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Academic literature on the topic 'Naïve phage library'

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Published: 1 April 2023

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Journal articles on the topic "Naïve phage library"

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Sloth, Ane Beth, Babak Bakhshinejad, Malte Jensen, Camilla Stavnsbjerg, Mikkel Baldtzer Liisberg, Maria Rossing, and Andreas Kjaer. "Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing." Viruses 14, no. 11 (October 29, 2022): 2402. http://dx.doi.org/10.3390/v14112402.

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The principal presumption of phage display biopanning is that the naïve library contains an unbiased repertoire of peptides, and thus, the enriched variants derive from the affinity selection of an entirely random peptide pool. In the current study, we utilized deep sequencing to characterize the widely used Ph.DTM-12 phage display peptide library (New England Biolabs). The next-generation sequencing (NGS) data indicated the presence of stop codons and a high abundance of wild-type clones in the naïve library, which collectively result in a reduced effective size of the library. The analysis of the DNA sequence logo and global and position-specific frequency of amino acids demonstrated significant bias in the nucleotide and amino acid composition of the library inserts. Principal component analysis (PCA) uncovered the existence of four distinct clusters in the naïve library and the investigation of peptide frequency distribution revealed a broad range of unequal abundances for peptides. Taken together, our data provide strong evidence for the notion that the naïve library represents substantial departures from randomness at the nucleotide, amino acid, and peptide levels, though not undergoing any selective pressure for target binding. This non-uniform sequence representation arises from both the M13 phage biology and technical errors of the library construction. Our findings highlight the paramount importance of the qualitative assessment of the naïve phage display libraries prior to biopanning.
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Sabir, Jamal S. M., Ahmed Atef, Fotouh M. El-Domyati, Sherif Edris, Nahid Hajrah, Ahmed M. Alzohairy, and Ahmed Bahieldin. "Construction of naïve camelids VHH repertoire in phage display-based library." Comptes Rendus Biologies 337, no. 4 (April 2014): 244–49. http://dx.doi.org/10.1016/j.crvi.2014.02.004.

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Sommavilla, R., V. Lovato, A. Villa, D. Sgier, and D. Neri. "Design and construction of a naïve mouse antibody phage display library." Journal of Immunological Methods 353, no. 1-2 (February 2010): 31–43. http://dx.doi.org/10.1016/j.jim.2010.01.003.

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Wagner, Hanna, Sarah Wehrle, Etienne Weiss, Marco Cavallari, and Wilfried Weber. "A Two-Step Approach for the Design and Generation of Nanobodies." International Journal of Molecular Sciences 19, no. 11 (November 2, 2018): 3444. http://dx.doi.org/10.3390/ijms19113444.

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Nanobodies, the smallest possible antibody format, have become of considerable interest for biotechnological and immunotherapeutic applications. They show excellent robustness, are non-immunogenic in humans, and can easily be engineered and produced in prokaryotic hosts. Traditionally, nanobodies are selected from camelid immune libraries involving the maintenance and treatment of animals. Recent advances have involved the generation of nanobodies from naïve or synthetic libraries. However, such approaches demand large library sizes and sophisticated selection procedures. Here, we propose an alternative, two-step approach for the design and generation of nanobodies. In a first step, complementarity-determining regions (CDRs) are grafted from conventional antibody formats onto nanobody frameworks, generating weak antigen binders. In a second step, the weak binders serve as templates to design focused synthetic phage libraries for affinity maturation. We validated this approach by grafting toxin- and hapten-specific CDRs onto frameworks derived from variable domains of camelid heavy-chain-only antibodies (VHH). We then affinity matured the hapten binder via panning of a synthetic phage library. We suggest that this strategy can complement existing immune, naïve, and synthetic library based methods, requiring neither animal experiments, nor large libraries, nor sophisticated selection protocols.
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Kamstrup Sell, Danna, Ane Beth Sloth, Babak Bakhshinejad, and Andreas Kjaer. "A White Plaque, Associated with Genomic Deletion, Derived from M13KE-Based Peptide Library Is Enriched in a Target-Unrelated Manner during Phage Display Biopanning Due to Propagation Advantage." International Journal of Molecular Sciences 23, no. 6 (March 18, 2022): 3308. http://dx.doi.org/10.3390/ijms23063308.

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The nonspecific enrichment of target-unrelated peptides during biopanning remains a major drawback for phage display technology. The commercial Ph.D.TM-7 phage display library is used extensively for peptide discovery. This library is based on the M13KE vector, which carries the lacZα sequence, leading to the formation of blue plaques on IPTG-X-gal agar plates. In the current study, we report the isolation of a fast-propagating white clone (displaying WSLGYTG peptide) identified through screening against a recombinant protein. Sanger sequencing demonstrated that white plaques are not contamination from environmental M13-like phages, but derive from the library itself. Whole genome sequencing revealed that the white color of the plaques results from a large 827-nucleotide genomic deletion. The phenotypic characterization of propagation capacity through plaque count- and NGS-based competitive propagation assay supported the higher propagation rate of Ph-WSLGYTG clone compared with the library. According to our data, white plaques are likely to arise endogenously in Ph.D. libraries due to mutations in the M13KE genome and should not always be viewed as exogenous contamination. Our findings also led to the conclusion that the deletion observed here might be an ancestral mutation already present in the naïve library, which causes target-unrelated nonspecific enrichment of white clone during biopanning due to propagation advantage.
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Killeen, G. F., B. D. Foy, R. H. Frohn, D. Impoinvil, A. Williams, and J. C. Beier. "Enrichment of a single clone from a high diversity library of phage-displayed antibodies by panning withAnopheles gambiae(Diptera: Culicidae) midgut homogenate." Bulletin of Entomological Research 93, no. 1 (January 2003): 31–37. http://dx.doi.org/10.1079/ber2002216.

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AbstractA high diversity library of recombinant human antibodies was selected on complex antigen mixtures from midguts of femaleAnopheles gambiaeGiles. The library of phage-displayed single chain variable region fragment constructs, derived from β-lymphocyte mRNA of naïve human donors, was repeatedly selected and reamplified on the insoluble fraction of midgut homogenates. Five rounds of panning yielded only one midgut-specific clone, which predominated the resulting antibody panel. InA. gambiae, the epitope was found throughout the tissues of females but was absent from the midgut of males. The cognate antigen proved to be detergent soluble but very sensitive to denaturation and could not be isolated or identified by Western blot of native electrophoresis gels or by immunoprecipitation. Nevertheless, immunohistology revealed that this sex-specific epitope is associated with the lumenal side of the midgut. Severe bottlenecking may limit the utility of phage display selection from naïve libraries for generating diverse panels of antibodies against complex mixtures of antigens from insect tissues. These results suggest that the selection of sufficiently diverse antibody panels, from which mosquitocidal or malaria transmission-blocking antibodies can be isolated, may require improved selection methods or specifically enriched pre-immunized libraries.
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Qiu, Yu-Lou, Qing-Hua He, Yang Xu, Arun K. Bhunia, Zhui Tu, Bo Chen, and Yuan-Yuan Liu. "Deoxynivalenol-mimic nanobody isolated from a naïve phage display nanobody library and its application in immunoassay." Analytica Chimica Acta 887 (August 2015): 201–8. http://dx.doi.org/10.1016/j.aca.2015.06.033.

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Park, Sae-Gwang, Yong-Joo Jeong, Yong-Yi Lee, Ik-Jung Kim, Su-Kil Seo, Eui-Joong Kim, Heung-Chae Jung, et al. "Hepatitis B virus-neutralizing anti-pre-S1 human antibody fragments from large naïve antibody phage library." Antiviral Research 68, no. 3 (December 2005): 109–15. http://dx.doi.org/10.1016/j.antiviral.2005.06.012.

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English, Hejiao, Jessica Hong, and Mitchell Ho. "Ancient species offers contemporary therapeutics: an update on shark VNAR single domain antibody sequences, phage libraries and potential clinical applications." Antibody Therapeutics 3, no. 1 (January 2020): 1–9. http://dx.doi.org/10.1093/abt/tbaa001.

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ABSTRACT The antigen binding variable domain (VNAR) of the shark immunoglobulin new antigen receptor (IgNAR) evolved approximately 500 million years ago and it is one of the smallest antibody fragments in the animal kingdom with sizes of 12–15 kDa. This review discusses the current knowledge of the shark VNAR single domain sequences and ongoing development of shark VNARs as research tools as well as potential therapeutics, in particular highlighting the recent next-generation sequencing analysis of 1.2 million shark VNAR sequences and construction of a large phage displayed shark VNAR library from six naïve adult nurse sharks (Ginglymostoma cirratum). The large phage-displayed VNAR single domain library covers all the four known VNAR types (Types I–IV) and many previously unknown types. Ongoing preclinical development will help define the utility of shark VNAR single domains as a potentially new family of drug candidates for treating cancer and other human diseases.
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Feng, Mingqian, Hejiao Bian, Xiaolin Wu, Tianyun Fu, Ying Fu, Jessica Hong, Bryan D. Fleming, Martin F. Flajnik, and Mitchell Ho. "Construction and next-generation sequencing analysis of a large phage-displayed VNAR single-domain antibody library from six naïve nurse sharks." Antibody Therapeutics 2, no. 1 (November 7, 2018): 1–11. http://dx.doi.org/10.1093/abt/tby011.

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ABSTRACT Background Shark new antigen receptor variable domain (VNAR) antibodies can bind restricted epitopes that may be inaccessible to conventional antibodies. Methods Here, we developed a library construction method based on polymerase chain reaction (PCR)-Extension Assembly and Self-Ligation (named “EASeL”) to construct a large VNAR antibody library with a size of 1.2 × 1010 from six naïve adult nurse sharks (Ginglymostoma cirratum). Results The next-generation sequencing analysis of 1.19 million full-length VNARs revealed that this library is highly diversified because it covers all four classical VNAR types (Types I–IV) including 11% of classical Type I and 57% of classical Type II. About 30% of the total VNARs could not be categorized as any of the classical types. The high variability of complementarity determining region (CDR) 3 length and cysteine numbers are important for the diversity of VNARs. To validate the use of the shark VNAR library for antibody discovery, we isolated a panel of VNAR phage binders to cancer therapy-related antigens, including glypican-3, human epidermal growth factor receptor 2 (HER2), and programmed cell death-1 (PD1). Additionally, we identified binders to viral antigens that included the Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) spike proteins. The isolated shark single-domain antibodies including Type I and Type II VNARs were produced in Escherichia coli and validated for their antigen binding. A Type II VNAR (PE38-B6) has a high affinity (Kd = 10.1 nM) for its antigen. Conclusions The naïve nurse shark VNAR library is a useful source for isolating single-domain antibodies to a wide range of antigens. The EASeL method may be applicable to the construction of other large diversity gene expression libraries.
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Dissertations / Theses on the topic "Naïve phage library"

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Hald, Rikke. "Generation and characterisation of a naive human antibody phage display library : a resource for clinically relevant reagents /." Cph. : Department of Pharmacology, The Danish University of Pharmaceutical Sciences, 2004. http://www.dfh.dk/phd/defences/rikkehald.htm.

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Huang, Shih-Tsung, and 黃仕聰. "Development of Fully Human Anti-HDGF Antibody from Phage-Displayed Human Naïve ScFv Library." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/92wr6a.

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博士
國立中山大學
海洋生物科技博士學位學程
107
Hepatocellular carcinoma (HCC), a deadly disease worldwide. For advanced HCC therapy, Sorafenib is the only conventional drug, however, low response rate, drug resistance, and strong side effects had been reported in Sorafenib therapy. Therefore, investigation of novel therapeutic strategy is a critical issue. HDGF is a cancerous factor in various cancer types including HCC. To develop anti-HDGF neutralizing antibody, phage display technology provides an effective in vitro selection strategy to identify fully human antibody. In the biopanning, thirteen HDGF affinity phage clones had been identified from phage display human naïve scFv library using unique Fc fusion protein/protein G dynabeads method. After fully human IgG construction and production, these antibodies were further confirmed binding affinity using ELISA, immunofluorescence, and HDGF conditional knockdown Huh7 cell line. Among them, hmAb-7 exhibited multiple anti-cancer activity, including cell growth, colony formation, invasion and sphere formation in Huh7, HepG2, and SK-Hep1 cells. The anti-cancer effects of hmAb-7 might participated with downregulation of PI3K/AKT/mTOR signaling pathway. The hmAb-7 inhibits of invasion through MMP-2 down-regulation; sphere formation was eliminated through downregulation of cancer stemness genes. In continuously cultured Huh7 and HepG2 cells, these cells present higher colony and spheroid forming features, however, the cancerous behavior able to abolish through hmAb-7 treatment. In sorafenib resistant Huh7 cells, hmAb-7 presents colony and sphere inhibition ability. Furthermore, the Huh7 xenograft model in NOD/SCID mice was performed and the data indicated that hmAb-7 slightly inhibited tumor growth (p = 0.1091) and prolong the overall survival for 14 days. Although anti-HDGF hmAb-7 single treatments not significantly inhibit tumor growth in vivo, but based on the cancerous inhibition effects in vitro, combination therapy might provide an approach to enhance therapeutic effect. Furthermore, a HDGF sandwich ELISA platform with well linear range between 10-0.15625 ng/ml has been established and able to detect the HDGF level in human and rat serum. Anti-HDGF antibody was also used for extended applications, included in analgesic application and allow to treat cancer stemness and Sorafenib drug resistant Huh7 cells (Huh7-SR). Our finding indicated anti-HDGF hmAb-7 exhibited analgesic effect in rat chronic constrictive injury (CCI) model plus with Adenoviral HDGF gene delivery. Besides, hmAb-7 not only shown sphere and colony inhibitory effects in continuous spheroid cell cultured Huh7 and HepG2 cells, but also inhibited cancerous behaviors in Huh7-SR cells. Finally, adenovirus mediated anti-HDGF-scFv gene delivery suppressed the colony and sphere formation in both Huh7 and Huh7-SR cells. The adenovirus mediated scFv gene delivery provided a novel approach for anti-HDGF therapy and allowed for further basic studies.
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Book chapters on the topic "Naïve phage library"

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Zhu, Zhongyu, and Dimiter S. Dimitrov. "Construction of a Large Naïve Human Phage-Displayed Fab Library Through One-Step Cloning." In Therapeutic Antibodies, 129–42. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-554-1_6.

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Omar, Noorsharmimi, and Theam Soon Lim. "Construction of Naive and Immune Human Fab Phage-Display Library." In Methods in Molecular Biology, 25–44. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7447-4_2.

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Wang, Xin, and Brian B. Cao. "Screening of Specific Internalization Fab Fragment from Human Naive Phage Library by Combinational Bio-Panning." In Therapeutic Antibodies, 161–74. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-554-1_8.

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