Ag nanoclusters as probes for turn-on fluorescence recognition of TpG dinucleotide with a high selectivity

CpG dinucleotide in DNA has a great tendency to mutate to TpG dinucleotide and this transition can cause some serious diseases. In this work, fluorescent Ag nanoclusters (Ag NCs) were employed as useful inorganic fluorophores for the potential of selectively discriminating TpG dinucleotide from CpG dinucleotide. Opposite the base Y of interest in YpG dinucleotide (Y = C or T), a bulge site was introduced so as to make the base Y to be unpaired and ready for Ag⁺ binding. Such that the unpaired Y and context base pairs can provide a specific space suitable for creating fluorescent Ag NCs. We found that in comparison with CpG dinucleotide, TpG dinucleotide is much more efficient in growing fluorescent Ag NCs. Therefore, mutation of CpG dinucleotide to TpG can be identified by a turn-on fluorescence response and a high selectivity. More interestingly, Ag NCs exhibit a better performance in the TpG recognition over the other dinucleotides (Y = A and G) than the previously used organic fluorophores. Additionally, the effectiveness of the bulge site design in discriminating these dinucleotides was evidenced by control DNAs having the abasic site structure. We expect that a practical method for TpG dinucleotide recognition with a high selectivity can be developed using the bulge site-grown fluorescent Ag NCs as novel probes.     

Kinetic approach for the purification of nucleotides with magnetic separation

The isolation of β‐nicotinamide adenine dinucleotide is of great importance since it is widely used in different scientific and technologic fields such as biofuel cells, sensor technology, and hydrogen production. In order to isolate β‐nicotinamide adenine dinucleotide, first 3‐aminophenyboronic acid functionalized magnetic nanoparticles were prepared to serve as a magnetic solid support and subsequently they were used for reversible adsorption/desorption of β‐nicotinamide adenine dinucleotide in a batch fashion. The loading capacity of the 3‐aminophenyboronic acid functionalized nanoparticles for β‐nicotinamide adenine dinucleotide adsorption was 13.0 μmol/g. Adsorption kinetic and isotherm studies showed that the adsorption process followed a pseudo‐second‐order kinetic model and the experimental data can be represented using Langmuir isotherm model. The 3‐aminophenyboronic acid functionalized magnetic nanoparticles were proposed as an alternative support for the β‐nicotinamide adenine dinucleotide purification. The results elucidated the significance of magnetic separation as a fast, relatively simple, and low‐cost technique. Furthermore, the magnetic supports can be reused at least five times for purification processes.     

Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme

We conducted 16 parallel in vitro selection experiments to isolate catalytic DNAs from a common DNA library for the cleavage of all 16 possible dinucleotide junctions of RNA incorporated into a common DNA/RNA chimeric substrate sequence. We discovered hundreds of sequence variations of the 8-17 deoxyribozyme--an RNA-cleaving catalytic DNA motif previously reported--from nearly all 16 final pools. Sequence analyses identified four absolutely conserved nucleotides in 8-17. Five representative 8-17 variants were tested for substrate cleavage in trans, and together they were able to cleave 14 dinucleotide junctions. New 8-17 variants required Mn2+ to support their broad dinucleotide cleavage capabilities. We hypothesize that 8-17 has a tertiary structure composed of an enzymatic core executing catalysis and a structural facilitator providing structural fine tuning when different dinucleotide junctions are given as cleavage sites.     

Artificial electron carriers for photoenzymatic synthesis under visible light

NAD analogues can be employed as artificial electron carriers for photoenzymatic synthesis under visible light. Four different NAD analogues that have a 3-substituted pyridine ring have been investigated. 3-Acetylpyridine adenine dinucleotide and 3-pyridinealdehyde adenine dinucleotide were photochemically reduced much more efficiently than NAD, while their reduced products showed coenzyme activity comparable to natural NAD.     

Typing dinucleotide repeat loci using microplate array diagonal gel electrophoresis: proof of principle

Polymorphic dinucleotide repeat loci ('microsatellite markers') are found in varying abundance throughout the genomes of most organisms. They have been extensively used for genetic studies, but conventional techniques used for their genotyping require sophisticated equipment. Microplate array diagonal gel electrophoresis (MADGE) has previously been extended to economical high-throughput genotyping of trinucleotide and tetranucleotide microsatellite amplicons. However, the capability of this technique to resolve the alleles of dinucleotide repeat loci has not been explored previously. Here we show that a modified microsatellite-MADGE approach can provide sufficient resolution for dinucleotide repeat typing. This enables economical and convenient set up for analysis of single markers in many samples in parallel, suitable, for example, for population association studies.     

A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures

A 5'-C-allylthymidine derivative was prepared from thymidine by the application of a stereoselective allylation procedure and its 5'(S)-configuration was confirmed. From this nucleoside derivative, appropriately protected building blocks were prepared and coupled using standard phosphoramidite chemistry to afford a dinucleotide with two 5'-C-allylgroups. This molecule was used as a substrate for a ring-closing metathesis (RCM) reaction and after deprotection, a 1 : 1 mixture of E- and Z-isomers of a cyclic dinucleotide with an unsaturated 5'-C-to-5'-C connection was obtained. Alternatively, a hydrogenation of the double bond and deprotection afforded a saturated cyclic dinucleotide. An advanced NMR-examination confirmed the constitution of this molecule and indicated a restriction in its overall conformational freedom. After variation of the protecting group strategy, a phosphoramidite building block of the saturated cyclic dinucleotide with the 5'-O-position protected as a pixyl ether and the phosphate protected as a methyl phosphotriester was obtained. This building block was used in the preparation of two 14-mer oligonucleotides with a central artificial bend due to the cyclic dinucleotide moiety. These were found to destabilise duplexes, slightly destabilise bulged duplexes but, to some extent, stabilise a three-way junction in high Mg(2+)-concentrations.     

Cofactor modified electrodes

Studies are underway to see if flavin adenine dinucleotide or nicotinamide adenine dinucleotide cofactors can be attached to electrode surfaces to give rapid rates of electron transfer and in some cases reconstitution of enzyme activity with appropriate apoenzymes. Such electrodes may find widespread application in analytical chemistry.     

Determination of nicotinamide-adenine dinucleotide and thiazole-4-carboxamide-adenine dinucleotide in human leukocytes by reversed-phase high-performance liquid chromatography.

A high-performance liquid chromatographic assay for cellular nicotinamide-adenine dinucleotide and thiazole-4-carboxamide-adenine dinucleotide is presented that is appropriate for analysis of these dinucleotides in extracts of Ficoll-purified human leukemic cells. The separation, which is effected by reversed-phase chromatography, is highly reproducible and the limit of quantitation is as low as 10-15 pmol. The stability of these compounds in neutralized perchloric acid extracts is addressed and the applicability of the procedure to clinical specimens is demonstrated.     

Amperometric measurement of hexacyanoferrate(III)-coupled dehydrogenase reactions.

The electrochemical oxidations of hexacyanoferrate II ion and reduced nicotinamide adenine dinucleotide at carbon electrodes are described. Amperometric methods for nicotinamide adenine dinucleotide oxidoreductase analyses by amperometric monitoring of hexacyanoferrate II are reported for lactic dehydrogenase in serum.     

Probing possible left- and right-handed poly(dinucleotide) helical conformations from (n–h) plots. models for polysequential nucleotides

Introducing the concept of the “dinucleotide” as the helical repeat, theoretical attempts have been made to determine possible single and double stranded helical structures by using helical parameter calculations and model building investigations. By virtue of its flexible framework, the dinucleotide repeat offers a much greater scope of finding new secondary structural forms for nucleic acids. Considering only those conformations which show tendency for at least partial base overlap as does the dinucleotide helical repeat, it has been possible to predict poly(dinucleotide) helical models in which successive phosphodiesters as well as nucleotide conformations alternate. More important, the recently found left-handed Z-type polynucleotide helix is characterized rather uniquely on the helical parameter plot. The results further suggest the possibility of other Z-type helices obtainable by alternative conformations for the exocyclic C4'–C5' bond and sugar pucker. Near neighbor long range conformational correlations between the dinucleotide repeat and the phosphodiester linking them have been established similar to poly(mononucleotide) helices. Need for considering higher repeats such as trinucleotide has been suggested to obtain models for looped out helical conformations.     

Sample preparation workflow for the liquid chromatography tandem mass spectrometry based analysis of nicotinamide adenine dinucleotide phosphate cofactors in yeast†

The accurate quantification of the highly unstable intracellular cofactor nicotinamide adenine dinucleotide phosphate in its oxidized and reduced forms demands a thorough evaluation of the analytical workflow and dedicated methods reflecting their solution chemistry as well as the biological importance of their ratio. In this work, we present a workflow for the analysis of intracellular levels of oxidized and reduced nicotinamide adenine dinucleotide phosphate in the yeast Pichia pastoris, including hot aqueous extraction, chromatographic separation in reversed‐phase conditions employing a 100% wettable stationary phase, and subsequent tandem mass spectrometric analysis. A thorough evaluation and optimization of the sample preparation procedure resulted in excellent biological repeatabilities (on average <10%, N = 3) without employing an internal standardization approach. As a consequence, the methodology proved to be appropriate for the relative assessment of intracellular levels of oxidized and reduced nicotinamide adenine dinucleotide phosphate in different P. pastoris strains. The ratio of reduced versus oxidized nicotinamide adenine dinucleotide phosphate was significantly higher in an engineered strain overexpressing glucose‐6‐phosphate dehydrogenase than in the corresponding wildtype strain. Interestingly, a difference was also observed in the nicotinamide adenine dinucleotide phosphate pool size, which was significantly higher in the wildtype than in the modified strain.     

Creation of bioorthogonal redox systems depending on nicotinamide flucytosine dinucleotide

Many enzymes catalyzing biological redox chemistry depend on the omnipresent cofactor, nicotinamide adenine dinucleotide (NAD). NAD is also involved in various nonredox processes. It remains challenging to disconnect one particular NAD-dependent reaction from all others. Here we present a bioorthogonal system that catalyzes the oxidative decarboxylation of l-malate with a dedicated abiotic cofactor, nicotinamide flucytosine dinucleotide (NFCD). By screening the multisite saturated mutagenesis libraries of the NAD-dependent malic enzyme (ME), we identified the mutant ME-L310R/Q401C, which showed excellent activity with NFCD, yet marginal activity with NAD. We found that another synthetic cofactor, nicotinamide cytosine dinucleotide (NCD), also displayed similar activity with the ME mutants. Inspired by these observations, we mutated d-lactate dehydrogenase (DLDH) and malate dehydrogenase (MDH) to DLDH-V152R and MDH-L6R, respectively, and both mutants showed fully active with NFCD. When coupled with DLDH-V152R, ME-L310R/Q401C required only a catalytic amount of NFCD to convert l-malate. Our results opened the window to engineer bioorthogonal redox systems for a wide variety of applications in systems biology and synthetic biology.     

生化教材中存在44年的瑕疵——吡啶环上氮原子的化合价

Understanding redox reactions in reaction of nicotinamide adenine dinucleotide (NAD⁺) and nicotinamide adenine dinucleotide phosphate (NADP⁺) requires a clear grasp of the textbook content. The reactions in nicotinamide coenzymes with reduced and oxidized forms have been compared in various biochemistry textbooks. Incorrect interpretations usually emphasize the valence changes that at nitrogen in the pyridine ring of a nicotinamide from +5 to +3. Actually, the valence of nitrogen in pyridine ring is -3. We have gathered shreds of evidences and provide here possible suggestions and caution for readers and instructors.     

Delta-amino group hydroxylation of L-ornithine during coelichelin biosynthesis

The nonribosomally produced hydroxamate siderophore coelichelin from Streptomyces coelicolor contains the nonproteinogenic amino acids N(5)-hydroxyornithine and N(5)-hydroxyformylornithine that are important for iron assembly. The hydroxylation of the delta-amino group of L-ornithine is catalyzed by the flavin-dependent monooxygenase CchB. During the redox reaction nicotinamide adenine dinucleotide phosphate (NADPH) and molecular oxygen are consumed and flavin adenine dinucleotide (FAD) is needed as a cofactor. During this work the monooxygenase was biochemically characterized and it could be shown that the hydroxylation of l-ornithine is most likely the first step in the biosynthesis of the siderophore coelichelin.     

Monitoring the preparation of NAD analogs by reversed-phase high-performance liquid chromatography

Summary Pig brain NAD glycohydrolase immobilized on Affi-Gel 10 or nylon 6 was used for the conversion of NAD into 3-acetylpyridine adenine dinucleotide (APAD) or 3-aminopyridine adenine dinucleotide (AAD). A reversed-phase chromatographic system consisting of a C₁₈ Resolve column and phosphate buffer (pH 6.2)-methanol as the mobile phase was used to monitor the production of APAD and AAD.     

20 Beta-hydroxysteroid dehydrogenase of neonatal pig testis: cofactor requirement and stereospecificity of hydrogen transfer from nicotinamide adenine dinucleotide phosphate, reduced form

The cofactor requirement of purified 20 beta-hydroxysteroid dehydrogenase from cytosol fraction of neonatal pig testis, in the reduction of 17 alpha-hydroxyprogesterone was investigated. The enzyme required beta-nicotinamide adenine dinucleotide phosphate, reduced form (beta-NADPH) as the preferred cofactor, with an apparent Km value of 17 microM. Furthermore, alpha-nicotinamide adenine dinucleotide phosphate, reduced form (alpha-NADPH), beta-3'-NADPH and beta-nicotinamide adenine dinucleotide (beta-NADH) were also utilized as hydrogen donors in the reduction at relatively high concentration with apparent Km values of 85.2 microM, 179.2 microM and 1.00 mM, respectively. The optimum pH was 5.5 when beta-NADPH was used as the cofactor, while it was 6.0 when beta-NADH was used. The hydrogen transfer from the beta-NADPH to the product, 17 alpha,20 beta-dihydroxypregn-4-en-3-one catalyzed by 20 beta-hydroxysteroid dehydrogenase was stereospecific, and the 4-pro-S-hydrogen of the nicotinamide moiety was transferred to the product.     

亚油酸与核黄素或FAD激发态之间电荷转移的直接证据

根据荧光显微镜方法,我们首次发现核黄素(维生素B2)主要分布在细胞核的膜上和核的内部,故核黄素光敏化与辐射化的靶位置主要集中在细胞核内;当核黄素的浓度较大时,细胞膜上也有药物的分布,即在高浓度时,细胞膜也是光敏化与辐射敏化的作用位点一。应用308nn激光光解时间分辨吸收方法,以亚油酸作为脂质的模型化合物,研究了亚油酸与核黄素和黄素腺嘌呤二核苷酸(FAD)的激发三重态之间的电荷转移过程,首次给出了电荷转移的直接证据。     

Computational Approach to Explore the B/A Junction Free Energy in DNA

Protein–DNA interactions induce conformational changes in DNA such as B‐ to A‐form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B–A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol^?1 for the A‐philic GG step and 1.59 kcal mol^?1 for the B‐philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B‐ to A‐form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.     

Novel nicotinamide adenine dinucleotide analogues as selective inhibitors of NAD-dependent enzymes

Three novel dinucleotide analogues of nicotinamide adenine dinucleotide (NAD⁺) have been synthesised from d-ribonolactone. These compounds incorporate a thiophene moiety in place of nicotinamide and are hydrolytically stable. They have been evaluated as inhibitors of adenosine diphosphate ribosyl cyclase, glutamate dehydrogenase and Sir2 acyltransferase activities. Enzyme specificity and a high level of inhibition was observed for the dehydrogenase.     

Crystal structure of the complex of trichosanthin with NADPH at 0.172 nm resolution

The orthorhombic crystal structure of the complex of trichosanthin with nicotinamide adenine dinucleotide phosphate has been determined by molecular replacement method using one of the molecules of the monoclinic crystal structure of trichosanthin at 0.27 nm resolution as the search model. The crystallographic refinement at 0.172 nm resolution led to a final R-factor of 17.4% with root-mean-square deviations of 0.0013 nm and 3.8 from the ideal bond lengths and bond angles, respectively. The quality of the structure, the polypeptide chain fold and the comparison of it with that of the monoclinic trichosanthin structure, the location of nicotinamide adenine dinucleotide phosphate, the active site structure as well as the solvent structure are described.