Improving metal ion specificity during in vitro selection of catalytic DNA

Metal ions play important roles in both the structure and function of catalytic DNA and RNA. While most natural catalytic RNA molecules (ribozymes) are active in solutions containing Mg(2+), in vitro selection makes it possible to search for new catalytic DNA/RNA that are specific for other metal ions. However, previous studies have indicated that the in vitro selection protocols often resulted in catalytic DNA/RNA that were equally active or sometimes even more active with metal ions other than the metal ion of choice. To improve the metal ion specificity during the in vitro selection process, we implemented a negative selection strategy where the nucleic acid pool was subjected to a solution containing competing metal ions. As a result, those nucleic acids that were active with those metal ions are discarded. To demonstrate the effectiveness of the negative selection strategy, we carried out two parallel in vitro selections of Co(2+)-dependent catalytic DNA. When no negative selection was used in the selection process, the resulting catalytic DNA molecules were more active in solutions of Zn(2+) and Pb(2+) than in Co(2+). On the other hand, when the negative selection steps were inserted between the normal positive selection steps, the resulting catalytic DNA molecules were much more active with Co(2+) than in other metal ions including Zn(2+) and Pb(2+). These results suggest strongly that in vitro selection can be used to obtain highly active and specific transition metal ion-dependent catalytic DNA/RNA, which hold great promise as versatile and efficient endonucleases as well as sensitive and selective metal ion sensors.     

Sequence specificity of alkali-labile DNA damage photosensitized by suprofen

On irradiation at UVB wavelengths, in aerated neutral aqueous solution, the anti-inflammatory drug suprofen (SP) photosensitizes the production of alkali-labile cleavage sites in DNA much more efficiently than direct strand breaks. It is active at submillimolar concentrations despite having no significant binding affinity for DNA. Gel sequencing studies utilizing 32P-end-labeled oligonucleotides have revealed that piperidine-sensitive lesions are formed predominantly at the positions of guanine (G) bases, with the extent of modification being UV dose- and SP concentration-dependent. Quite distinct patterns of G-specific damage are observed in single-stranded and duplex DNA molecules. The uniform attack at all G residues in single-stranded DNA, which is enhanced in D2O, is compatible with a Type-II mechanism. SP is a known generator of singlet oxygen whose participation in the reaction is supported by the effects of quenchers and scavengers. In duplex DNA, piperidine-induced cleavage occurs with high selectivity at the 5'-G of GG and (less prominently) GA doublets. This behavior is characteristic of a Type-I process involving electron transfer from DNA to photoexcited SP molecules. The ability of SP to sensitize the formation of Type-I and Type-II photo-oxidation products from 2'-deoxyguanosine attests to the feasibility of competing mechanisms in DNA.     

Sequence specificity of hydrogen-bonded molecular duplexes

Hydrogen-bonded molecular duplexes, 1.3 and 1.4, each of which contains a mismatched binding site (acceptor-to-acceptor in 1.3, and donor-to-donor in 1.4), were designed and synthesized based on duplex 1.2. One- and two-dimensional NMR studies demonstrated that, despite their single mismatched binding sites, the backbones of duplexes 1.3 and 1.4 still stayed in register through the formation of the remaining five H-bonds. The backbones of 1.3 and 1.4 adjusted to the presence of the mismatched binding sites by slightly twisting around these sites, which alleviate any head-on repulsive interactions between two H-bond donors (amide O) or between two acceptors (amide H). After 1 equiv of single strand 2, which forms a perfectly matched duplex 1.2 with single strand 1, was added into the solution of either 1.3 or 1.4, only 1.2 and single strand 3 or 4, were detected. Isothermal titration calorimetry (ITC, in chloroform containing 5% DMSO) indicated that duplexes 1.3 and 1.4 were significantly (>40 times) less stable than the corresponding perfectly hydrogen-bonded duplex 1.2. These NMR and ITC results indicate that the pairing of two complementary single strands is not affected by another very similar single strand that contains only one wrong H-bond donor or acceptor, which demonstrates that the self-assembly of this class of H-bonded duplexes is a highly sequence-specific process. The role of these H-bonded duplexes as predictable and programmable molecular recognition units for directing intermolecular interactions has thus been established.     

Diaminobipyridine-TDI polyureas: Synthesis,metal complexes,and catalytic activity

In this article we report the synthesis of a polyurea containing the chelating ligand bipyridine and concentrate on some of the catalytic properties of its palladium complexes.     

Catalytic proficiency of ubiquitin conjugation enzymes: balancing pK(a) suppression, entropy, and electrostatics

Biological organisms orchestrate coordinated responses to external stimuli through temporal fluctuations in protein-protein interaction networks using molecular mechanisms such as the synthesis and recognition of polyubiquitin (polyUb) chains on signaling adaptor proteins. One of the pivotal chemical steps in ubiquitination involves reaction of a lysine amino group with a thioester group on an activated E2, or ubiquitin conjugation enzyme, to form an amide bond between Ub and a target protein. In this study, we demonstrate a nominal 14-fold range for the rate of the chemical step, k(cat), catalyzed by different E2 enzymes using non-steady-state, single-turnover assays. However, the observed range for k(cat) is as large as ～100-fold for steady-state, single-turnover assays. Biochemical assays were used in combination with measurement of the underlying protein-protein interaction kinetics using NMR line-shape and ZZ-exchange analyses to determine the rate of polyUb chain synthesis catalyzed by the heterodimeric E2 enzyme Ubc13-Mms2. Modest variations in substrate affinity and k(cat) can achieve functional diversity in E2 mechanism, thereby influencing the biological outcomes of polyubiquitination. E2 enzymes achieve reaction rate enhancements through electrostatic effects such as suppression of substrate lysine pK(a) and stabilization of transition states by the preorganized, polar enzyme active site as well as the entropic effects of binding. Importantly, modestly proficient enzymes such as E2s maintain the ability to tune reaction rates; this may confer a biological advantage for achieving specificity in the diverse cellular roles for which these enzymes are involved.     

pH- and metal-dependent structural diversity from mononuclear to two-dimensional polymers based on a flexible tricarboxylate ligand

Six complexes based on a flexible tripodal ligand H₃TTTA (2,2′,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid) have been hydrothermally synthesized and structurally characterized. X-ray single-crystal diffractions reveal that they have rich structural chemistry: mononuclear, [Zn(HTTTA)(2,2′-bpy)(H₂O)₃]_n (1); dimeric metallamacrocycle, [Zn(HTTTA)(2,2′-bipy)(H₂O)]_n (2) and [Cd(HTTTA)(2,2′-bipy)(H₂O)·H₂O]_n (3); two-dimensional networks with binodal (3,6)-connected CdI₂ topology based on linear trinuclear M₃(μ²-CO²)₄(μ₂-CO₂)₂ SBUs (Secondary Building Units), [M₃(TTTA)₂(2,2′-bipy)₂(H₂O)_m·nH₂O]_n (M=Zn·4, m=0, n=4; Cd·5 and Mn·6, m=2; n=2). The value of pH and the metal ions has large influences on the resulting structures. The flexible tricarboxylic acid exhibits four coordination modes from monodentate to μ⁶-bridge. Fluorescence and magnetic properties of the complexes have also been investigated in details.     

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2‐aminopurine (2AP) as an energy trap in short (3‐ to 20‐base) single‐ and double‐stranded DNA oligomers is reviewed. Variation of 2AP’s neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3′ end, (3) approximate equality of efficiencies for 3′ to 5′ and 5′ to 3′ directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de‐excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross‐strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ?60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single‐stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor–acceptor distance, the experimental dependence clearly disagrees with Förster 1/r⁶ dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base–base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular “fiber optic” face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this “fiber optic” a challenge.     

Preparation, characterization, and catalytic activity of rare earth metal oxide nanoparticles

In present study, a series of rare earth metal oxide (CeO₂, Pr₂O₃, and Nd₂O₃) nanoparticles have been prepared by sol–gel route using Ce(NO₃)₃·6H₂O, Pr(NO₃)₃·6H₂O and Nd(NO₃)₃·6H₂O, and citric acid as precursor materials. Powder X-ray diffraction, scanning electron microscopy, and transmission electron microscopy are employed to characterize the size and morphology of the nano oxide particles. The particles are spherical in shape and the average particle size is of the order of 11–30 nm. Their catalytic activity was measured on the thermal decomposition of ammonium perchlorate and composite solid propellants (CSPs) by thermogravimetry (TG), TG coupled with differential thermal analysis (TG–DTA), and ignition delay measurements. The ignition delays and activation energies are found to decrease when rare earth metal oxide nanoparticles were incorporated in the system. Addition of metal oxide nanoparticles to AP led to shifting of the high temperature decomposition peak toward lower temperature and the burning rate of CSPs was also found to enhance. However, E _a activation energy for decomposition was also found to decrease with each catalyst.     

Deubiquitinating enzymes: their functions and substrate specificity

Conjugation of one or more molecules of ubiquitin to target proteins can signify one of several fates, including degradation by the 26S proteasome, or trafficking via the secretory or endocytic pathways. Whereas much attention in recent years has focussed on the mechanisms of forming these different ubiquitin conjugates, far less is known about the removal of ubiquitin, which is performed by deubiquitinating enzymes (DUBs). While it has been appreciated for some 10 years that DUBs constitute large gene families in eukaryotes, and known for much longer that ubiquitination is a reversible process, information on the exact role of DUBs has been slow in coming. This review will attempt to summarise results from the last few years that shows that DUBs are an essential regulatory step of both protein degradation by the proteasome, and of other ubiquitin-dependent processes, by virtue of their ability to regulate protein ubiquitination in a target-specific manner.     

Polyamide-bound metal complex catalysts: Synthesis,characterization and catalytic properties

A series of polyamides having different numbers of methylene groups in their repeating units have been synthesized by interfacial polycondensation of terephthaloyl chloride with piperazine and aliphatic diamines H₂N(CH₂)_nNH₂ (n = 2, 6, 10). These materials, which have high thermal stability, were used for immobilization of rhodium and platinum complexes. Chloroplatinic acid and the compounds PtCl₂(CH₃CN)₂ and [RhCl(CO)₂]₂ were used as precursors of the supported catalysts. Low molecular weight analogues of the polyamides were prepared for a study of the coordination mode between the metal ion and the polymer by IR spectroscopy. The results suggest that the carbonyl oxygen of the polyamide is the site of coordination to both rhodium and platinum. The bound catalysts exhibited high activity in hydrosilylation of hexene-1. The activities of the rhodium complexes were found to be dependent on the structure of the polyamide support, decreasing with increasing distance between the amide groups, and closely paralled the changes in the degree of crystallinity of the polymers. Repeated use of the polymers bearing rhodium complexes showed that the bond between the metal and polyamide is fairly stable.     

Syntheses,crystal structures,and DNA binding and catalytic properties of two transition metal coordination polymers constructed from 5-aminoisophthalic acid and bis-benzimidazole ligands

Two mixed-ligand transition metal coordination polymers, {[Co(aip)(bbp)]·(H₂O)} _n (1) and {[Ni₂(aip)(Hbbop)₂]·(H₂O)₂} _n (2) (H₂aip = 5-aminoisophthalic acid, bbp = 1,3-bis(benzoimidazol-2-yl)propane, H₂bbop = 1,3-bis(benzimidazol-2-yl)-2-oxapropane), were synthesized and characterized by elemental analyses, IR spectra, single-crystal X-ray diffraction, and thermogravimetric analyses. Complex 1 has a 1D chain structure, while 2 has a 3-connected 2D network with (6³) topology. Both structures are further connected by hydrogen bonds and π–π stacking interactions to form the 3D supramolecular architectures. DNA binding and catalytic properties of the two complexes were investigated.     

Biochemical applications of ultrathin films of enzymes, polyions and DNA

This feature article summarizes recent applications of ultrathin films of enzymes and DNA assembled layer-by-layer (LbL). Using examples mainly from our own research, we focus on systems developed for biocatalysis and biosensors for toxicity screening. Enzyme-poly(L-lysine) (PLL) films, especially when stabilized by crosslinking, can be used for biocatalysis at unprecedented high temperatures or in acidic or basic solutions on electrodes or sub-micron sized beads. Such films have bright prospects for chiral synthesis and biofuel cells. Excellent bioactivity and retention of enzyme structure in these films facilitates their use in detailed kinetic studies. Biosensors and arrays employing DNA-enzyme films show great promise in predicting genotoxicity of new drug and chemical product candidates. These devices combine metabolic biocatalysis, reactive metabolite-DNA reactions, and DNA damage detection. Catalytic voltammetry or electrochemiluminescence (ECL) can be used for high throughput arrays utilizing multiple LbL "spots" of DNA, enzyme and metallopolymer. DNA-enzyme films can also be used to produce nucleobase adduct toxicity biomarkers for detection by LC-MS. These approaches provide valuable high throughput tools for drug and chemical product development and toxicity prediction.     

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.

Orotidine 5'-phosphate decarboxylase (ODCase) is the most proficient enzyme known, enhancing the rate of decarboxylation of orotidine 5'-phosphate (OMP) by a factor of 10(17), which corresponds to a DeltaDeltaG++ of approximately 24 kcal/mol. Ground-state destabilization through local electrostatic stress has been recently proposed as the basis of catalytic rate enhancement for a mechanism that is the same as in solution. We have carried out gas-phase ab initio quantum mechanical calculations combined with a free energy method, a continuum solvent model, and molecular dynamics simulations to assess an alternative mechanism. Although we are not able to reproduce the experimentally observed DeltaDeltaG++ quantitatively, we present evidence that this DeltaDeltaG++ is very large, in the range found experimentally. We thus conclude that the preferred mechanism may well be different from that in solution, involving an equilibrium pre-protonation of OMP C5 by a catalytic lysine residue that greatly reduces the barrier to subsequent decarboxylation.     

铈基介孔金属有机骨架固定化酶的构建及催化性能

金属有机骨架(MOF)材料由于其孔隙率高、比表面积大以及具有发达的内联通孔道结构等优点,可以作为优良的生物分子固定化载体。通过表面活性自组装策略制备了铈基介孔MOF(Ce-MOF-F),表征结果表明,该材料有大的比表面积和呈辐射状的介孔孔道结构。以其为载体、南极假丝酵母脂肪酶B(CALB)为模型酶,通过物理吸附法制备了生物催化剂CALB@Ce-MOF-F,对该固定化酶的酶载量和催化性能进行了研究。在优化条件下,CALB的负载量为162.0mg/g载体,水解活性为899.1U/g蛋白。与游离CALB相比,CALB@Ce-MOF-F表现出对高温、酸碱和有机溶剂等有更强的耐受性;将Ce-MOF-F用于多种酶的固定化,研究其作为载体的普适性,结果表明,介孔Ce-MOF-F对洋葱伯克氏菌脂肪酶(BCL)和漆酶有良好的固定效果,可以作为良好载体,并能对酶起到较好的保护作用。     

Isolation, Mapping, DNA Sequence and RFLPs Studies of Random Single-Copy DNA Segments on Human X Chromosome

Using the total human/mouse DNA as the probe, screening has been carried out three times with in situ plaque hybridization to obtain the single-copy DNA sequence from the human X chromosome genomic library. The effective rate of screening is 1. 45%. DNAs from clones containing single-copy inserts have been analyzed by a panel of hybrid cells with or without human X chromosome. Three segments, designated by DXFD52,73,75, are mapped to the X chromosome. DXFD52 has been precisely localized on Xq12-q13 with in situ chromosomal hybridization. DXFD52 has been partially sequenced. The results indicate that DXFD52 is a new isolated single-copy segment on the X chromosome. Great progress in the RFLPs study with DXFD52 has been achieved in the population of Chongqing, Sichuan Province. The results show that the DXFD52 can be used to detect the RFLP with Hind Ⅲ, Bgl Ⅱ, and Hinf Ⅰ. DXFD52 will be a potential "landmark" for the construction of the complete linkage map of human genome and the analysis of genomic s     

Stereospecific synthesis and catalytic activity of L-histidylidene metal complexes

We report on the synthesis, metal coordination, and catalytic impact of histidylidene, a histidine-derived N-heterocyclic carbene (NHC) ligand. The histidinium salt 3, comprising methyl substituents at both heterocyclic nitrogens and protected at the C- and N-terminus of the amino acid, was rhodated and iridated by a transmetallation protocol using Ag(2)O. Ambient temperature and short reaction times were pivotal for full retention of configuration at the α-carbon. The stereospecificity of the reaction was conveniently probed by (31)P NMR spectroscopy after transmetallation with rhodium(I) and coordination of enantiopure (S)-Ph-binepine. The histidylidene rhodium complexes are highly efficient catalysts for the mild hydrosilylation of ketones. For the cationic complexes [Rh(cod)(histidylidene)(phosphine)](+), lowering the temperature shifted the rate-limiting step of the catalytic reaction to an earlier stage that is not enantioselective. Hence the asymmetric induction-which is governed by the chiral phosphine-did not improve at low temperature.