Sequential Gene Silencing Using Wavelength‐Selective Caged Morpholino Oligonucleotides

Spectrally differentiated caged morpholino oligonucleotides (cMOs) and wavelength‐selective illumination have been used to sequentially inactivate organismal gene function. The efficacy of these reverse‐genetic chemical probes has been demonstrated in zebrafish embryos, and these reagents have been employed to examine the mechanisms of mesoderm patterning.     

Quantitative parameters of cooperative interactions of oligonucleotides within tandem complexes

Quantitative parameters of cooperative interactions of deoxyribooligonucleotides within perfect complementary complexes with a nick in one strand and imperfect complexes containing one mismatched base pair in the nick were obtained. One complementary strand was represented by 22-mer oligonucleotides, while the other, by two short 8-mer oligonucleotides forming a tandem complex with the central part of the 22-mer. In the tandem complexes, the 8-mers form contacts of the following types: 5"-Py*pPy-3", 5"-Pu*pPy-3", and 5"-Pu*pPu-3", where p is phosphate, Py and Pu are pyrimidine and purine nucleosides, respectively, and * stands for a nick. In each incompletely complementary complex, the mismatched base pair in the nick is formed by the 3"-end nucleoside of the 8-mer oligonucleotide and by the nucleoside located in the middle of the 22-mer oligonucleotide. The alkylating 4-[N-(2-chloroethyl)-N-methylamino]phenyl}methylamino group (RCl) is linked through the 5"-end phosphate of the 8-mers (reagents) close to 3"-ends of the 22-mers. The dependences of the limit extents of alkylation of 22-mers (targets) at zero and saturating concentrations of the neighbor oligonucleotides (effectors) on the initial concentration of RCl-derivatives of oligonucleotides (reagents) were used to calculate the association constants K _X of the reagent with the target. The ratio of these constants was used to determine the parameters of contact cooperativity , which characterize the interactions at the junction of two oligonucleotides within the tandem complexes.     

Phosphoramidites and solid supports based on N-substituted 2,4-dihydroxybutyramides: universal reagents for synthesis of modified oligonucleotides

A general and convenient method for synthesis of modified oligonucleotides by use of new non-nucleoside phosphoramidites is reported. A chiral 1,3-diol backbone of the modifying reagents is generated either from (R)-(+)-α-hydroxy-γ-butyrolactone or (R)-(−)-pantolactone. Aliphatic amines were acylated with the lactones to give the corresponding N-substituted 2,4-dihydroxybutyramides. After protection of a side chain, if necessary, the diols were converted into phosphoramidites or solid supports suitable for use in oligonucleotide synthesis. The reagents allow single, multiple or combined introduction of various functions (e.g., alkylamine, imidazole and pyrene residues) into synthetic oligonucleotides. The structures of the conjugates were confirmed by MALDI-TOF mass spectrometry.     

Liquid‐Phase RNA Synthesis by Using Alkyl‐Chain‐Soluble Support

Recent progress in the RNA therapeutics has increased demand for the synthesis of large quantities of oligoribonucleotides. The assembly of RNA oligomers relies mainly on solid‐phase approaches. These allow rapid product purification and the ability to drive a target reaction to completion through the use of excess reagents. Despite the known advantages of solid‐phase synthesis, some issues in the process remain to be addressed, such as low and limited scale, reagent accessibility, and the use of a very large excess of reagents. Herein, we report a highly efficient and practical method of liquid‐phase synthesis of RNA oligomers by using alkyl‐chain‐soluble support. We demonstrate the utility of the liquid‐phase method through 21‐mer RNA synthesis on a gram scale.     

Oligonucleotides containing new fluorescent 1-phenylethynylpyrene and 9,10-bis(phenylethynyl)anthracene uridine-2′-carbamates: synthesis and properties

The synthesis of two novel fluorescent uridine-2′-carbamate phosphoramidites is described. The reagents carrying fluorescent polyaromatic hydrocarbons 1-phenylethynylpyrene (PEPy) or 9,10-bis(phenylethynyl)anthracene (BPEA) are suitable for oligonucleotide synthesis. Prepared oligonucleotide conjugates show strong dye emissions at 401 and 485 nm, but low FRET rate when located in the oligonucleotide duplex. The dyes show considerable compensation of the usual carbamate duplex destabilization. The possible explanation of both effects is binding of PEPy and BPEA to the minor groove of the DNA duplex.     

Ionic strength of electrospray droplets affects charging of DNA oligonucleotides

The fundamental aspects of charging in electrospray ionization (ESI) are hotly debated. In the present study, ESI charging of DNA oligonucleotides was explored in both positive (ESI+) and negative (ESI?) polarity using mass spectrometry detection. Single‐stranded 12‐mer CCCCAATTCCCC in buffer solution (aqueous NH₄Ac, 100 mM) produced similar charge state distribution (CSD) in either ESI+ or ESI?. Similarity of CSD in ESI+ and ESI? was also observed for the double‐stranded 12‐mer CGCGAATTCGCG. By adding typical low‐vapor reagents (e.g. m‐nitro benzyl alcohol, m‐NBA; sulfolane) into the same buffer solution (<0.5% w/v), both CCCCAATTCCCC and CGCGAATTCGCG revealed strong supercharging (SC) effect in ESI?, while very little or no SC effect was observed in ESI+. With either sulfolane or m‐NBA, the CGCGAATTCGCG duplex dissociated into single strands in ESI?. No SC was observed in both ESI+ and ESI? for thermally denatured CGCGAATTCGCG duplex in NH₄Ac buffer without the reagents. These findings are difficult to reconcile with the earlier model, which attributes SC in aqueous buffer solution to the conformational changes of analytes. Our observations suggest that the ionic strength of ESI droplets strongly affects the CSD of biopolymers such as DNA oligonucleotides and that SC effect is related to the depletion of ionic strength during the ESI process. Copyright © 2014 John Wiley & Sons, Ltd.     

Investigation of surface oligonucleotide-binding proteins of eucaryotic cells by affinity modification with reactive oligonucleotide derivatives

Interactions between oligodeoxyribonucleotides (ODN) with different sequences and cell proteins were examined using the affinity modification by [³²P]-labeled reactive oligonucleotide derivatives. 3"-Terminal ribouridine oxidized with sodium periodate, 4-[(N-2-chloroethyl-N-methyl)amino]benzylamine, and the maleimide residue were used as reactive groups. All the compounds used are specific reagents. The set of the discovered nucleic acid-binding (NA-binding) proteins depends on the chemical properties of the affinity reagent. The presence of the hydrophobic group at the 5"-terminus of the ODN molecule is the key factor determining the variety of the discovered NA-binding proteins. The cells of different origin (A431, HeLa, KB, MCF-7, Hap-2, K562, Cos-7, NIH/3T3, human-lung primary epithelial cells, and porcine kidney primary cells) are characterized by the same set of NA-binding proteins whose affinity modifications depends on the conditions of incubation of oligonucleotides with the cells. Treatments of cells disturbing the integrity of the cellular membrane (scrapping, treatment with trypsin, or cell permeabilization with streptolysin O or saponin), disrupt interactions between NA-binding proteins from native cells and ODN.     

Molecular Lamps and Molecular Golf Balls

The concave shielding of the active site of enzymes has been transferred to standard reagents of organic chemistry and concave reagents have been synthesized which possess a lamp-like geometry (concave 1,10-phenanthrolines 1–2, concave pyridines 3). The special concave geometry of these reagents is responsible for their selectivity in metal ion catalyzed (Pd-catalyzed allylations, Cu(I)-catalyzed cyclopropanations) and base catalyzed (acylation of alcohols by ketenes) reactions. For an easier recovery, these reagents have been attached to Merrifield polymers and to dendrimers. Higher generations of dendrimers loaded with concave reagents will possess a golf ball geometry.     

In vitro metabolism of 2′-ribose unmodified and modified phosphorothioate oligonucleotide therapeutics using liquid chromatography mass spectrometry

Antisense oligonucleotides (ASOs) have been touted as an emerging therapeutic class to treat genetic disorders and infections. The evaluation of metabolic stability of ASOs during biotransformation is critical due to concerns regarding drug safety. Because the effects of the modifications in ASOs on their metabolic stabilities are different from unmodified ASOs, studies that afford an understanding of these effects as well as propose proper methods to determine modified and unmodified ASO metabolites are imperative. An LC–tandem mass spectrometry method offering good selectivity with a high-quality separation using 30 mm N,N-dimethylcyclohexylamine and 100 mm 1,1,1,3,3,3-hexafluoro-2-propanol was utilized to identify each oligonucleotide metabolite. Subsequently, the method was successfully applied to a variety of in vitro systems including endo/exonuclease digestion, mouse liver homogenates, and then liver microsomes, after which the metabolic stability of unmodified versus modified ASOs was compared. Typical patterns of chain-shortened metabolites generated by mainly 3′-exonucleases were observed in phosphodiester and phosphorothioate ASOs, and endonuclease activity was identically observed in gapmers that showed relatively more resistance to nuclease degradation. Overall, the degradation of each ASO occurred more slowly corresponding to the degree of chemical modifications, while 5′-exonuclease activities were only observed in gapmers incubated in mouse liver homogenates. Our findings provide further understanding of the impact of modifications on the metabolic stability of ASOs, which facilitates the development of future ASO therapeutics.     

光学分析试剂

光学分析试剂是建立有关光学分析方法的物质基础,在许多领域中具有极强的应用背景。本文介绍若干种光学分析试剂尤其是高分子显色剂的研究进展。     

X-Ray and NMR Structural Data of Ethynylbenziodoxolones (EBXs) Reagents and Their Analogues

First synthesized in 1991, EthynylBenziodoXolones (EBXs) – cyclic hypervalent iodine reagents derived from 2-iodobenzoic acid – are now among the most versatile electrophilic alkynylation reagents. Due to their cyclic structure, these reagents exhibit enhanced stability compared to previously used alkynyl iodonium salts. Over the last decade, both the iodoheterocycle and the arene ring have been extensively modified to fine-tune the reactivity of the reagents, resulting in new analogues such as Ethynylbenziodoxoles (EBxs) or N-heterocyclic reagents. In this article, we have for the first time compiled the structural data available for EBXs and their analogues, focusing especially on X-Ray and NMR data. For selected compounds, molecular electrostatic potentials (MEP) have also been calculated. When considering the tight relationship between structure and reactivity in hypervalent iodine reagents, the collected data is expected to be highly useful for further developments in the field.     

Increased Affinity of 2′‐O‐(2‐Methoxyethyl)‐Modified Oligonucleotides to RNA through Conjugation of Spermine at Cytidines

Structural modification at the 2′‐O‐position of riboses in oligonucleotide therapeutics is of critical importance for their use as drugs. To date, the methoxyethyl (MOE) substituent is the most important and features in dozens of antisense oligonucleotides that have been tested in clinical trials. Yet, the search for new improved modifications continues in a quest for increased oligonucleotide potency, improved transport in vivo and favorable metabolism. Recently, we described how the conjugation of spermine groups to pyrimidines in oligonucleotides vastly increases their affinity for complementary RNAs through accelerated binding kinetics. Here we describe how spermines can be linked to the exocyclic amino groups of cytidines in MOE‐oligonucleotides employing a straightforward ‘convertible nucleoside approach’ during solid phase synthesis. Singly‐ or doubly‐modified oligonucleotides show greatly enhanced affinity for complementary RNA, with potential for a new generation of MOE‐based oligonucleotide drugs.     

Stabilization of ATP reagents containing firefly <Emphasis Type="Italic">L. mingrelica</Emphasis> luciferase by polyols

ATP reagents containing 2–20% of ethylene glycol, glycerol, or PEG-8000 have been prepared. Polyols inhibit the activity of the ATP reagents by 20–40%, and addition of 0.75 mM Triton X-100 prevents this inhibition. The optimal polyol concentration is 10%. The kinetics of thermoinactivation of the ATP reagents in solution at 37, 20, and 4°C has been studied. At all temperatures, the stability of ATP reagents increases two-to fivefold in the presence of polyols. A solution of ATP reagents kept at 4°C for 180 h retains 100% activity. The activity half-life is 15 days.     

Copper(I) thiolate catalysts in asymmetric conjugate addition reactions

[structure: see text] Full conversion and enantioselectivities up to 83% have been obtained in the conjugate addition reactions of diethyl zinc to Michael acceptors catalyzed by well-defined (chiral) copper(I) aminoarenethiolates. Interesting differences between organozinc or Grignard reagents have been found: for cyclic enones R(2)Zn reagents afford better results, whereas earlier work showed that RMgX reagents react more selectively with acyclic enones.     

Added-metal-free catalytic nucleophilic addition of Grignard reagents to ketones

On the basis of the investigation of the combinational effect of quaternary ammonium salts and organic bases, an added-metal-free catalytic system for nucleophilic addition reactions of a variety of Grignard reagents to diverse ketones in THF solvent has been developed to produce tertiary alcohols in good to excellent yields. By using tetrabutylammonium chloride (NBu(4)Cl) as a catalyst and diglyme (DGDE) as an additive, this system strongly enhances the efficiency of addition at the expense of enolization and reduction. NBu(4)Cl should help to shift the Schlenk equilibrium of Grignard reagents to the side of dimeric Grignard reagents to favor the additions of Grignard reagents to ketones via a favored six-membered transition state to form the desired tertiary alcohols, and DGDE should increase the nucleophilic reactivities of Grignard reagents by coordination. This catalytic system has been applied in the efficient synthesis of Citalopram, an effective U.S. FDA-approved antidepressant, and a recyclable version of this catalytic synthesis has also been devised.     

Continuous‐Flow Electrochemical Generator of Hypervalent Iodine Reagents: Synthetic Applications

An efficient and reliable electrochemical generator of hypervalent iodine reagents has been developed. In the anodic oxidation of iodoarenes to hypervalent iodine reagents under flow conditions, the use of electricity replaces hazardous and costly chemical oxidants. Unstable hypervalent iodine reagents can be prepared easily and coupled with different substrates to achieve oxidative transformations in high yields. The unstable, electrochemically generated reagents can also easily be transformed into classic bench‐stable hypervalent iodine reagents through ligand exchange. The combination of electrochemical and flow‐chemistry advantages largely improves the ecological footprint of the overall process compared to conventional approaches.     

Synthetic application of water-soluble hypervalent iodine reagents in aqueous media

Along with the vigorous development of hypervalent iodine chemistry, water-soluble hypervalent iodine reagents have received considerable attentions in recent years. In order to obtain water-soluble hypervalent iodine reagents, two strategies have been employed including introduction of hydrophilic functional groups onto the phenyl ring and formation of complex of iodosylbenzene with crown ether. And, it is observed that four kinds of hypervalent iodine reagents exhibit more or less solubility in water including hypervalent iodine reagents containing hydrophilic ligands, diaryliodonium salts, oligomeric iodosylbenzene sulfate, and iodylbenzene and its derivatives. In this review, we summarize these water-soluble hypervalent iodine reagents and their broad synthetic applications in aqueous media.     

Simple and efficient method for the synthesis of highly substituted imidazoles using zeolite-supported reagents

Cu(II) nitrate impregnated zeolite has been used as an efficient supported reagent for an improved and rapid one-pot synthesis of 2,4,5-trisubstituted and 1,2,4,5-tetrasubstituted imidazoles in excellent yields. Condensation in the presence of supported reagents with operational simplicity, inexpensive reagents, high yield of products, and the use of non-toxic reagents makes this synthetic protocol, an attractive one.     

Investigation of short lived radicals in aromatic nucleophilic substitution by use of nitroso compounds as scavengers

Radical intermediates formed in reaction of substituted nitrobenzene compounds with nucleophilic reagents have been trapped by t-nitrosobutane to yield nitroxide radicals which have been characterized in situ by ESR. The formation of short-lived radicals originating from reagents and solvents has been shown.     

有机高价碘化学简介及其应用

近几十年来,有机高价碘化学蓬勃发展,有机高价碘试剂也受到化学合成工作者的广泛关注,关于有机高价碘试剂的反应性研究也获得了迅猛发展。有机高价碘试剂作为绿色、高效、多功能化的氧化剂,通常容易制备且操作简单,与已有的合成方法相比,该类试剂参与的反应表现出了许多独特的优点,并且具有与汞、铬、铅、铊等重金属试剂类似的反应性,但却没有这些试剂所带来的毒性和环境污染问题。本文介绍了有机高价碘化学的起源与发展,高价碘试剂的结构特点与分类,高价碘试剂在有机合成、材料化学及工业合成中的应用。