Visualizing the higher order folding of a catalytic RNA molecule

The higher order folding process of the catalytic RNA derived from the self-splicing intron of Tetrahymena thermophila was monitored with the use of Fe(II)-EDTA-induced free radical chemistry. The overall tertiary structure of the RNA molecule forms cooperatively with the uptake of at least three magnesium ions. Local folding transitions display different metal ion dependencies, suggesting that the RNA tertiary structure assembles through a specific folding intermediate before the catalytic core is formed. Enzymatic activity, assayed with an RNA substrate that is complementary to the catalytic RNA active site, coincides with the cooperative structural transition. The higher order RNA foldings produced by Mg(II), Ca(II), and Sr(II) are similar; however, only the Mg(II)-stabilized RNA is catalytically active. Thus, these results directly demonstrate that divalent metal ions participate in general folding of the ribozyme tertiary structure, and further indicate a more specific involvement of Mg(II) in catalysis.     

SELEX技术筛选毒死蜱单链DNA适体

试验旨在利用SELEX技术体外筛选毒死蜱的特异性适体。体外合成全长为91 nt的ssDNA文库,以链亲和素修饰的凝胶为载体、毒死蜱为靶分子进行SELEX(配体指数增强系统进化技术)筛选。利用荧光标记法测定适体的筛选效率、亲和力和特异性,通过MFOLD分析软件对亲和力较高的适体进行二级结构预测和结合位点分析。结果表明,经过15轮筛选后,DNA文库的筛选效率达到44.00%;最终获得9条ssDNA适体,其中适体N23对毒死蜱具有最高的亲和力,其结合活性显著高于N23与水胺硫磷、丙溴磷、氧化乐果的结合活性;二级结构表明茎环结构可能是毒死蜱与适体相互作用的结构基础。     

In vitro Selection of DNA Aptamers and Fluorescence-Based Recognition for Rapid Detection Listeria monocytogenes

Aptamers are specific nucleic acid sequences that can bind to a wide range of nucleic acid and non-nucleic acid targets with high affinity and specificity. Nucleic acid aptamers are selected in vitro from single stranded DNA or RNA ligands containing random sequences of up to a few hundred nucleotides. Systematic evolution of ligands by exponential enrichment (SELEX) was used to select and PCR amplify DNA sequences (aptamers) capable of binding to and detecting Listeria monocytogenes, one of the major food-borne pathogens. A simplified affinity separation approach was employed, in which L. monocytogenes in exponential (log) phase of growth was used as the separation target. A fluorescently-labeled aptamer assay scheme was devised for detecting L. monocytogenes. This report described a novel approach to the detection of L. monocytogenes using DNA aptamers. Aptamers were developed by nine rounds of SELEX. A high affinity aptamer was successfully selected from the initial random DNA pool, and its secondary structure was also investigated. One of aptamers named e01 with the highest affinity was further tested in aptamer-peroxidase and aptamer-fluorescence staining protocols. This study has proved the principle that the whole-cell SELEX could be a promising technique to design aptamer-based molecular probes for dectection of pathogenic microorganisms without tedious isolation and purification of complex markers or targets.     

RNA structure: reading the ribosome

The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.     

溶藻弧菌适配子亲和力测定条件的优化及其特异性研究

[目的]优化溶藻弧菌适配子亲和力的测定条件,并验证适配子的亲和特异性。[方法]采用地高辛-过氧化物酶显色系统,通过正交试验确定亲和力测定的适宜条件,并在该条件下进行特异性验证。[结果]优化后亲和力的测定条件为：菌浓度3.0×10^8个/ml,结合时间40 min,结合温度28℃;经验证,该适配子对溶藻弧菌具有较高的亲和特异性。[结论]获得了溶藻弧菌适配子亲和力测定的优化条件,并证明了该适配子与溶藻弧菌具有较好的亲和特异性,为溶藻弧菌的SELEX筛选及其快速检测提供了参考。     

适配体的研究进程与思考

适配体（aptamer）是指利用指数富集的配体系统进化（SELEX）技术，从人工合成的寡核苷酸文库中筛选获得的能够与靶分子特异结合的短单链DNA和RNA分子。筛选得到的适配体可以与DNA，RNA，蛋白质或其它靶分子结合，影响这些靶分子的性质，从而起到改变与靶分子相关的生物学功能的效果。而且研究发现，适配体在与靶分子相互作用时，不仅序列，它们所形成的三维结构也尤其重要。同时，适配体在生物医药研究方面显示出广阔的应用前景。介绍了适配体的发展历程，以及一些典型适配体的生物学功效。提出了RNA适配体三维结构在与靶分子进行相互作用时可能发挥重要作用，以期为RNA适配体的筛选提供理论思考。     

适配体的研究进程与思考*

 适配体（aptamer）是指利用指数富集的配体系统进化（SELEX）技术，从人工合成的寡核苷酸文库中筛选获得的能够与靶分子特异结合的短单链DNA和RNA分子。筛选得到的适配体可以与DNA，RNA，蛋白质或其它靶分子结合，影响这些靶分子的性质，从而起到改变与靶分子相关的生物学功能的效果。而且研究发现，适配体在与靶分子相互作用时，不仅序列，它们所形成的三维结构也尤其重要。同时，适配体在生物医药研究方面显示出广阔的应用前景。介绍了适配体的发展历程，以及一些典型适配体的生物学功效。提出了RNA适配体三维结构在与靶分子进行相互作用时可能发挥重要作用，以期为RNA适配体的筛选提供理论思考。     

Synthetic genetic polymers capable of heredity and evolution

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.     

Adaptive recognition by nucleic acid aptamers

Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined at high resolution for a number of aptamers in complex with their cognate ligands. Structures of aptamer complexes reveal the key molecular interactions conferring specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity. These basic principles of discriminatory molecular interactions in aptamer complexes parallel recognition events central to many cellular processes involving nucleic acids.     

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA 's, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNA's.     

RNA二级结构预测及其在分子分类研究中的应用

文中通过比较RNA二级结构与一级结构和三维结构的差异,说明了RNA二级结构用于系统发育和分子分类研究的优点,并介绍了目前构建RNA二级结构的常用方法以及各种方法的优缺点,并对用于RNA二级结构折叠的软件作了简单介绍。最后从4个方面详细阐述了RNA二级结构在分子分类研究中的应用,即:RNA二级结构应用于分子分类研究的理论和方法;应用RNA二级结构分类与形态分类的区别;三种RNA二级结构在分子分类中的研究现状;RNA二级结构对序列信息的校正与补充。     

Biochemical basis of oxidative protein folding in the endoplasmic reticulum

The endoplasmic reticulum (ER) supports disulfide bond formation by a poorly understood mechanism requiring protein disulfide isomerase (PDI) and ERO1. In yeast, Ero1p-mediated oxidative folding was shown to depend on cellular flavin adenine dinucleotide (FAD) levels but not on ubiquinone or heme, and Ero1p was shown to be a FAD-binding protein. We reconstituted efficient oxidative folding in vitro using FAD, PDI, and Ero1p. Disulfide formation proceeded by direct delivery of oxidizing equivalents from Ero1p to folding substrates via PDI. This kinetic shuttling of oxidizing equivalents could allow the ER to support rapid disulfide formation while maintaining the ability to reduce and rearrange incorrect disulfide bonds.     

核酸适配体生物传感技术在沙门氏菌定量检测中的应用

沙门氏菌是一种重要的人畜共患病病原菌,在世界各地的食物中毒中,该菌引起的中毒事件数量位居前列。目前,基于抗原/抗体、核酸适配体、细胞等传感元件的生物传感技术已被广泛应用于沙门氏菌的定量检测中。其中,核酸适配体是一种短的核酸序列,具有特异性强、亲和力高、合成速度快、重现性好、修饰方便等优点。核酸适配体的这些优点可能会取代抗体,成为分析领域中的潜在识别探针。因此,核酸适配体生物传感技术在沙门氏菌定量检测中具有独特优势。主要综述了核酸适配体生物传感技术在沙门氏菌定量检测中的应用研究。首先对沙门氏菌及其常用检测方法进行简单介绍,其次介绍沙门氏菌核酸适配体的SELEX筛选方法,重点对基于核酸适配体的比色、荧光、表面增强拉曼散射(SERS)、电化学等生物传感技术在沙门氏菌定量检测中的应用进行详细论述,最后对核酸适配体生物传感技术应用于沙门氏菌定量检测的发展前景进行展望。     

Mutants of bovine pancreatic trypsin inhibitor lacking cysteines 14 and 38 can fold properly

It is a generally accepted principle of biology that a protein's primary sequence is the main determinant of its tertiary structure. However, the mechanism by which a protein proceeds from an unfolded, disordered state to a folded, relatively well-ordered, native conformation is obscure. Studies have been initiated to examine the "genetics" of protein folding, with mutants of bovine pancreatic trypsin inhibitor (BPTI) being used to explore the nature of the specific intramolecular interactions that direct this process. Previous work with BPTI chemically modified at cysteines 14 and 38 indicated that transient disulfide bond formation by these residues contributed to efficient folding at 25 degrees C. In the present work, mutants of BPTI in which these cysteines were replaced by alanines or threonines were made and the mutant proteins were produced by a heterologous Escherichia coli expression system. At 25 degrees C in vitro, the refolding behavior of these mutants was characterized by a pronounced lag. However, when expressed at 37 degrees C in E. coli, or when refolded at 37 degrees or 52 degrees C in vitro, the mutant proteins folded readily into the native conformation, albeit at a rate somewhat slower than that exhibited by wild-type BPTI. These results indicate that, at physiological temperatures, BPTI lacking cysteines 14 and 38 can refold quantitatively.     

Direct observation of chaperone-induced changes in a protein folding pathway

How chaperone interactions affect protein folding pathways is a central problem in biology. With the use of optical tweezers and all-atom molecular dynamics simulations, we studied the effect of chaperone SecB on the folding and unfolding pathways of maltose binding protein (MBP) at the single-molecule level. In the absence of SecB, we find that the MBP polypeptide first collapses into a molten globulelike compacted state and then folds into a stable core structure onto which several alpha helices are finally wrapped. Interactions with SecB completely prevent stable tertiary contacts in the core structure but have no detectable effect on the folding of the external alpha helices. It appears that SecB only binds to the extended or molten globulelike structure and retains MBP in this latter state. Thus during MBP translocation, no energy is required to disrupt stable tertiary interactions.     

The ribosome modulates nascent protein folding

Proteins are synthesized by the ribosome and generally must fold to become functionally active. Although it is commonly assumed that the ribosome affects the folding process, this idea has been extremely difficult to demonstrate. We have developed an experimental system to investigate the folding of single ribosome-bound stalled nascent polypeptides with optical tweezers. In T4 lysozyme, synthesized in a reconstituted in vitro translation system, the ribosome slows the formation of stable tertiary interactions and the attainment of the native state relative to the free protein. Incomplete T4 lysozyme polypeptides misfold and aggregate when free in solution, but they remain folding-competent near the ribosomal surface. Altogether, our results suggest that the ribosome not only decodes the genetic information and synthesizes polypeptides, but also promotes efficient de novo attainment of the native state.     

A single-molecule study of RNA catalysis and folding

Using fluorescence microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules. The dye-labeled and surface-immobilized ribozymes used were shown to be functionally indistinguishable from the unmodified free ribozyme in solution. A reversible local folding step in which a duplex docks and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing the determination of the rate constants and characterization of the transition state. A rarely populated docked state, not measurable by ensemble methods, was observed. In the overall folding process, intermediate folding states and multiple folding pathways were observed. In addition to observing previously established folding pathways, a pathway with an observed folding rate constant of 1 per second was discovered. These results establish single-molecule fluorescence as a powerful tool for examining RNA folding.     

Reformation of functional liver polyribosomes from ribosome monomers in the absence of RNA synthesis

The administration to rats of the ethyl analog of methionine, ethionine, results in the rapid decrease in the hepatic concentration of adenosine triphosphate followed by an extensive disaggregation of polysomes to ribosome monomers and a concomitant inhibition of protein synthesis. These effects are readily reversed by the injection of methionine or precursors of adenine nucleotides such as adenine. The reformation of liver polyribosomes in such animals following the administration of adenine plus methionine was found to occur under conditions in which new RNA synthesis was markedly inhibited. Free messenger RNA without attached ribosomes must be capable of remaining functionally active in the liver cytoplasm for many hours.     

RNA mimics of green fluorescent protein

Green fluorescent protein (GFP) and its derivatives have transformed the use and analysis of proteins for diverse applications. Like proteins, RNA has complex roles in cellular function and is increasingly used for various applications, but a comparable approach for fluorescently tagging RNA is lacking. Here, we describe the generation of RNA aptamers that bind fluorophores resembling the fluorophore in GFP. These RNA-fluorophore complexes create a palette that spans the visible spectrum. An RNA-fluorophore complex, termed Spinach, resembles enhanced GFP and emits a green fluorescence comparable in brightness with fluorescent proteins. Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs.     

The structural basis of ribozyme-catalyzed RNA assembly

Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.