibility to estimate the electron structure as well as the local characteristics of latent tracks induced by nuclear particles. Dependencies of the shape of photoluminescence bands can be investigated experimentally for different kinds of nuclear particles within a wide energy range. Application of combined experimental and theoretical approach of investigation of solid-state nuclear track detector (SSNTD) physical properties, and determination of nuclear particle characteristics (charge, atomic number, etc.) are discussed.     

Mesoscopic models for DNA stretching under force: New results and comparison with experiments

We investigate the dynamical behavior of simple networks, namely loops with an additional internal regulating connection. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a generalized method and within a single framework, we study different continuous models and different types of regulatory functions, and establish conditions under which the system can display stable oscillations or stable fixed points. These conditions depend only on general features such as the degree of cooperativity of the regulating interactions and the logical structure of the interactions. There are no simple rules for deciding when Boolean and continuous dynamics agree with each other, but we identify several relevant criteria.      

Accurate ab initio anharmonic force field and heat of formation for silane

From large basis set coupled cluster calculations and a minor empirical adjustment, an anharmonic force field for silane has been derived that is consistently of spectroscopic quality (±1 cm^?1 on vibrational fundamentals) for all isotopomers of silane studied. Inner-shell polarization functions have an appreciable effect on computed properties and even on anharmonic corrections. From large basis set coupled cluster calculations and extrapolations to the infinite-basis set limit, we obtain TAE₀ = 303.80 ± 0.18 kcal mol^?1, which includes an anharmonic zero-point energy (19.59 kcal mol^?1), inner-shell correlation (—0.36 kcal mol^?1), scalar relativistic corrections (— 0.70 kcal mol^?1) and atomic spin-orbit corrections (—0.43 kcal mol^?1). In combination with the recently revised ΔH ^o _{f, o}[Si(g)], we obtain ΔH ^o _f.o[SiH₄(g)] = 9.9 ± 0.4 kcal mol^?1 in between the two established experimental values.     

Molecular force field and structure of water: Recent microwave results

Recently, microwave studies of the rotational spectra of water and its various isotopic species have been reported. These studies provide rotational constants and among others the quartic distortion constants, which depend on the quadratic part of the vibrational potential function. These data are collected and discussed, and the molecular force field and structure of water is considered in light of this recent microwave data. The quartic distortion data gives force constants which are very reasonable considering the difficulties in the distortion analysis of these light molecules, where as many as 22 parameters are being evaluated to fit the observed spectrum. The infrared and microwave data are combined within the theoretical framework of the small oscillations model and the results compare favorably with the true harmonic force field. The infrared and microwave valence bond force constants of H₂O are (mdyn/Å):

$\text{?}{}_{\mathrm{r}}\text{=7.746, ?}{}_{\mathrm{\theta }}\text{=0.700, ?}{}_{\mathrm{rr}}\text{=?0.093, ?}{}_{\mathrm{r\theta }}\text{=0.379}$

The results further confirm the usefulness of rotation-vibration data in the determination of force constans, and show that even for water with extremely large anharmonicity effects, a very representative force field can be obtained by combining ground state infrared and microwave data.Various molecular structures have been evaluated, and the average structures in the ground vibrational state for H₂O, D₂O and T₂O are found to be:

$\text{〈r〉}\text{〈θ}\text{O-H=0.9724}\text{A}\text{?}\text{HOH=104.50°}\text{O-D=0.9687}\text{A}\text{?}\text{DOD=104.35°}\text{O-T=0.9671}\text{A}\text{?}\text{TOT=104.26°}$

A one-dimensional approximation to the anharmonicity effects is applied to determine the equilibrium molecular structure of H₂O from the average structure data. The result is as follows:

$\text{r}{}_{\mathrm{e}}\text{=0.9587}\text{A}\text{?}\text{and θ}{}_{\mathrm{e}}\text{=103.9°}$

     

Percolation in a network with long-range connections: Implications for cytoskeletal structure and function

Cell shape, signaling, and integrity depend on cytoskeletal organization. In this study we describe the cytoskeleton as a simple network of filamentary proteins (links) anchored by complex protein structures (nodes). The structure of this network is regulated by a distance-dependent probability of link formation as P=p/d^s, where p regulates the network density and s controls how fast the probability for link formation decays with node distance (d). It was previously shown that the regulation of the link lengths is crucial for the mechanical behavior of the cells. Here we examined the ability of the two-dimensional network to percolate (i.e. to have end-to-end connectivity), and found that the percolation threshold depends strongly on s. The system undergoes a transition around s=2. The percolation threshold of networks with s<2 decreases with increasing system size L, while the percolation threshold for networks with s>2 converges to a finite value. We speculate that s<2 may represent a condition in which cells can accommodate deformation while still preserving their mechanical integrity. Additionally, we measured the length distribution of F-actin filaments from publicly available images of a variety of cell types. In agreement with model predictions, cells originating from more deformable tissues show longer F-actin cytoskeletal filaments.