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Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing.

التفاصيل البيبلوغرافية
العنوان: Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing.
المؤلفون: Sloth AB; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Bakhshinejad B; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Jensen M; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Stavnsbjerg C; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Liisberg MB; Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark., Rossing M; Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark.; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Kjaer A; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
المصدر: Viruses [Viruses] 2022 Oct 29; Vol. 14 (11). Date of Electronic Publication: 2022 Oct 29.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI
مواضيع طبية MeSH: Peptide Library* , High-Throughput Nucleotide Sequencing*, Peptides/chemistry ; Amino Acids/genetics ; Nucleotides
مستخلص: 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.
References: J Control Release. 2011 Mar 30;150(3):248-55. (PMID: 21295090)
Methods. 2001 Feb;23(2):169-78. (PMID: 11181036)
Signal Transduct Target Ther. 2017 May 12;2:17010. (PMID: 29263914)
Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9751-4. (PMID: 1946398)
Nucleic Acids Res. 2018 May 18;46(9):e52. (PMID: 29420788)
Anal Biochem. 1996 Jun 15;238(1):1-13. (PMID: 8660577)
Amino Acids. 2018 May;50(5):577-592. (PMID: 29435721)
Hum Immunol. 2012 May;73(5):465-9. (PMID: 22406255)
J Mol Biol. 1996 Jul 5;260(1):9-21. (PMID: 8676395)
Nat Biotechnol. 2019 Apr;37(4):420-423. (PMID: 30778233)
Nature. 1965 Jun 5;206(988):994-8. (PMID: 5320272)
Nucleic Acids Res. 2016 Jan 4;44(D1):D1127-32. (PMID: 26503249)
Biochemistry. 1991 Dec 24;30(51):11775-81. (PMID: 1751494)
Amino Acids. 2017 Aug;49(8):1293-1308. (PMID: 28664268)
Molecules. 2011 Feb 15;16(2):1625-41. (PMID: 21326140)
J Mol Biol. 2002 Oct 4;322(5):1039-52. (PMID: 12367527)
Mol Ther Nucleic Acids. 2015;4:e223. (PMID: 28110747)
J Bacteriol. 1994 Jul;176(14):4296-305. (PMID: 8021215)
Hum Immunol. 2013 Jan;74(1):28-31. (PMID: 23000375)
FEBS Lett. 1992 Mar 16;299(3):243-6. (PMID: 1544500)
Methods Mol Biol. 2014;1088:19-33. (PMID: 24146394)
J Mol Biol. 2005 Dec 2;354(3):666-78. (PMID: 16259997)
Mol Divers. 1996 May;1(3):165-76. (PMID: 9237207)
J Biol Chem. 1992 Jan 15;267(2):1231-8. (PMID: 1730647)
Front Microbiol. 2015 Apr 28;6:340. (PMID: 25972845)
ACS Chem Biol. 2020 Nov 20;15(11):2907-2915. (PMID: 33125222)
Nucleic Acids Res. 2014 Feb;42(3):1784-98. (PMID: 24217917)
Expert Opin Drug Deliv. 2008 Aug;5(8):825-36. (PMID: 18712993)
Genome Res. 2004 Jun;14(6):1188-90. (PMID: 15173120)
Anal Biochem. 2012 Feb 15;421(2):622-31. (PMID: 22178910)
J Biol Chem. 1988 Dec 25;263(36):19690-6. (PMID: 3058705)
Science. 1985 Jun 14;228(4705):1315-7. (PMID: 4001944)
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100. (PMID: 2172928)
Int J Mol Sci. 2022 Mar 18;23(6):. (PMID: 35328728)
J Biomed Biotechnol. 2010;2010:101932. (PMID: 20339521)
J Bacteriol. 1997 Oct;179(20):6464-71. (PMID: 9335297)
J Mol Biol. 1983 Feb 15;164(1):73-87. (PMID: 6188841)
Appl Microbiol Biotechnol. 2008 Oct;80(5):925-36. (PMID: 18716770)
Methods. 2012 Sep;58(1):47-55. (PMID: 22819855)
فهرسة مساهمة: Keywords: M13 phage; Ph.D.TM-12 peptide library; biopanning; compositional bias; deep sequencing; departure from randomness; next-generation sequencing; phage display; principal component analysis
المشرفين على المادة: 0 (Peptide Library)
0 (Peptides)
0 (Amino Acids)
0 (Nucleotides)
تواريخ الأحداث: Date Created: 20221111 Date Completed: 20221114 Latest Revision: 20230130
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC9697088
DOI: 10.3390/v14112402
PMID: 36366500
قاعدة البيانات: MEDLINE
الوصف
تدمد:1999-4915
DOI:10.3390/v14112402