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In-situ synthesis of quantum dots in the nucleus of live cells

National Science Review 2024年第3期11卷 172-182页

作者： Yusi Hu Zhi-Gang Wang Haohao Fu chuanzheng zhou Wensheng Cai Xueguang Shao Shu-Lin Liu Dai-Wen Pang State Key Laboratory of Medicinal Chemical Biology Frontiers Science Centre for New Organic MatterTianjin Key Laboratory of Biosensing and Molecular Recognition Research Centre for Analytical Sciences College of Chemistry School of Medicine and Frontiers Science Centre for Cell Responses Nankai University Haihe Laboratory of Sustainable Chemical Transformations

The cell nucleus is the main site for the storage and replication of genetic material, and the synthesis of substances in the nucleus is rhythmic, regular and strictly regulated by physiological processes. However,whether exogenous substances, such as nanoparticles, can be synthesized in situ in the nucleus of live cells has not been reported. Here, we have achieved in-situ synthesis of CdSxSe1-xquantum dots（QDs） in the nucleus by regulation of the glutathione（GSH） metabolic pathway. High enrichment of GSH in the nucleus can be accomplished by the addition of GSH with the help of the Bcl-2 protein. Then, high-valence Se is reduced to low-valence Se by glutathione-reductase-catalyzed GSH, and interacts with the Cd precursor formed through Cd and thiol-rich proteins, eventually generating QDs in the nucleus. Our work contributes to a new understanding of the syntheses of substances in the cell nucleus and will pave the way for the development of advanced ‘supercells’.

关键词： glutathione live cell nucleus quantum dot intracellular synthesis

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DNA damage in nucleosomes

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Science China Chemistry 2019年第5期62卷 561-570页

作者： Mengtian Ren Jing Bai Zhen Xi chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai University

Eukaryotic genomic DNA is packed into chromatin, whose fundamental structural unit is the nucleosome. As DNA-histone protein complexes, nucleosomes show different properties toward exogenous and endogenous DNA-damaging agents. This review summarizes nucleosome DNA damage due to different sources, including alkylating agents, radicals, UV radiation and reactive DNA damage intermediates. In most cases, the histone core protects the associated DNA against damage via its structure and/or scavenging of damaging agents. In contrast, histones react with damaged DNA and, in some instances, catalyze DNA damage in the nucleosome. The biological consequence of nucleosome DNA damage and future prospects in this field are briefly discussed.

关键词： DNA damage DNA alkylation DNA-protein cross-link nucleosome radical reactive intermediate

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Transesterification Reaction and the Repair of Embedded Ribonucleotides in DNA Are Suppressed in Nucleosome Core Particles

Transesterification Reaction and the Repair of Embedded Ribo...

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第十一届全国化学生物学学术会议

作者： Mengtian Ren chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai University

Ribonucleotides can be incorporated into DNA through many different cellular processes. Embedded ribonucleotides lead to genomic instability through spontaneous ribonucleotide cleavage via internal transesterification. Ribonucleotides misincorporated in genomic DNA can be removed by RNase HII through the ribonucleotide excision repair(RER) pathway.[1] Herein, based on in vitro reconstituted nucleosome core particles(NCPs) containing a single ribonucleotide at different positions, we studied the kinetics of ribonucleotide cleavage via the internal transesterification reaction and repair of the ribonucleotides by RNase HII in NCPs. Our results show that ribonucleotide cleavage via the internal transesterification in NCPs is suppressed compared to that in free DNA. Ribonucleotide repair by RNase HII in NCPs exhibits a strong correlation between the translational and rotational positions of the ribonucleotides.[2-3] Hence, misincorporated ribonucleotides in NCPs exhibit decreased transesterification rates and repair efficiency, which may result in numerous and persistent ribonucleotides in genomic DNA, and thus exert other deleterious effects on DNA.

关键词： Nucleosome Core Particles Ribonucleotides Transesterification Reaction RNase HII

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Synthesis of Inositol Hexakisphosphate Deravatives to Study Hexakisphosphate-Dependent CRL-CSN Complex Assembly

Synthesis of Inositol Hexakisphosphate Deravatives to Study ...

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第十届全国化学生物学学术会议

作者： ChuanlongZang chuanzheng zhou Feng Rao State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai University Department of Biology South University of Science and Technology of China

Inositol hexakisphosphate（IP6） has been found to be associated with ubiquitination mediated protein degradation. Cullin Ring E3 ligases（CRL） are activated by neddylation and regulated by dynamic complex formation with the deneddylase COP9 signalosome（CSN）. IP6 was proposed to fulfill its function by regulating CRL-CSNinteraction. To reveal the role of IP6 underlying CRL-CSN complex assembly, biotinylated IP6 derivatives were synthesized and were used to probe the orientation of IP6 at the CRL-CSN interface. Together with biochemical and computational studies, the data suggest that IP6 is bound primarily by a positively charged surfaced on CSN2, with its 2’-phosphate interacting with Roc1 to bridge CRL-CSN complexes.

关键词： Inositol hexakisphosphate Cullin Ring E3 ligases COP9 signalosome CRL-CSN complex

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Synthesis of 5-Methylene Pyrrolone Derivatives for Cysteine Bioconjugation

Synthesis of 5-Methylene Pyrrolone Derivatives for Cysteine ...

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第十届全国化学生物学学术会议

作者： GuoceAn Yingqian Zhang chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai UniversityCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)

Cysteine is especially attractive for site-specific chemical modification owing to its high nucleophilicity at physiological conditions and relatively low natural abundance. In our previous studies, we found 5-methylene pyrrolone (5MP) is highly thiol-specific and tracelessly removable bioconjugation molecule. 5MPs exhibit significantly improved stability under physiologically relevant conditions and cysteine specificity compared to commonly used analogues, maleimides. The reversible property of thiol-5MP conjugate render this approach invaluable in some cases. However, in many other situations, stable bioconjugation on cysteine is desired. Here, some 5MP derivatives[(1), R, R, R=CH/Br ] were synthesized and their reactivity with BME were evaluated. The effect of substitutions on the reactivity of 5MP toward thiol and stability of 5MP-thiol conjugates were summarized.

关键词： Bioconjugation 5-methylene pyrrolone Cysteine

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The Synthesis and Biological Properties of C4'-CF3 Modified Ribonucleotides

The Synthesis and Biological Properties of C4'-CF3 Modified ...

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第十届全国化学生物学学术会议

作者： Fengmin Guo Zhen Xi chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai University

Due to the specific properties of fluorine atom, such as small size, high electronegativity, carbon-fluorine bone strength and sensitivity of 19 F NMR, the introduction of fluorine atom(s) into biomolecules can bring about remarkable and profound physical, chemical and biological properties.1 In this study, C4’-CF modified ribonucleotides were synthesized2. NMR and calculation studies showed that C4’-CF modification constrained the ribose sugar moiety in DNA-like(South puckering) conformation. The unique conformation of this modified nucleotide in both oligo-DNA and oligo-RNA was further confirmed by biophysical studies. Potential applications of this C4’-CF modified ribonucleotides were demonstrated as well.

关键词： Synthesis Fluorinated nucletides Biological properties

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Synthesis,Biophysical and Biochemical Studies of C4’-OCH3 Modified Ribonucleotides

Synthesis,Biophysical and Biochemical Studies of C4’-OCH3 M...

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第十一届全国化学生物学学术会议

作者： Chaochao Fan Zhen Xi chuanzheng zhou State Key of Laboratory of Element-organic Chemistry college of ChemistryNankai University

C4′-modified ribonucleotides have recently attracted great interests.[1] C4′ modifications introduce stereoelectronic effect and thus modulate the conformation of the ribose, without losing the 2′-OH. For instance, we have synthesized C4′-Me modified rU（C4′-Me-rU） and found it is constrained in an unusual South conformation.[2, 3] Methoxy group generally render different electronic effects than methyl group. Herein, we synthesized 4’-OCH3-rU and introduced it into oligonucleotides based on solid phase synthesis（Figure 1）. The structure of 4’-OCH3-rU was studied by NMR, and the biophysical and biochemical properties of these modified oligonucleotides were examined.

关键词： ribonucleotide ribose confirmation chemical modifications

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2-（2-azidoethyl）-2,5-di-（4,5-Dimethoxy-2-nitro-benzyloxy）-2,5-dihydr ofuran as a potential photoaffinity crosslinking reagent

2-（2-azidoethyl）-2,5-di-（4,5-Dimethoxy-2-nitro-benzyloxy...

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第十届全国化学生物学学术会议

作者： Jiahui Li Mengdi Shang Xiaoping zhou Zhen Xi chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai University

Photoaffinity crosslinking is widely used in biomolecules interaction studies. A few photoreactive groups, such as azide, diazirine and benzophenone, have introduced to fulfill such a purpose. However, all of these groups suffer from low cross-linking efficiency as a result of either low reactivity or photodecomposition. We design and synthesized 2-（2-azidoethyl）-2,5-di-（4,5-Dimethoxy-2-nitro-benzyloxy）-2,5-dihydrofuran as a new photoaffinity crosslinking reagent. The azid function on this molecule allow it to be readily anchored to alkyne modified biomolecules. Photo irradiation of the molecule at 350 nm furnish cis-enedione, which is quite stable but crosslink with primary amines quickly and quantitatively. The unique property make this molecule prominent in mapping out protein residues involved in protein–DNA interactions and to trapping/identifying proteins that interact with DNA.

关键词： Photoaffinity crosslinking DNA-protein interaction target protein

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Thiol Specific and Tracelessly Removable Bioconjugation via Michael Addition to 5-Methylene Pyrrolones

Thiol Specific and Tracelessly Removable Bioconjugation via ...

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第十届全国化学生物学学术会议

作者： Yingqian Zhang Xiaoping zhou Yonghui Xie Zhen Xi chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai UniversityCollaborative Innovation Center of Chemical Science and Engineering （Tianjin）

Maleimide analogue, 5-methylene pyrrolones （5MPs） are highly thiol-specific and tracelessly removable bioconjugation tools. 5MPs are easily prepared from primary amines in one step. 5 MPs exhibit significantly improved stability and cysteine specificity compared to maleimides. Michael addition of thiol to 5MPs occurs rapidly without generating a stereocenter, leading to quite clean conjugation reactions. The conjugates efficiently release thiols via retro-Michael reaction in alkaline buffer（pH ≥ 9.5） or via thiol exchange. This unique property makes 5MPs valuable for the controlled release of conjugated cargo and temporary thiol protection. The utilization of 5MPs for protein immobilization and pull-down of active complexes is illustrated using E. coli. acetohydroxyacid synthase isozyme Ⅰ.

关键词： Bioconjugation Maleimide Cysteine

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Oxidation of 8-Oxoguanosine Leads to DNA-Protein Crosslinks in Nucleosome Core Particles

Oxidation of 8-Oxoguanosine Leads to DNA-Protein Crosslinks ...

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第十届全国化学生物学学术会议

作者： Jing Bai Yingqian Zhang Zhen Xi chuanzheng zhou State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of ChemistryNankai UniversityCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)

8-oxoguanine(8-oxo-G) is a major product of oxidative DNA damage. 8-oxo-G is labile for further oxidation to produce OGox which is a strong electrophile and thus highly reactive toward nucleophiles such as water, amine function of lysine. Through site-specific incorporation of 8-oxo-G in nucleosome core particles(NCPs) followed by oxidation using KFe(CN), OGox was in situ generated in NCPs. We found OGox leads to nearly quantitative DNA-protein crosslinks(DPCs) within NCPs. Mechanistic studies using chemical models and mutated histones demonstrate that DPCs form mainly by conjugation of OGox with N-terminal amine, serine and lysine as well. The DPCs are stable and can not repaired by DNA glycosylase hOGG1. These results suggest that DPCs formation from the oxidation of 8-oxo-G will provide insight into the relationship between DNA oxidative damage and mutagenesis.

关键词： DNA-protein crosslinks 8-Oxoguanine Nuclesome

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