Primer Extension Reaction Assays for Incorporation of Deoxynucleotide Analogue into DNA

Incorporation of deoxynucleotide analogues into DNA is important for the expansion of DNA functions. Primer extension reactions are commonly used for the assay of such reaction events. However, current assay protocols generally rely on radiolabeling, fluorescence reporter labeling, or removal of specific deoxynucleotide triphosphate in the reaction mixture. Herein we report on the design of two novel assay protocols that utilize a dideoxynucleotide‐terminated template strand and a phosphorothiolate‐modified deoxynucleotide‐terminated template strand. We designed and synthesized a deoxyuridine triphosphate analogue (dU*TP) containing 2‐bromoisobutyryl group and demonstrated that it could be well recognized by ?29DNA polymerase, E. coli DNA polymerase I Klenow Fragment, Bst DNA polymerase Large Fragment, and E. coli DNA polymerase I Klenow Fragment (exo⁽), which translated to effective incorporation of dU*TP into DNA. dU*TP was also successfully incorporated into extremely long single‐stranded DNA at high‐density using ?29 DNA polymerase by rolling circle amplification.     

Synthesis of brassinosteroids analogues from laxogenin and their plant growth promotion

Four steroid saponins (2–5) and three derivatives (6–8) were synthesised from laxogenin. Four of them were new compounds: (25R)-3β-(2,3,4,6-tetra-O-acetyl-β-d-galactopyranosyloxy)-5α-spirostan-6-one (3), (25R)-3β-(β-d-galactopyranosyloxy)-5α-spirostan-6-one (5), 3β,16-diacetyl-26-hydroxy-5α-cholestan-6,22-dione (6) and 16-acetyl-3β,26-dihydroxy-5α-cholestan-6,22-dione (7). All the compounds showed plant growth-promoting activity in the radish hypocotyl elongation and cotyledon expansion bioassay. Above all, 2 and 6 were found to be more active.     

Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides

[Chemical reaction: See text] Nucleosides bearing a branched ribose have significant promise as therapeutic agents and biotechnological and biochemical tools. Here we describe synthetic entry into a new subclass of these analogues, 2'-C-beta-difluoromethylribonucleosides. We constructed the glycosylating agent 4 in three steps from 1,3,5-tri-O-benzoyl-alpha-D-ribofuranose 1. The key steps included nucleophilic addition of difluoromethyl phenyl sulfone to 2-ketoribose 2 followed by mild and efficient reductive desulfonation. Ribofuranose 4 glycosylated bis(trimethylsilyl)uracil directly, giving difluoromethyluridine 7 efficiently after deprotection. Conversion of 4 to the corresponding ribofuranosyl bromide allowed efficient access to C, A, and G analogues. A related approach starting from methyl D-ribofuranose offered synthetic entry into the diastereomeric manifold, 2'-C-alpha-difluoromethyl-arabino-alpha-pyrimidine. To incorporate 2'-C-beta-difluoromethyluridine into an oligodeoxynucleotide we converted 7 to the bisphosphate and carried out successive ligation reactions using T4 RNA ligase and T4 DNA ligase. Analogous to natural RNA linkages, the resulting oligonucleotide undergoes hydroxide-catalyzed backbone scission at the difluoromethyluridine residue via internal transphosphorylation.     

Synthesis of highly modified DNA by a combination of PCR with alkyne-bearing triphosphates and click chemistry

We report the combination of "click chemistry" with PCR by using alkyne-modified triphosphates for efficient and homogeneous labeling of DNA. A series of modified PCR products of different lengths (300, 900, and 2000 base pairs) were prepared by using a variety of alkyne- and azide-containing triphosphates and different polymerases. After intensive screening of real-time PCR methods, protocols were developed that allow the amplification of genes by using these modified triphosphates with similar efficiency to that of standard PCR. The click reaction on the highly modified PCR fragments provided conversion rates above 90 % and resulted in the functionalization of hundreds of alkynes on large DNA fragments with superb selectivity and efficiency.     

Synthesis of acyclic nucleotide analogues possessing a difluoromethylene phosphonyl group at the side chain

A synthetic approach to a new type of acyclic nucleotide analogues 8 and 9 was examined. The design was based on acyclic modification of MRS 2179, a P2Y₁-antagonist, and replacement of one of two phosphate groups characterized by MRS 2179 with an isosteric difluoromethylenephosphonyl group. The nucleotide analogues 8 and 9 were enantio-divergently prepared as their ester-protecting derivatives from a highly differentiated 1,5-pentanediol derivative possessing a difluoromethylenephosphonyl group at the 3-position.     

姜黄素类似物的合成及其生物活性的测定

实验合成了姜黄素的Knoevenagel缩合物4-(2-呋喃次甲基)姜黄素C1,氨基硫脲Schiff 碱配体E1,及其Schiff 碱配体的Zn(Ⅱ)配合物D1.采用DPPH法测定了产品清除自由基的能力,结果表明产品C1对DPPH自由基清除率为82.0%.在pH7.2的Tris-Hcl缓冲溶液中,采用紫外光谱和荧光光谱研究了C1与鲱鱼精DNA的相互作用,结果表明,C1与DNA是通过嵌插模式发生相互作用的,其键合常数为Kq =9.31×103.     

Synthesis and characterization of nonaqueous dispersion particles with photolabile α‐heptadecylphenacyl ester stabilizer chains

We describe a new method for the synthesis of core–shell photolabile nanoparticles. The synthesis begins with the batch emulsion copolymerization of n‐butyl methacrylate (BMA) and ethylene glycol dimethacrylate to form small (20‐nm‐diameter) crosslinked particles with a narrow size distribution. These seeds are then used for a second‐stage emulsion copolymerizations in which BMA and various polar monomers, including methacrylic acid, are added under monomer‐starved conditions. After characterization of the particles, they are transferred to an N,N‐dimethylformamide solution. The cesium salt of the carboxylic acid groups is reacted with 2‐bromo‐1‐phenyl‐octadecan‐1‐one to convert various fractions of the ? COOH groups to the corresponding 2‐benzoylheptadecyl ester groups. These aliphatic ester groups render the surface sufficiently hydrophobic that the particles can be dispersed in common aliphatic hydrocarbons solvents to yield colloidal dispersions, sterically stabilized by the dangling aliphatic chains. Ester groups with a phenyl ketone attached to the β‐carbon are photolabile. Irradiation of the particles with UV light detaches the sterically stabilizing chains from the particle and transforms the surface groups back to COOH groups. This leads to flocculation of the particles. The emphasis in this article is on the optimization of the particle synthesis and the characterization of the particles obtained. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2642–2657, 2001     

2‐Substituted dATP Derivatives as Building Blocks for Polymerase‐Catalyzed Synthesis of DNA Modified in the Minor Groove

2′‐Deoxyadenosine triphosphate (dATP) derivatives bearing diverse substituents (Cl, NH₂, CH₃, vinyl, ethynyl, and phenyl) at position 2 were prepared and tested as substrates for DNA polymerases. The 2‐phenyl‐dATP was not a substrate for DNA polymerases, but the dATPs bearing smaller substituents were good substrates in primer‐extension experiments, producing DNA substituted in the minor groove. The vinyl‐modified DNA was applied in thiol–ene addition and the ethynyl‐modified DNA was applied in a CuAAC click reaction to form DNA labelled with fluorescent dyes in the minor groove     

Green approaches for the synthesis of nucleotides,their conjugates and analogues

Abstract

We have developed original one-pot and protecting group-free approaches, which are also user-friendly and reliable, to synthesize nucleotides and derivatives starting from nucleoside 5’-monophosphates. Both methods present convenient set-up, i.e., non-dry solvents and reagents, substrates in their sodium or acid form, and commercially available and cheap phosphorus reagents as sodium and potassium salts.     

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.     

Synthesis and cytotoxic activity of novel curcumin analogues

Five novel curcumin analogues bearing different substituents at 4-position of phenyl group were synthesized. Their structures were confirmed by NMR and HRMS spectrum. Their cytotoxic activities against six tumor cell lines were tested by the standard MTT assay in vitro. The results indicated that four analogues （1A-1C, 1E） with solubilizing moieties showed selective potent cytotoxicity against HepG2, HeLa and CT26 cell lines, and analogue 1A and 1C exhibited more potent cytotoxicity than curcumin against CT26 cell line. It was suggested that introduction of appropriate substituents to 4-position of phenyl group might be a potential option for structural modification of curcumin.     

Synthesis, DNA polymerase incorporation, and enzymatic phosphate hydrolysis of formamidopyrimidine nucleoside triphosphates

The nucleoside triphosphates of N6-(2-deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy.dGTP) and its C-nucleoside analogue (beta-C-Fapy.dGTP) were synthesized. The lability of the formamide group required that nucleoside triphosphate formation be carried out using an umpolung strategy in which pyrophosphate was activated toward nucleophilic attack. The Klenow fragment of DNA polymerase I from Escherichia coli accepted Fapy.dGTP and beta-C-Fapy.dGTP as substrates much less efficiently than it did dGTP. Subsequent extension of a primer containing either modified nucleotide was less affected compared to when the native nucleotide is present at the 3'-terminus. The specificity constants are sufficiently large that nucleoside triphosphate incorporation could account for the level of Fapy.dG observed in cells if 1% of the dGTP pool is converted to Fapy.dGTP. Similarly, polymerase-mediated introduction of beta-C-Fapy.dG could be useful for incorporating useful amounts of this nonhydrolyzable analogue for use as an inhibitor of base excision repair. The kinetic viability of these processes is enhanced by inefficient hydrolysis of Fapy.dGTP and beta-C-Fapy.dGTP by MutT, the E. coli enzyme that releases pyrophosphate and the corresponding nucleoside monophosphate upon reaction with structurally related nucleoside triphosphates.     

An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection

The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of this task, as they do not exhibit good brightness in aqueous buffer media, develop aggregation and/or are not easily conjugated to oligodeoxynucleotides (ODNs) while keeping their photophysics intact. Herein, an important modification strategy was employed for a well-known fluorophore, 2-(4-(diethylamino)phenyl)-3-hydroxychromone (dEAF). Although this push–pull dye absorbs intensively in the visible range and shows emission with large Stokes shifts in all organic solvents, it is strongly quenched in water. This Achilles’ heel prompted us to implement a new strategy to obtain a series of dyes that retain all the photophysical features of dEAF in water, conjugate readily with oligonucleotides, and furthermore demonstrate sensitivity to hydration, thus paving the way for a high-performance fluorogenic DNA hybridization probe.     

Synthesis and optical characteristics of 4-styrylpyridinium dyes and their conjugates with antibody

Two new styryl-type dyes modified with the succinimide ester group were prepared for conjugation with antibodies. The optical characteristics of the obtained compounds in different solvents were studied, and the solvatochromic properties of these dyes were revealed. The applicability of the dyes as protein labels was demonstrated in cyto-fluorometry and fluorescence microscopy.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

Development of a facile and sensitive HPLC‐FLD method via fluorescence labeling for triterpenic acid bioavailability investigation

Triterpenic acids are widely distributed in many fruits and are known for their medicinal benefits. The study of bioavailability has been an important task for a better understanding of the triterpenic acids. Although many methods based on fluorescence labeling for triterpenic acid determination have been established, these reported methods needed anhydrous conditions, which are not suitable for the convenient study of triterpenic acid bioavailability. Inspired by that, a versatile method, which overcomes the difficulty of the reported methods, has been first developed in this study. The novel method using 2‐[12‐benzo[b ]acridin‐5‐ (12H)‐yl]‐acetohydrazide (BAAH) as the fluorescence labeling reagent coupled with high‐performance liquid chromatography with fluorescence detection was first developed for the study of triterpenic acid bioavailability. Furthermore, the labeling conditions have been optimized in order to achieve the best fluorescence labeling yield. Under the optimal conditions, the quantitative linear range of analytes was 2–1000 ng mL⁻¹, and the correlation coefficients were >0.9998. The detection limits for all triterpenic acid derivatives were achieved within the range of 0.28–0.29 ng mL⁻¹. The proposed method was successfully applied to the study of triterpenic acid bioavailability with excellent applicability and good reproducibility.     

Synthesis of unnatural 2- and 3-deoxyfuranose analogues

This Letter describes the synthesis of two racemic analogues of unnatural 3′-deoxy and 2′-deoxy sugars, where a phosphorus atom replaces the carbon atom in the 2′- or 3′-position. Two methods of four- and 5-steps were developed affording these new unnatural sugar analogues.     

Synthesis,characterization, and polymerization of propenyl ether analogues

A series of aromatic monomers bearing cationically polymerizable propenyl groups were prepared and characterized using the readily available starting materials: isoeugenol and o-allyl phenol. Monomers with both propenyl and vinyl ether functional groups were also synthesized by the reaction of these starting materials with chloroethyl vinyl ether. The reactivity of the resulting monomers in photoinitiated cationic polymerization was studied using differential scanning photocalorimetry and photogel point measurements. Their thermal properties were determined using thermogravimetric analysis. © 1994 John Wiley & Sons, Inc.