An efficient synthesis of highly functionalized dinucleotide cap analogs

An efficient synthesis of new cap analogs containing aminoallyl linkers such as m⁷G[5′]pppp[5′]U-aminoallyl and m₂^7,3′OG[5′]pppp[5′]U-aminoallyl is reported. The final cap analog has been isolated with high purity (>99.8%) after ion-exchange column purification.     

Chemical conjugation of an mRNA cap analogue with a cell-penetrating peptide as a potential membrane permeable translation inhibitor

We present a versatile method for chemical conjugation of a dinucleotide cap analogue with a cell-penetrating peptide. The final coupling reaction is between an azide-modified peptide (MPS-N₃)—a fragment that is responsible for transport of the conjugate through the cell membrane, with a biologically active compound—and an alkynylated cap structure, using the Cu(I)-catalyzed click reaction.     

Highly specific quantification of mRNA mutation in single cells based on RNase H cleavage-assisted reverse transcription(RT)-PCR

Accurate quantitation of site-specific mRNA mutation in single cells or in peripheral blood is of great significance for both biological and biomedical studies.How to eliminate the false-positive interference from the abundant normal mRNA is still a big challenge.Herein,we have proposed an LNA(locked nucleic acid)-assisted high-specificity strategy which can selectively guide the RNase H to cleave only the wildtype mRNA(wtRNA) while the mutant mRNA(mutRNA) will remain intact.The intact mutRNA ca...     

Synthesis of photolabile dUTP analogues and their enzymatic incorporation for DNA labeling

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Synthesis of a new class of ribose functionalized dinucleotide cap analogues for biophysical studies on interaction of cap-binding proteins with the 5' end of mRNA

mRNAs of primitive eukaryotes such as Caenorhabditis elegans and Ascaris summ possess two different caps at their 5' terminus. They have either a typical cap which consists of 7-methylguanosine linked via a 5',5'-triphosphate bridge to the first transcribed nucleotide (MMG cap) or an atypical hypermethylated form with two additional methyl groups at the N2 position (TMG cap). Studies on interaction between the 5' end of mRNA and proteins that specifically recognize its structure have been carried out for several years and they often require chemically modified cap analogues. Here, we present the synthesis of five novel dinucleotide MMG and TMG cap analogues designed for binding studies using biophysical methods such as electron spin resonance (ESR) and surface plasmon resonance (SPR). New analogues were prepared by derivatization of the 2',3'-cis diol of the second nucleotide in the cap structure with levulinic acid, and coupling of the obtained acetal through its carboxylic group with 4-amino-2,2,6,6-tetramethylpiperidine-1-oxyl (4-amino TEMPO), ethylenediamine (EDA) or (+)-biotinyl-3,6,9-trioxaundecanediamine (amine-PEO(3)-biotin).     

Synthesis of isoprenoid chain-contained chemical probes for an investigation of molecular interactions by using quartz crystal microbalance

Five probes including four that contained isoprenoid chain were synthesized. These probes were assembled onto the gold-coated quartz crystal chips for analysis of their interactions with four yeast proteins by using the quartz crystal microbalance technology. Results showed that 3-phosphoglycerate phosphokinase and triosephosphate isomerase had clear interactions with certain probes, while glutathione reductase and phosphoglucose isomerase gave much lower interaction signals. It also suggested that 3-phosphoglycerate phosphokinase had two sites interacting with the probe attached with a geranyl moiety. Further molecule simulation experiments provided supportive information on these intermolecular interactions. Together, our data suggested that there are hydrophobic interactions, with relatively good selectivity, between isoprenoid chain and proteins.     

Synthesis and evaluation of two novel rhodamine-based fluorescence probes for specific recognition of Fec+ ion

Two low cytotoxic fluorescence probes Rb1 and Rb2 detecting Fe³⁺ were synthesized and evaluated. Rb1 and Rb2 exhibited an excellent selectivity to Fe³⁺, which was not disturbed by Ag⁺, Li⁺, K⁺, Na⁺, NH₄⁺, Fe²⁺, Pb²⁺, Ba²⁺, Cd²⁺, Ni²⁺, Co²⁺, Mn²⁺, Zn²⁺, Mg²⁺, Hg²⁺, Ca²⁺, Cu²⁺, Ce³⁺, AcO^?, Br^?, Cl^?, HPO₄^2?, HSO₃^?, I^?, NO₃^?, S₂O₃^2?, SO₃^2? and SO₄^2? ions. The detection limits were 1.87 × 10^?7 M for Rb1 and 5.60 × 10^?7 M for Rb2, respectively. 1:1 stoichiometry and 1:2 stoichiometry were the most likely recognition mode of Rb1 or Rb2 towards Fe³⁺, and the corresponding OFF–ON fluorescence mechanisms of Rb1 and Rb2 were proposed.     

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis

Messenger RNAs (mRNAs) with phosphorothioate modification (PS‐mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell‐free translation system. Protein synthesis from PS‐mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22‐fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5′‐end to the initiation codon. Single‐turnover analysis of PS‐mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non‐natural mRNA.     

Strategies for the Dynamic Integration of Combinatorial Synthesis and Screening

Selection and amplification of only those components with the desired property–the integration of combinatorial chemistry and screening makes this possible. If the components of a combinatorial library are in a reversible equilibrium, the desired components can be selected and amplified by shifting the equilibrium of the mixture (see schematic representation).     

苯丙氨酸衍生物分子印迹聚合物的制备及手性拆分研究

以分子印迹技术合成分子印迹聚合物，作为手性色谱柱的固定相来拆分苯丙氨酸衍生物的对映异构体。采用了新型的交联剂及光引发剂。模板分子和可聚合的功能单体形成配合物是分子印迹聚合物必不可少的条件。模板分子与功能单体的比例为1:4时，获得了良好的分离效果，分离因子α为1.69。光聚合方式合成的分子印迹聚合物比热聚合方式合成的拆分能力要高。且聚合的温度越低，聚合物分离效果越好。     

Polymer–Lipid Nanoparticles for Systemic Delivery of mRNA to the Lungs

Therapeutic nucleic acids hold great promise for the treatment of disease but require vectors for safe and effective delivery. Synthetic nanoparticle vectors composed of poly(β‐amino esters) (PBAEs) and nucleic acids have previously demonstrated potential utility for local delivery applications. To expand this potential utility to include systemic delivery of mRNA, hybrid polymer–lipid nanoformulations for systemic delivery to the lungs were developed. Through coformulation of PBAEs with lipid–polyethylene glycol (PEG), mRNA formulations were developed with increased serum stability and increased in vitro potency. The formulations were capable of functional delivery of mRNA to the lungs after intravenous administration in mice. To our knowledge, this is the first report of the systemic administration of mRNA for delivery to the lungs using degradable polymer–lipid nanoparticles.     

Synthesis of a cell-permeable analogue of a glycosylphosphatidylinositol (GPI) intermediate that is toxic to the living bloodstream form of Trypanosoma brucei

The synthesis of two cell-permeable analogues related to a GPI intermediate is described for studies with living trypanosomes and human (HeLa) cells. One of the analogues is metabolised by the former GPI pathway and is toxic to the parasite Trypanosoma brucei but not to human cells.     

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

We report the design, synthesis, and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy, and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed with Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively slow FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.     

A novel ratiometric fluorescent probe based on coumarin derivative for the recognition of Al(III) and its application on test strips

A novel ratiometric probe (L) which was composed of chromone and coumarin moieties has been designed and synthesized for sensing Al³⁺ in EtOH in view of the internal charge transfer (ICT) mechanism. The free probe L exhibited a strong fluorescence emission at 477 nm, and the fluorescence emission here almost disappeared after adding Al³⁺ (10 equiv.) while a new peak appeared at 524 nm. This may be due to the enhancement of intramolecular electron transfer efficiency from donor to acceptor. In addition, this probe L could be form a 1:1 complex with Al³⁺, which could be explained by the ESI-MS spectra, and L had a low detection limit for Al³⁺ with a binding constant of 1.32 × 10⁴ M⁻¹. More importantly, L could be applied to a solid probe for rapid detection of Al³⁺ with a significant color change.     

Synthesis of Components for the Generation of Constitutional Dynamic Analogues of Nucleic Acids

The introduction of dynamic covalent polymers, in which the monomer units are linked by reversible covalent bonds and can undergo component exchange, opens up new possibilities for the generation of functional materials. Extending this approach to the generation of dynamic biopolymers in aqueous media, which are able to adapt constitution (sequence, length) to external factors (e.g., environment, medium, template), would provide an alternative approach to the de novo design of functional dynamic bio‐macromolecules. As a first step towards this goal, various mono‐ and bifunctionalised (hetero‐ and homotopic) nucleic acid‐derived building blocks of type I – X have been synthesised for the generation of dynamic main‐chain and side‐chain reversible nucleic acid analogues. Hydrazide‐ and/or acetal (protected carbonyl)‐functionalised components were selected, which differ in terms of flexibility, length, net formal charge, and hydrazide/acetal substituents, in order to explore how such factors may affect the properties (structure, solubility, molecular recognition features) of the polymer products that may be generated by polycondensation.     

Facile Route for the Synthesis of Nucleobase Analogs

Various nucleobases, 5-heteroaryl substituted 2,4-alkoxy, and/or aryloxy pyrimidines were prepared in an easy method.