5(6)-羧基荧光素标记2''-脱氧尿苷的合成

以5-碘-2'-脱氧尿嘧啶为起始原料,5(6)-羧基荧光素为荧光标记物,经6步反应合成了5(6)-羧基荧光素标记的2'-脱氧尿苷,并利用高效液相色谱(HPLC),1H NMR和13C NMR对目标化合物的纯度和结构进行了表征.     

含长碳烷基核苷氢亚磷酸酯衍生物的合成与表征

通过将抗病毒药物核苷(3'-叠氮-2',3'-二脱氧胸苷AZT或2',3'-二脱氢-2',3'-二脱氧胸苷d4T)与三氯化磷反应, 然后在不同的醇解试剂作用下, 一锅法合成得到6个含长链烷基的核苷氢亚磷酸二酯衍生物, 并采用³¹P NMR, ¹H NMR, ¹³C NMR和ESI-MS对其结构进行了表征.     

5(6)-羧基荧光素标记2′-脱氧尿苷的合成

以5-碘-2'-脱氧尿嘧啶为起始原料, 5(6)-羧基荧光素为荧光标记物, 经6步反应合成了5(6)-羧基荧光素标记的2′-脱氧尿苷, 并利用高效液相色谱(HPLC), ¹H NMR和¹³C NMR对目标化合物的纯度和结构进行了表征.     

2-甲氧基-3-氟-4-碘吡啶的合成

2-甲氧基-3-氟-4-碘吡啶是一个重要的医药化工中间体,其合成路线未见文献报道。以2-甲氧基-3-氟-5-氯吡啶为起始原料,经氢解和碘代两步反应合成标题化合物,总收率62.8%,其结构经¹H NMR, ¹³C NMR和MS确证。     

用于DNA合成测序的可断裂连接单元研究现状

DNA测序技术是遗传基因组相关疾病研究的基础。合成测序是DNA二代测序技术中非常重要的一种。合成测序技术能够有效地实现大规模平行测序,大大提高测序通量的同时也降低成本,目前已得到广泛的应用。在合成测序中,首先需要合成荧光素标记的核苷酸,作为能够参与DNA链延伸的循环可逆终端。已有文献报道的可逆终端结构主要包括单位点修饰(MRT)和双位点修饰(DRT)两种类型。DRT类型可逆终端的最大优势是DNA聚合酶容易识别且合成路线简单,能够较好地应用于DNA合成测序。在此过程中可断裂连接单元将核苷酸和荧光素连接起来,它的性质直接决定了测序的效率、读长等关键指标。本文主要对目前用于DNA合成测序的可断裂连接单元研究现状进行介绍,并对其发展前景进行了展望。     

伊贝沙坦的合成

以环戊酮为起始原料,与氰胺、戊酰化物反应得到N-(1-氰基环戊基)戊酰胺(2); 2经双氧水水解得到1-戊酰胺基环戊烷-1-羟酰胺(3);化合物3依次经分子内环合、酸化和缩合制得4'-[(2-丁基-4-氧-1,3-二氮杂螺环[4,4]壬-1-烯-3-基)甲基]联苯-2-甲腈(5);化合物5与叠氮钠发生叠氮化反应合成了伊贝沙坦(6),总收率40.7 %,纯度99.5 %,其结构经¹H NMR、 ¹³C NMR和HR-MS(ESI)确证。      

新型含1,2,3-三氮唑的染料木素糖缀合物的合成

以染料木素为起始原料,经两步反应制得中间体7-O-炔丙基染料木素(3);以CuI为催化剂,3与叠氮乙酰基糖经Click反应合成了7-O-［1-(2,3,4,6-四-O-乙酰基-β-D-糖苷)1H-1,2,3-三氮唑-4-甲基］-染料木素(5a~5c); 5a~5c经去乙酰基制得三种含1,2,3-三氮唑的氮苷染料木素糖缀合物(6a~6c)。3, 5和6均为新化合物,其结构经¹H NMR, ¹³C NMR和HR-MS表征。     

5-二茂铁基吡唑啉衍生物的合成及性质

以甲酰基二茂铁和2-乙酰基吡啶为原料, 合成了3个1-芳香酰基-3-(2-吡啶基)-5-二茂铁基-2-吡唑啉衍生物(3~5), 通过红外光谱、质谱、¹H NMR、¹³C NMR和元素分析对其进行了表征, 并对化合物4的单晶结构进行了解析. 研究了该类化合物的电化学性质及紫外、荧光光谱, 并借助密度泛函理论(DFT)计算从理论上加以解释.     

基于ESIPT机理香豆素荧光化合物的合成和光学性质

以3-碘苯酚为原料,经过甲酰化反应、Knoevenagel缩合反应、Sonogashira偶联和还原反应得到以香豆素为母体的目标化合物7-（甲氧基苯乙炔基）香豆素-3-甲醇(5)。化合物5的结构经过¹H NMR, ¹³C NMR和MS(ESI)分析表征确认。并对化合物5的光学性质进行了研究,结果表明：化合物5具有典型的 ESIPT 发光机理,可以构建比率计量型双光子荧光探针。      

新型芳基修饰的尿苷型荧光探针的合成及其性能

4-氟苯乙酮经二氧化硒氧化得到4-氟苯甲酰甲酸(1); 1与盐酸氨基脲在碱性条件下经环合反应制得5-(4-氟苯基)-6-氮杂嘧啶(2); 2与1-乙酰氧基-2,3,5-三苯甲酰氧基-1-β-D-呋喃核糖在无水乙腈中反应得2′,3′,5′-三苯甲酰氧基-5-(4-氟苯基)-6-氮杂尿苷(3); 3在甲醇中水解合成了一种新型荧光核苷探针--5-(4-氟苯基)-6-氮杂尿苷(4),其结构经¹H NMR, ¹³C NMR和MS(ESI)表征。并研究了4的性能。结果表明：4在水中的量子产率高达0.81,对极性变化敏感;4可选择性识别Pd²⁺,在5.0×10^-7~5.0×10^-6 mol·L^-1能定量检测Pd²⁺。     

Design and synthesis of a chemically cleavable fluorescent nucleotide, 3'-O-allyl-dGTP-allyl-bodipy-FL-510, as a reversible terminator for DNA sequencing by synthesis

We report the construction of a novel chemically cleavable fluorescent labeling system based on an allyl group to modify nucleotide for DNA sequencing by synthesis (SBS). We have found that an allyl moiety can be used successfully as a linker to tether a fluorophore to a 3'-O-allyl-modified nucleotide, forming a chemically cleavable reversible terminator, 3'-O-allyl-dGTP-allyl-Bodipy-FL-510, for application in SBS. The fluorophore and the 3'-allyl group on a DNA extension product, which is generated by incorporating 3'-O-allyl-dGTP-allyl-Bodipy-FL-510, are removed simultaneously in 30 s by Pd-catalyzed deallylation in aqueous buffer solution. The resulting DNA product is successfully used as a primer for further extension in polymerase reaction. This one-pot dual-deallylation reaction thus allows the reinitiation of the polymerase reaction and increases the SBS efficiency.     

A One‐Pot Chemically Cleavable Bis‐Linker Tether Strategy for the Synthesis of Heterodimeric Peptides

Heterodimeric peptides linked by disulfide bonds are attractive drug targets. However, their chemical assembly can be tedious, time‐consuming, and low yielding. Inspired by the cellular synthesis of pro‐insulin in which the two constituent peptide chains are expressed as a single‐chain precursor separated by a connecting C‐peptide, we have developed a novel chemically cleavable bis‐linker tether which allows the convenient assembly of two peptide chains as a single “pro”‐peptide on the same solid support. Following the peptide cleavage and post‐synthetic modifications, this bis‐linker tether can be removed in one‐step by chemical means. This method was used to synthesize a drug delivery‐cargo conjugate, TAT‐PKCi peptide, and a two‐disulfide bridged heterodimeric peptide, thionin (7‐19)‐(24‐32R), a thionin analogue. To our knowledge, this is the first report of a one‐pot chemically cleavable bis‐linker strategy for the facile synthesis of cross‐bridged two‐chain peptides.     

Structural evolution of environmentally responsive cationic liposome-DNA complexes with a reducible lipid linker

Environmentally responsive materials (i.e., materials that respond to changes in their environment with a change in their properties or structure) are attracting increasing amounts of interest. We recently designed and synthesized a series of cleavable multivalent lipids (CMVLn, with n = 2-5 being the number of positive headgroup charges at full protonation) with a disulfide bond in the linker between their cationic headgroup and hydrophobic tails. The self-assembled complexes of the CMVLs and DNA are a prototypical environmentally responsive material, undergoing extensive structural rearrangement when exposed to reducing agents. We investigated the structural evolution of CMVL-DNA complexes at varied complex composition, temperature, and incubation time using small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS). A related lipid with a stable linker, TMVL4, was used as a control. In a nonreducing environment, CMVL-DNA complexes form the lamellar (L(α)(C)) phase, with DNA rods sandwiched between lipid bilayers. However, new self-assembled phases form when the disulfide linker is cleaved by dithiothreitol or the biologically relevant reducing agent glutathione. The released DNA and cleaved CMVL headgroups form a loosely organized phase, giving rise to a characteristic broad SAXS correlation profile. CMVLs with high headgroup charge also form condensed DNA bundles. Intriguingly, the cleaved hydrophobic tails of the CMVLs reassemble into tilted chain-ordered L(β') phases upon incubation at physiological temperature (37 °C), as indicated by characteristic WAXS peaks. X-ray scattering further reveals that two of the three phases (L(βF), L(βL), and L(βI)) constituting the L(β') phase coexist in these samples. The described system may have applications in lipid-based nanotechnologies.     

An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR

Single-step aqueous cross-coupling reactions of nucleobase-halogenated 2'-deoxynucleosides (8-bromo-2'-deoxyadenosine, 7-iodo-7-deaza-2'-deoxyadenosine, or 5-iodo-2'-deoxy-uridine) or their 5'-triphosphates with 4-boronophenylalanine or 4-ethynylphenylalanine have been developed and used for efficient synthesis of modified 2'-deoxynucleoside triphosphates (dNTPs) bearing amino acid groups. These dNTPs were then tested as substrates for DNA polymerases for construction of functionalized DNA through primer extension and PCR. While 8-substituted adenosine triphosphates were poor substrates for DNA polymerases, the corresponding 7-substituted 7-deazaadenine and 5-substituted uracil nucleotides were efficiently incorporated in place of dATP or dTTP, respectively, by Pwo (Pyrococcus woesei) DNA polymerase. Nucleotides bearing the amino acid connected through the less bulky acetylene linker were incorporated more efficiently than those directly linked through a more bulky phenylene group. In addition, combinations of modified dATPs and dTTPs were incorporated by Pwo polymerase. Novel functionalized DNA duplexes bearing amino acid moieties were prepared by this two-step approach. PCR can be used for amplification of duplexes bearing large number of modifications, while primer extension is suitable for introduction of just one or several modifications in a single DNA strand.     

A novel linker for solid-phase synthesis cleavable under neutral conditions

A novel linker cleavable under neutral conditions has been developed for the solid-phase synthesis of base-labile compounds. The linker is comprised of a 3-azidomethyl-4-hydroxybenzyl alcohol moiety, and the azidomethyl group in the linker is readily converted to an aminomethyl group by treatment with a phosphine reagent in the presence of water to result in an intramolecular cyclization to release the compounds. Using the linker, a base-labile dinucleoside methyl phosphate was synthesized on a highly cross-linked polystyrene (HCP) support and cleaved successfully from the resin without decomposition of the product.     

Design and synthesis of a photocleavable fluorescent nucleotide 3'-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis

DNA sequencing by synthesis (SBS) using reversible fluorescent nucleotide terminators is potentially an efficient approach to address the limitations of current DNA sequencing techniques. Here, we report the design and synthesis of a 3'-O-allyl photocleavable fluorescent nucleotide analogue, 3'-O-allyl-dGTP-PC-Bodipy-FL-510, as a reversible terminator for SBS. The nucleotide is efficiently incorporated by DNA polymerase into a growing DNA strand to terminate the polymerase reaction. After that, the fluorophore is photocleaved quantitatively by irradiation at 355 nm, and the allyl group is rapidly and efficiently removed by using a Pd-catalyzed reaction under DNA-compatible conditions to regenerate a free 3'-OH group to reinitiate the polymerase reaction. Two cycles of such steps were successfully demonstrated to sequence a homopolymeric region of a DNA template, facilitating the development of SBS as a viable approach for high-throughput DNA sequencing.     

Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.     

Reversible formation of hybrid nanostructures via an organic linkage

A reversible formation of hybrid nanostructures has been successfully achieved via an organic linker containing a cleavable disulfide bond, which provides a general route to the preparation of controllable composite architectures using particles of distinct compositions.     

A Useful Disulfide Linker for Single‐Bead Analysis of Peptide Libraries

A disulfide‐linker for conventional peptide synthesis, attached to a PEGA‐resin, has been developed. Reductive hydrolysis cleaves the linker within minutes, liberating the synthesized peptide for rapid sequencing by tandem mass spectrometry. The method has been tested for ten peptides in a single‐bead fashion.