Synthetic hosts by monomolecular imprinting inside dendrimers

Synthetic host systems capable of selectively binding guest molecules are of interest for applications ranging from separations and chemical or biological sensing to the development of biomedical materials. Such host systems can be efficiently prepared by 'imprinting' polymers or inorganic materials with template molecules, which, upon removal, leave behind spatially arranged functional groups that act as recognition sites. However, molecularly imprinted polymers have limitations, including incomplete template removal, broad guest affinities and selectivities, and slow mass transfer. An alternative strategy for moulding desired recognition sites uses combinatorial libraries of assemblies that are made of a relatively small number of molecules, interconverting in dynamic equilibrium; upon addition of a target molecule, the library equilibrium shifts towards the best hosts. Here we describe the dynamic imprinting of dendritic macromolecules with porphyrin templates to yield synthetic host molecules containing one binding site each. The process is based on our general strategy to prepare cored dendrimers, and involves covalent attachment of dendrons to a porphyrin core, cross-linking of the end-groups of the dendrons, and removal of the porphyrin template by hydrolysis. In contrast to more traditional polymer imprinting, our approach ensures nearly homogeneous binding sites and quantitative template removal. Moreover, the hosts are soluble in common organic solvents and amenable to the incorporation of other functional groups, which should facilitate further development of this system for novel applications.     

Taq酶体外合成DNA时模板错位机制的探讨

利用Taq DNA聚合酶体外合成DNA过程中,当反应体系中缺少与模板链互补配对的dNTP底物时,产物合成并不会在底物缺失位点处终止,聚合反应继续进行.为研究此复制缺陷现象,设计一系列模板用于DNA体外酶促合成.除了已知的碱基错配机制,笔者发现存在另一种"模板错位"机制,即模板中与底物非Watson-Crick互补配对的碱基位点首先进行收缩滑动,形成模板bulge结构后再继续进行酶促合成反应.这项研究有助于提高DNA样品合成保真度以及继续深入探索体外DNA合成的详细机制.     

模板作用与金刚石的选择性生长

用生命科学中的DNA(或RNA)模板和碱基(或氨基酸)模块的概念,从物理学角度说明模板对大尺度有序结构特别是亚稳相的生长,对自由能相差很小的异构体的选择生长所具有的重要作用.金刚石和石墨表面具有模板的特征,它们将主导自身外延层的生长方式.异质衬底的某些局域微观结构可以作为新相生长成核的局域模板;不同材料、不同的处理方法及不同的化学环境下的衬底具有不同的局域微观结构,从而决定了多晶薄膜的取向优势.     

Telomerase primer specificity and chromosome healing

Chromosome healing by de novo telomere addition at nontelomeric sites has been well characterized in several organisms. The Tetrahymena telomerase ribonucleoprotein uses an internal RNA template to catalyse d(TTGGGG)n telomere addition to the 3' end of telomeric sequence in vitro and in vivo. Studies of telomerase RNA indicated that hybridization of the RNA template region, 5'-CAACCCCAA-3', to the 3' end of single-stranded telomeric oligonucleotides might be important for primer recognition and utilization. The apparent requirement of telomerase for pre-existing telomeric sequence has raised questions regarding its role in chromosome healing. We report here that Tetrahymena telomerase can specifically elongate single-stranded DNA oligonucleotides whose termini are not complementary to the RNA template sequence 5'-CAACCCCAA-3'. These data suggest that telomerase may be able to heal chromosomes directly in vivo.     

Template-directed synthesis of a genetic polymer in a model protocell

Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles that retain encapsulated oligonucleotides and are capable of growth and division. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.     

A DNA-fuelled molecular machine made of DNA

Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible--for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product.     

Rab25基因siRNA表达载体的构建鉴定及在人卵巢癌细胞A2780中的表达

为研究Rab25基因的功能及卵巢癌的基因治疗,构建针对Rab25基因的siRNA表达载体。转染细胞A2780后观察其对Rab25基因表达的抑制作用,为探索卵巢癌基因治疗的新途径打好基础。根据基因库上的Rab25 mRNA序列,设计并合成两端含有酶切位点的64个碱基的寡核苷酸链。寡核苷酸链退火后用T4DNA连接酶连接到线性化的pSUPER质粒中,并对重组质粒（命名为pSUPER/Rab25siRNA）进行酶切及序列鉴定,后转染卵巢癌细胞A2780,RT-PCR检测转染前后Ra25的表达情况。双酶切证实RaB25sinRNA表达载体克隆构建成功,插入片段测序结果与合成的siRNA结果一致。RT-PCR检测显示转染卵巢癌细胞A2780后有效抑制了Rab25基因的表达。成功构建Rab25siRNA表达载体,为卵巢癌基因治疗开辟新途径。     

MNP-端粒酶反义寡核苷酸复合物诱导HL-60细胞凋亡

反义寡核苷酸具有抑制细胞基因表达作用,对于病毒感染及癌症的治疗具有潜在疗效,然而由于其在生物介质中的不稳定性和低穿透率,常需要修饰于一定的载体上,纳米粒子便是其良好的载体,修饰后可提高反义寡核苷酸的稳定性,研究应用FACS,MTT比色法,电子显微镜,原子力显微镜,细胞集落法研究MNP-端粒酶反义寡核苷酸复合物体外诱导HL-60细胞（人急性早幼粒细胞白血病细胞系）细胞凋亡情况,研究结果表明：通过MTT比色法检测可知不同的药物浓度对细胞的生长有明显的抑制影响;实验组细胞在诱导后于流式细胞术检测中产生了亚二倍体峰（凋亡峰）;通过集落形成及电镜观察都有明显的凋亡现象产生,因此认为MNP-端粒酶反义寡核苷酸复合物具有诱导HL-60细胞凋亡的作用。     

A ribozyme composed of only two different nucleotides

RNA molecules are thought to have been prominent in the early history of life on Earth because of their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, owing to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unit. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyse the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalysed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.     

An LFA-3 cDNA encodes a phospholipid-linked membrane protein homologous to its receptor CD2

Recently the human T cell erythrocyte receptor CD2 has been shown to bind human erythrocytes through LFA-3, a heavily glycosylated surface protein of broad tissue distribution. CD2-LFA-3 interactions are important for cytolytic conjugate formation, for thymocyte adhesion, and for T cell activation. A complementary DNA clone encoding LFA-3 was isolated using a complementary DNA clone encoding LFA-3 was isolated using a novel transient expression system of mouse cells. The cDNA encodes a phospholipid-linked membrane protein whose extracellular domain shares significant homology with CD2. As CD2 is homologous with the neural cell adhesion molecule NCAM in immunoglobulin-like domains, cellular adhesion molecules in both neural and lymphoid tissues could have a common ancestor.     

Overview of the Alliance for Cellular Signaling

The Alliance for Cellular Signaling is a large-scale collaboration designed to answer global questions about signalling networks. Pathways will be studied intensively in two cells--B lymphocytes (the cells of the immune system) and cardiac myocytes--to facilitate quantitative modelling. One goal is to catalyse complementary research in individual laboratories; to facilitate this, all alliance data are freely available for use by the entire research community.     

Quasi-planar nucleus structure in apoferritin crystallization

First-order phase transitions of matter, such as condensation and crystallization, proceed through the formation and subsequent growth of 'critical nuclei' of the new phase. The thermodynamics and kinetics of the formation of these critical nuclei depend on their structure, which is often assumed to be a compact, three-dimensional arrangement of the constituent molecules or atoms. Recent molecular dynamics simulations have predicted compact nucleus structures for matter made up of building blocks with a spherical interaction field, whereas strongly anisotropic, dipolar molecules may form nuclei consisting of single chains of molecules. Here we show, using direct atomic force microscopy observations, that the near-critical-size clusters formed during the crystallization of apoferritin, a quasi-spherical protein, and which are representative of the critical nucleus of this system, consist of planar arrays of one or two monomolecular layers that contain 5-10 rods of up to 7 molecules each. We find that these clusters contain between 20 and 50 molecules each, and that the arrangement of the constituent molecules is identical to that found in apoferritin crystals. We anticipate that similarly unexpected critical nucleus structures may be quite common, particularly with anisotropic molecules, suggesting that advanced nucleation theories should treat the critical nucleus structure as a variable.     

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups.

Shortened forms of the group I intron from Tetrahymena catalyse sequence-specific cleavage of exogenous oligonucleotide substrates. The association between RNA enzyme (ribozyme) and substrate is mediated by pairing between an internal guide sequence on the ribozyme and a complementary sequence on the substrate. RNA substrates and cleavage products associate with a binding energy greater than that of base-pairing by approximately 4 kcal-mol-1 (at 42 degrees C), whereas DNA associates with an energy around that expected for base-pairing. It has been proposed that the difference in binding affinity is due to specific 2'-OH groups on an RNA substrate forming stabilizing tertiary interactions with the core of the ribozyme, or that the RNA.RNA helix formed upon association of an RNA substrate and the ribozyme might be more stable than an RNA.DNA helix of the same sequence. To differentiate between these two models, chimaeric oligonucleotides containing deoxynucleotide residues at successive positions along the chain were synthesized, and their equilibrium binding constants for association with the ribozyme were measured directly by a new gel electrophoresis technique. We report here that most of the extra binding energy can be accounted for by discrete RNA-ribozyme interactions, the 2'-OH group on the sugar residue three nucleotides from the cleavage site contributing the most interaction energy. Thus, in addition to the well documented binding of RNA to RNA by base-pairing, 2'-OH groups within a duplex can also mediate association between RNA molecules.     

Total synthesis of marine natural products without using protecting groups

The field of organic synthesis has made phenomenal advances in the past fifty years, yet chemists still struggle to design synthetic routes that will enable them to obtain sufficient quantities of complex molecules for biological and medical studies. Total synthesis is therefore increasingly focused on preparing natural products in the most efficient manner possible. Here we describe the preparative-scale, enantioselective, total syntheses of members of the hapalindole, fischerindole, welwitindolinone and ambiguine families, each constructed without the need for protecting groups--the use of such groups adds considerably to the cost and complexity of syntheses. As a consequence, molecules that have previously required twenty or more steps to synthesize racemically in milligram amounts can now be obtained as single enantiomers in significant quantities in ten steps or less. Through the extension of the general principles demonstrated here, it should be possible to access other complex molecular architectures without using protecting groups.     

DNA-guided crystallization of colloidal nanoparticles

Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks-to realize novel magnetic, plasmonic and photonic metamaterials, for example. A conceptually simple idea for overcoming this problem is the use of 'encodable' interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles' surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only approximately 4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.     

Catalysis for fluorination and trifluoromethylation

Recent advances in catalysis have made the incorporation of fluorine into complex organic molecules easier than ever before, but selective, general and practical fluorination reactions remain sought after. Fluorination of molecules often imparts desirable properties, such as metabolic and thermal stability, and fluorinated molecules are therefore frequently used as pharmaceuticals or materials. But the formation of carbon-fluorine bonds in complex molecules is a significant challenge. Here we discuss reactions to make organofluorides that have emerged within the past few years and which exemplify how to overcome some of the intricate challenges associated with fluorination.     

Organoplatinum crystals for gas-triggered switches

Considerable effort is being devoted to the fabrication of nanoscale devices. Molecular machines, motors and switches have been made, generally operating in solution, but for most device applications (such as electronics and opto-electronics), a maximal degree of order and regularity is required. Crystalline materials would be excellent systems for these purposes, as crystals comprise a vast number of self-assembled molecules, with a perfectly ordered three-dimensional structure. In non-porous crystals, however, the molecules are densely packed and any change in them (due, for example, to a reaction) is likely to destroy the crystal and its properties. Here we report the controlled and fully reversible crystalline-state reaction of gaseous SO2 with non-porous crystalline materials consisting of organoplatinum molecules. This process, including repetitive expansion-reduction sequences (on gas uptake and release) of the crystal lattice, modifies the structures of these molecules without affecting their crystallinity. The process is based on the incorporation of SO2 into the colourless crystals and its subsequent liberation from the orange adducts by reversible bond formation and cleavage. We therefore expect that these crystalline materials will find applications for gas storage devices and as opto-electronic switches.