单分子技术研究T7解旋酶的解旋与换链

单分子荧光共振能量转移(smFRET)和磁镊(MT)技术目前广泛应用于研究分子马达.相较于常规技术,其具有高精度及动态观测的优点.本文研究对象为T7解旋酶,是六聚体解旋酶的典型代表.研究表明,这种解旋酶主要消耗脱氧胸苷三磷酸(dTTP)提供能量,且仅能沿着5′-3′单向进行行走和解旋工作.目前对于六聚体解旋酶的解旋和换链机制的认知仍然存在着诸多问题,因此本文主要以此作为切入点开展研究.首先通过运用smFRET技术研究T7解旋酶在不同DNA底物上的解旋现象,发现其需要3′-尾链参与到解旋工作中,但其为单链或双链结构并无明显区别;通过改变脱氧核糖核酸(DNA)序列中的GC含量,发现T7解旋酶随着序列中GC含量的升高会更容易在解旋过程中发生回退现象,导致解旋长度明显缩短;通过进一步分析发生回退先的实验数据,发现T7解旋酶除了可以瞬时回退到叉形DNA岔口或脱落外,还可以缓慢回退到叉形DNA岔口;运用MT技术研究该解旋酶,同样发现这种缓慢回退现象的存在.根据T7解旋酶解旋DNA遵循的单向性和极性,其只能沿着5′到3′方向进行行走和解旋.因此,本文推测这种缓慢回退的现象可能是解旋酶从5′-链转移至3′-链上,即发生换链过程;最后,本文提出了T7解旋酶在解旋过程中进行换链的模型,将有助于进一步理解环状六聚体解旋酶行使其功能的分子机制.     

An Insight into the Helicase Functioning Through the Hydrogen Isotope Effects

The replacement of hydrogen atoms by deuterium in hydrogen bonds of base pairs AT and GC decreases the rate of unwinding DNA by more than 30% per each unzipped base pair. In active helicases this isotope effect refers to the ratio of the rate constants for unzipping closed base pairs in protiated and deuterated DNA. In passive helicases the effect is controlled by ratio of equilibrium constants for opening and closing base pairs in protiated and deuterated DNA. Hydrogen/deuterium isotope effects on the unwindening of double strand DNA seems to explain, at least partly, biological and pharmacological effects of heavy water on living organisms and may be used as a means to explore new facets of the helicase functioning.     

A motor that makes its own track: helicase unwinding of DNA

We study the unwinding of DNA by helicase proteins as a representative system in which a motor protein interacts with a mobile obstacle. In our discrete model, the interaction between the helicase and the DNA fork is characterized by an interaction potential. For the case of a hard-wall potential, the helicase opens the DNA by rectifying thermal fluctuations which spontaneously open base pairs. A potential with nonzero range describes the destabilization of the double strand by the enzymatic action of the helicase. We derive solutions for the opening speed as a function of the potential shape and relate our results to experiments on helicase motion.     

Nucleic acid hydration: a volumetric perspective

Hydration represents a major force governing the conformational preferences and drug binding properties of nucleic acids. Volumetric measurements have proven useful in characterizing the hydration properties of nucleic acid structures and their complexes with other molecules. In this paper, we present an overview of recent developments in the field of volumetric investigations of nucleic acids. We discuss, in particular, the volumetric properties of nucleic acids, their molecular components and analogs, conformational transitions of DNA and RNA, and drug–DNA interactions. We emphasize the importance of hydration as a major contributor to the energetics of molecular recognition. We also emphasize the need of expanding the field of volumetric characterizations of nucleic acid structures in an effort to gain further insight into the molecular origins of various nucleic acid recognition processes, including helix-to-coil and helix-to-helix conformational transitions, as well as drug–DNA and protein–DNA interactions.     

全内反射瞬逝场照明高精度磁镊及其在DNA解旋酶研究中的应用

传统磁镊的测量精度受限于磁球的布朗涨落, 当磁力小于约10 pN时, 磁球的布朗涨落明显增大, 对应磁镊的空间分辨率显著下降. 为了提高传统磁镊在小力条件下的测量精度, 本文将全内反射荧光技术引入到磁镊技术中, 并建立相适应的“磁球-手柄-荧光微球-待测生物分子”单分子连接系统, 在小力条件下(小于10 pN)获得纳米量级的测量精度. 应用改进的磁镊对DNA发卡的折叠-去折叠态的转变过程进行了研究, 依据DNA发卡的折叠-去折叠态转变的性质对全内反射场的穿透深度进行了校正, 并结合实验结果对改进后的磁镊的测量精度进行分析. 观察了Bloom解旋酶的解旋动力学过程, 获得初步实验结果, 证实了改进的磁镊在单分子研究中的实用性. 关键词： 磁镊 全内反射荧光 DNA发卡 解旋酶     

Characterization of magnetic labels for bioassays

Magnetic nanoparticles differing by their size have been synthesized to use them for multiparametric testing, based on their differing magnetic properties. The nanoparticle has two essential roles: to act as a probe owing to its specific magnetic properties and to carry on its surface precursor groups for the covalent coupling of biological recognition molecules, such as antibodies, nucleic acids. A totally unique, newly patented, method has been used to characterize magnetic signatures using the MIAplex technology. The MIAplex reader, developed by Magnisense, measures the non-linear response of the magnetic labels when they are exposed to a multi-frequency alternating magnetic field. This specific signature based on d²B(H)/dH² was correlated to other more conventional magnetic detection methods (superconducting quantum interference devices (SQUID) and Mössbauer).     

Propidium Iodide and PicoGreen as Dyes for the DNA Fluorescence Correlation Spectroscopy Measurements

Many experimental designs, in which nucleic acid conformational changes are of interest, require reliable fluorescence labeling. The appropriate fluorescence probe should have suitable optical properties and, more importantly, should not interfere with the investigated processes. In order to avoid chemical modifications the fluorescence label needs to be associated with nucleic acid via weak non-covalent interactions. There are a number of fluorescent probes that change their fluorescent properties (i.e. their quantum yield and/or spectral characteristics) upon association with nucleic acid. Such probes are frequently used to detect, visualize and follow processes involving nucleic acid and its conformational changes. In order to obtain reliable data regarding macromolecule or aggregate topology a detailed knowledge of probe–nucleic acid interactions on the molecular level is needed. In this paper we show that the association of propidium iodide with DNA alters its conformation and that it selectively labels plasmid fragments and/or its subpopulations in a concentration-dependent meaner. Another dye, PicoGreen, exhibits better properties. It labels nucleic acid uniformly and without any concentration-dependent artifacts.     

核酸与有机小分子反应机理的荧光特性研究

核酸与有机小分子的反应机理对认识核酸的结构与功能具有重要作用,也是揭示核酸的生物功能与一些药物的作用机制的重要途径。研究核酸与有机小分子之间的相互作用对生命过程的模拟和生命本质的探索具有十分重要的意义,并对近年来该领域采用的荧光光谱法进行了综述,从温度、双分子猝灭过程的速率常数、荧光寿命以及吸收光谱的变化等方面作了论述,从而确定了核酸与有机小分子(染料和药物)之间相互作用的荧光猝灭类型;总结了结合常数、荧光给体-受体间的作用距离、作用力类型及结合方式的多种求算方法,并分别阐述了核酸与染料及药物在不同结合数下生成常数的计算方法。这对研究核酸与有机小分子之间的作用机理、开发新的核酸探针以及以核酸为靶标的药物分子的设计有一定的指导意义。     

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: Implications for DNA hybridization

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy —c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low-temperature/low-force compact (folded) structure and a high-temperature/high-force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c ≲ 2.479 a melting transition is possible; for c ≤ 2 the chain is always in the folded phase and for 2.479 ≲ c always in the unfolded phase. A force-induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single-molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double-stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ≈ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent [^(c)] \hat{{c}}, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.     

Preparation of cytocompatible luminescent and magnetic nanohybrids based on ZnO, Zn0.95Ni0.05O and core@shell ZnO@Fe2O3 polymer grafted nanoparticles for biomedical imaging

ZnO, Zn_0.95Ni_0.05O and core@shell ZnO@??-Fe₂O₃ nanoparticles (NPs) have been prepared by forced hydrolysis in polyol medium and then coated via the ??grafting from?? approach with poly(sodium-4-styrenesulfonate) and poly(sodium-4-styrenesulfonate?Cco?Csodium methacrylate) in the case of ZnO. The surface-initiated atom transfer radical polymerization occurred from the surface-functionalized NPs with ??-bromoisobutyric acid as initiator. The polymer chains were grown from the surface to yield hybrid NPs with a 1?C3-nm thick organic shell. FT-IR, TGA and electron microscopy evidenced the presence of a polymer layer on the surface of NPs. Magnetic and optical properties of bare and coated NPs have been measured. Eventually, the weak cytotoxicity of coated NPs on human endothelial cell allows considering their potentialities as new tools for nanomedicine and biomedical imaging.     

基于功能性核酸识别的荧光各向异性分析方法与应用

荧光各向异性方法又称荧光偏振法,基于相互作用的分子结合前后发射光退偏振的不同而实现对相互作用的研究或对目标物的检测。20世纪50年代Gregorio Weber用荧光各向异性法研究了氮磺酰氯与牛血清白蛋白和卵清白蛋白的作用,开启了该方法在生物化学研究中应用的先河。而20世纪90年代开始的功能性核酸(FNAs,包括核酸适配体和核酸酶等)的发现与合成,使基于功能性核酸的传感得到了广泛的应用。核酸适配体能够特异性识别目标分子,基于核酸识别的荧光各向异性分析方法具有高选择性、高灵敏度、高通量等优势,在研究蛋白质、核酸和小分子的相互作用中起到重要作用,然而如何提高结合前后的荧光各向异性信号变化,尤其是小分子识别前后,在基于功能性核酸识别的分析方法发展中是一个挑战。介绍了基于功能性核酸识别的荧光各向异性的方法应用于检测蛋白质、核酸及其他在生命活动中起重要作用的小分子的基本原理及设计理念。     

Effect of cooling conditions on the magnetic structure of multiferroic BiFeO3 synthesized by mechanical activation

We have studied the nuclear quadrupole interactions (NQI) of the ¹⁴N, ¹⁷O and ²H nuclei in the nucleobases cytosine, adenine, guanine and thymine in the free state as well as when they are bonded to the sugar ring in DNA, simulated through a CH₃ group attached to the nucleobases. The nucleobase uracil, which replaces thymine in RNA, has also been studied. Our results show that there are substantial indirect effects of the bonding with the sugar group in the nucleic acids on the NQI parameters e ² qQ/h and η. It is hoped that measurements of these NQI parameters in DNA will be available in the future to compare with our predictions. Our results provide the conclusion that for any property dependent on the electronic structures of the nucleic acids, the effects of the bonding between the nucleobases and the nucleic acid backbones have to be included.     

Electric-field-induced unwinding of ferroelectric helix in thin smectic C* layers with soft and rigid anchoring of molecules

The unwinding of a helical structure in thin films of a ferroelectric smectic liquid crystal (LC) by an external electric field has been theoretically studied using a discrete model in which every LC layer is characterized by a two-dimensional vector ξ _i (describing the orientation of molecules) and by the polarization P _i . It is established that the unwinding of the LC helix in thin films significantly differs from the well-known behavior of thick samples. In particular, discrete intermediate states (differing by an integer or half-integer number of turns) are formed in thin films for both weak and strong anchoring of molecules to a substrate surface. The physical factor responsible for this behavior is the presence of near-surface regions with thicknesses below the helix pitch and the corresponding uncompensated polarization.     

核酸功能化纳米探针在细胞荧光成像中的应用

核酸是携带遗传信息的物质,既存在于自然界中也能够通过成熟技术人工合成。通过体外筛选技术还可以筛选出具有特殊功能的核酸序列,例如核酸适体和脱氧核酶。核酸通过沃森-克里克碱基互补配对原则进行杂交,具有很强的专一性。无论是通过序列设计还是体外筛选,核酸探针在生物标志物的分析与成像应用方面都发挥着重要作用。纳米材料辅助构建核酸功能化纳米探针,可以保护负载的核酸探针不被核酸酶降解,并且无需转染试剂就能进入细胞,在细胞荧光成像应用上具有很大优势。为解决细胞内有些生物标志物含量低、难于检测的问题,目前已构建多种适用于细胞水平的成像信号放大方法来实现对低丰度生物标志物的高灵敏成像。本文主要综述了核酸功能化纳米探针在细胞荧光成像中的应用进展,包括反义寡核苷酸功能化纳米探针、核酸适体功能化纳米探针、脱氧核酶功能化纳米探针等,同时介绍了他们在成像信号放大中的应用。     

Interaction of nucleic acid segments as a result of modification of the network of hydrogen bonds of the solvent

It is shown that experimental results on the influence of various factors in the formation efficiency and structure of cholesteric liquid-crystal dispersions of nucleic acids cannot be consistently described using conventional theories of liquid crystal formation. A new model is proposed for the interaction of nucleic acid segments which allows for a change in the particular structure of the solvent hydrogen bonds in the presence of nucleic acid molecules. The conclusions of the model agree with existing spectroscopic and structural investigations of DNA dispersions. According to our model, interaction between nucleic acid molecules and solvent modifies proton tunneling processes in the latter, leading to effective interaction between the nucleic acids. A theoretical analysis of the model is made using a pseudospin formalism in which the effective interaction potential of the nucleic acid segments is calculated. It is shown that this potential may lead to nematic ordering for small distances between the nucleic acid molecules (R ≤ 30 Å) and cholesteric ordering for large distances.     

Human genetic deficits in glycan formation

Glycans are associated with most proteins found in secretions and on the surface of mammalian cells. Glycans of secreted glycoproteins affect many protein properties such as solubility, stability, protease sensitivity, and polarity, while glycans on cell surface glycoproteins are involved in various cellular functions including cell-cell and cell-matrix interactions during embryogenesis, immune reactions, and tumor development. Recent advances in human genomic research together with newly developed and sensitive methods for the analysis of glycan structures have elucidated the etiology of a growing number of human genetic diseases with aberrant glycan formation. Among these diseases, defects of protein N-glycosylation and O-mannosylation are reviewed here. The former is relatively common and the latter is rather uncommon. Both types of defects lead to severe abnormalities, which indicate the importance of glycosylation. Sequencing of the human genome is essentially complete and now glycobiology becomes an important area of postgenomic research. Glycobiology is expected to produce remarkable advances in the understanding and treatment of certain genetic diseases.     

Rare-earth-cation-induced change in the cholesteric twisting of neighboring nucleic acid molecules

Certain physicochemical characteristics of particles of the cholesteric liquid-crystal dispersions of complexes of double-stranded nucleic acids with rare earth elements have been determined. It is shown for the first time that the binding of the rare earth cations to linear nucleic acid molecules ordered in the structure of particles of the cholesteric liquid crystal dispersions is accompanied not only by amplification of the abnormal band in the circular dichroism spectrum, but also by the disappearance of the characteristic maximum on the X-ray scattering curves for small angles. The (cholesteric 1-cholesteric 2) transition induced by rare earth cations is an example of the operation of a microscopic machine consisting of spatially ordered nucleic acid molecules. Particles of the cholesteric liquid crystal dispersions of nucleic acid complexes with rare earth elements hold the abnormal optical properties for a long time.     

Sonolytic hydrolysis of peptides in aqueous solution upon addition of catechol

The sonolytic hydrolysis of peptides with addition of phenolic reagents to aqueous solutions is described. Sonolysis of an aqueous solution of peptides to which catechol (o-dihydroxybenzene) had been added resulted in hydrolytic products reflecting the amino acid sequence without any side reactions, while sonolysis without any additives resulted in oxidation analytes and degradation products caused by side reactions. Although the use of additives such as resorcinol (m-dihydroxybenzene), hydroquinone (p-dihydroxybenzene) and phenol was also effective in producing sequence related products, several degradation products were produced by side reactions. A characteristic of the sonolysis of peptides is that the N-terminal side of proline, Xxx-Pro, is more susceptible than other amino acid residues to the process. This characteristic of sonolysis is superior to that of acid hydrolysis in which cleavage at the C-terminal side of proline, Pro-Xxx is difficult, and where dehydration products result due to side reactions.     

One-pot green fabrication and antibacterial activity of thermally stable corn-like CNC/Ag nanocomposites

Corn-like cellulose nanocrystals/silver (CNC/Ag) nanocomposites were prepared by formic acid/hydrochloric acid hydrolysis of commercial microcrystalline cellulose (MCC), and redox reaction with silver ammonia aqueous solution (Ag(NH₃)₂(OH)) in one-pot green synthesis, in which the preparation and modification of CNCs were performed simultaneously and the resultant modified CNCs could be as reducing, stabilizing and supporting agents for silver nanoparticles. The influences of the Ag⁺ ion concentrations on the morphology, microstructure, and properties of the CNC/Ag nanocomposites were investigated. It is found that corn-like CNC/Ag nanocomposites containing Ag nanoparticles with diameter of about 20–40 nm were obtained. Compared to the MCCs, high crystallinity of 88.5 % and the maximum degradation temperature (T _max) of 364.5 °C can be achieved. Moreover, the CNC/Ag nanocomposites showed strong antibacterial activity against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Furthermore, such nanocomposites can act as bifunctional nanofillers to improve thermal stability, mechanical property, and antibacterial activity of commercial poly(3-hydroxybutyrate-co-3-hydroxyvalerate) and poly(lactic acid).