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Current Protocols in Nucleic Acid Chemistry最新文献

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Synthesis of β-Nicotinamide Riboside Using an Efficient Two-Step Methodology 高效两步法合成β-烟酰胺核苷
Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.43
Ning Zhang, Anthony A. Sauve
{"title":"Synthesis of β-Nicotinamide Riboside Using an Efficient Two-Step Methodology","authors":"Ning Zhang,&nbsp;Anthony A. Sauve","doi":"10.1002/cpnc.43","DOIUrl":"10.1002/cpnc.43","url":null,"abstract":"<p>A two-step chemical method for the synthesis of β-nicotinamide riboside (NR) is described. NR has achieved wide use as an NAD<sup>+</sup> precursor (vitamin B3) and can significantly increase central metabolite NAD<sup>+</sup> concentrations in mammalian cells. β-NR can be prepared with an efficient two-step procedure. The synthesis is initiated via coupling of commercially available 1,2,3,5-tetra-<i>O</i>-acetyl-β-<span>D</span>-ribofuranose with ethyl nicotinate in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf). <sup>1</sup>H NMR showed that the product was formed with complete stereoselectivity to produce only the β-isomer in high yield (&gt;90% versus starting sugar). The clean stereochemical result suggests that the coupling proceeds via a cationic <i>cis</i>-1,2-acyloxonium-sugar intermediate, which controls addition by nucleophiles to generate predominantly β-stereochemistry. The subsequent deprotection of esters in methanolic ammonia generates the desired product in 85% overall yield versus sugar. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.43","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35686098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Characterization of Quadruplex DNA Structure by Circular Dichroism 四重DNA结构的圆二色性表征
Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.23
Rafael del Villar-Guerra, Robert D. Gray, Jonathan B. Chaires
{"title":"Characterization of Quadruplex DNA Structure by Circular Dichroism","authors":"Rafael del Villar-Guerra,&nbsp;Robert D. Gray,&nbsp;Jonathan B. Chaires","doi":"10.1002/cpnc.23","DOIUrl":"10.1002/cpnc.23","url":null,"abstract":"<p>Circular dichroism (CD) is a phenomenon that arises from the differential absorption of left- and right-handed circularly polarized light, and may be seen with optically active molecules. CD spectroscopy provides useful spectral signatures for biological macromolecules in solution, and provides low-resolution structural information about macromolecular conformation. CD spectroscopy is particularly useful for monitoring conformational changes in macromolecules upon environmental perturbations. G-quadruplex structures show unique CD spectral signatures, and CD is an important tool for characterizing their formation and global structure. This protocol offers step-by-step methods for determining reliable and reproducible CD spectra of quadruplex structures and normalizing the spectra for presentation. CD spectra properly normalized with respect to quadruplex concentration and path length are required to facilitate accurate comparison of results among laboratories. The standard operating procedures proposed are recommended to make such comparison accurate and informative. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34776950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 54
Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages 含二硫代磷酸键的RNA类似物的固相合成
Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.40
Xianbin Yang
{"title":"Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages","authors":"Xianbin Yang","doi":"10.1002/cpnc.40","DOIUrl":"10.1002/cpnc.40","url":null,"abstract":"<p>The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.40","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35522060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes 高压下配体核酸稳定性定量分析设计靶向g -四联体药物
Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.39
Shuntaro Takahashi, Naoki Sugimoto
{"title":"Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes","authors":"Shuntaro Takahashi,&nbsp;Naoki Sugimoto","doi":"10.1002/cpnc.39","DOIUrl":"10.1002/cpnc.39","url":null,"abstract":"<p>Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (Δ<i>V</i>) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate Δ<i>V</i> values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (Δ<i>G</i>, Δ<i>H</i>, Δ<i>S</i>, and Δ<i>V</i>) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.39","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35522063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Synthesis of Bipartite Tetracysteine PNA Probes for DNA In Situ Fluorescent Labeling 用于DNA原位荧光标记的二部四半胱氨酸PNA探针的合成
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-12-24 DOI: 10.1002/cpnc.44
Ge-min Fang, Oliver Seitz
{"title":"Synthesis of Bipartite Tetracysteine PNA Probes for DNA In Situ Fluorescent Labeling","authors":"Ge-min Fang,&nbsp;Oliver Seitz","doi":"10.1002/cpnc.44","DOIUrl":"10.1002/cpnc.44","url":null,"abstract":"<p>“Label-free” fluorescent probes that avoid additional steps or building blocks for conjugation of fluorescent dyes with oligonucleotides can significantly reduce the time and cost of parallel bioanalysis of a large number of nucleic acid samples. A method for the synthesis of “label-free” bicysteine-modified PNA probes using solid-phase synthesis and procedures for sequence-specific DNA in situ fluorescent labeling is described here. The concept is based on the adjacent alignment of two bicysteine-modified peptide nucleic acids on a DNA target to form a structurally optimized bipartite tetracysteine motif, which induces a sequence-specific fluorogenic reaction with commercially available biarsenic dyes, even in complex media such as cell lysate. This unit will help researchers to quickly synthesize bipartite tetracysteine PNA probes and carry out low-cost DNA in situ fluorescent labeling experiments. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.44","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35686184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis of Oligodeoxynucleotides Containing a C8-2′-Deoxyguanosine Adduct Formed by the Carcinogen 3-Nitrobenzanthrone 含有致癌物质3-硝基苯并蒽酮形成的C8-2 ' -脱氧鸟苷加合物的寡脱氧核苷酸的合成
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-06-19 DOI: 10.1002/cpnc.28
Arindom Chatterjee, Chanchal K. Malik, Ashis K. Basu
{"title":"Synthesis of Oligodeoxynucleotides Containing a C8-2′-Deoxyguanosine Adduct Formed by the Carcinogen 3-Nitrobenzanthrone","authors":"Arindom Chatterjee,&nbsp;Chanchal K. Malik,&nbsp;Ashis K. Basu","doi":"10.1002/cpnc.28","DOIUrl":"10.1002/cpnc.28","url":null,"abstract":"<p>This unit describes the detailed procedure in five parts for the synthesis of the C8-2′-deoxyguanosine-3-aminobenzanthrone adduct located in a desired site in an oligonucleotide. The synthesis of the protected 2′-deoxyguanosine, <i>O</i>\u0000 <sup>6</sup>-benzyl-<i>N</i>\u0000 <sup>2</sup>-DMTr-3′-5′-bisTBDMS-C8-Br-2′-deoxyguanosine, is described in the first part. The synthesis of the reduced carcinogen 3-aminobenzanthrone is detailed in part two. The third part outlines the key step of the adduct formation between the reduced carcinogen and the protected nucleoside by a palladium-catalyzed cross coupling reaction. The final two parts describe phosphoramidite synthesis from the nucleoside-carcinogen adduct followed by its site-specific incorporation into DNA by solid-phase oligonucleotide synthesis. The adducted oligonucleotides are purified by reversed-phase HPLC and characterized by mass spectrometry. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.28","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35101790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences 合成DNA序列固相纯化的高通量工艺
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-06-19 DOI: 10.1002/cpnc.31
Andrzej Grajkowski, Jacek Cieślak, Serge L. Beaucage
{"title":"A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences","authors":"Andrzej Grajkowski,&nbsp;Jacek Cieślak,&nbsp;Serge L. Beaucage","doi":"10.1002/cpnc.31","DOIUrl":"10.1002/cpnc.31","url":null,"abstract":"<p>An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5′-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5′-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-<i>n</i>-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.31","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35099910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Engineered Polymerases with Altered Substrate Specificity: Expression and Purification 改变底物特异性的工程聚合酶:表达和纯化
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-06-19 DOI: 10.1002/cpnc.33
Ali Nikoomanzar, Matthew R. Dunn, John C. Chaput
{"title":"Engineered Polymerases with Altered Substrate Specificity: Expression and Purification","authors":"Ali Nikoomanzar,&nbsp;Matthew R. Dunn,&nbsp;John C. Chaput","doi":"10.1002/cpnc.33","DOIUrl":"10.1002/cpnc.33","url":null,"abstract":"<p>Polymerase engineering is making it possible to synthesize xeno-nucleic acid polymers (XNAs) with diverse backbone structures and chemical functionality. The ability to copy genetic information back and forth between DNA and XNA has led to a new field of science known as synthetic genetics, which aims to study the genetic concepts of heredity and evolution in artificial genetic polymers. Since many of the polymerases needed to synthesize XNA polymers are not available commercially, researchers must express and purify these enzymes as recombinant proteins from <i>E. coli</i>. This unit details the steps needed to express, purify, and evaluate the activity of engineered polymerases with altered substrate recognition properties. The protocol requires 6 days to complete and will produce ∼20 mg of pure, nuclease-free polymerase per liter of <i>E. coli</i> bacterial culture. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.33","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35099913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Carbocyclic C-C Bond Formation: Intramolecular Radical Ring Closure to Yield Diastereomerically Pure (7′S-Me- or 7′R-Me-) Carba-LNA Nucleotide Analogs 碳环C-C键形成:分子内自由基环闭合产生非对映纯(7'S-Me -或7'R-Me -)碳- rna核苷酸类似物
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-06-19 DOI: 10.1002/cpnc.29
Oleksandr Plashkevych, Ram Shankar Upadhayaya, Jyoti Chattopadhyaya
{"title":"Carbocyclic C-C Bond Formation: Intramolecular Radical Ring Closure to Yield Diastereomerically Pure (7′S-Me- or 7′R-Me-) Carba-LNA Nucleotide Analogs","authors":"Oleksandr Plashkevych,&nbsp;Ram Shankar Upadhayaya,&nbsp;Jyoti Chattopadhyaya","doi":"10.1002/cpnc.29","DOIUrl":"10.1002/cpnc.29","url":null,"abstract":"<p>In light of the impressive gene-silencing properties of carba-LNA modified oligo DNA and RNA, both in antisense RNA and siRNA approaches, which have been confirmed as proof-of-concept for biochemical applications in post-transcriptional gene silencing, we envision the true potential of carba-LNA modifications to be revealed soon. Herein we provide detailed protocols for synthesis of carba-LNA-A, -G, -<sup>5-Me</sup>C, and -T nucleosides on a medium/large scale (gram scale), as well as important guidelines for incorporation of these modified carba-LNAs into DNA or RNA oligonucleotides. Creation of a stereoselective C-C bond during the 5-<i>exo</i> radical intramolecular cyclization involves trapping of a C2′ radical intermediate intramolecularly by the vicinal double bond of a C4′-tethered ─CH<sub>2</sub>-CH═CH<sub>2</sub> group. All diastereomers of substituted carba-LNAs are now available in pure form. The present procedure allows carba-LNA to be commercialized for medicinal or biotechnological purposes. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.29","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35101789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stereoselective Synthesis of 4′-Selenonucleosides via the Seleno-Michael Reaction 硒-迈克尔反应立体选择性合成4′-硒核苷
Current Protocols in Nucleic Acid Chemistry Pub Date : 2017-06-19 DOI: 10.1002/cpnc.27
Pramod K. Sahu, Dnyandev B. Jarhad, Gyudong Kim, Lak Shin Jeong
{"title":"Stereoselective Synthesis of 4′-Selenonucleosides via the Seleno-Michael Reaction","authors":"Pramod K. Sahu,&nbsp;Dnyandev B. Jarhad,&nbsp;Gyudong Kim,&nbsp;Lak Shin Jeong","doi":"10.1002/cpnc.27","DOIUrl":"10.1002/cpnc.27","url":null,"abstract":"<p>5′-Homo-4′-selenonucleosides, a class of next-generation nucleosides, are synthesized from <span>D</span>-ribose via a 4-selenosugar intermediate. The key step in synthesizing this intermediate is a seleno-Michael reaction. 5′-Homo-4′-selenouridine and -adenosine are prepared using Pummerer-type and Vorbrüggen condensation, respectively. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.27","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35099911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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