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Wang S, Uchida N, Ueno K, Matsubara T, Sato T, Aida T, Ishida Y. Effects of the Magnetic Orientation of M13 Bacteriophage on Phage Display Selection. Chemistry 2023; 29:e202302261. [PMID: 37638672 DOI: 10.1002/chem.202302261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
Although phage display selection using a library of M13 bacteriophage has become a powerful tool for finding peptides that bind to target materials on demand, a remaining concern of this method is the interference by the M13 main body, which is a huge filament >103 times larger than the displayed peptide, and therefore would nonspecifically adhere to the target or sterically inhibit the binding of the displayed peptide. Meanwhile, filamentous phages are known to be orientable by an external magnetic field. If M13 filaments are magnetically oriented during the library selection, their angular arrangement relative to the target surface would be changed, being expected to control the interference by the M13 main body. This study reports that the magnetic orientation of M13 filaments vertical to the target surface significantly affects the selection. When the target surface was affinitive to the M13 main body, this orientation notably suppressed the nonspecific adhesion. Furthermore, when the target surface was less affinitive to the M13 main body and intrinsically free from the nonspecific adhesion, this orientation drastically changed the population of M13 clones obtained through library selection. The method of using no chemicals but only a physical stimulus is simple, clean, and expected to expand the scope of phage display selection.
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Affiliation(s)
- Shuxu Wang
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Noriyuki Uchida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kento Ueno
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yasuhiro Ishida
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Carter JG, Pfukwa R, Riley L, Tucker JHR, Rodger A, Dafforn TR, Klumperman B. Linear Dichroism Activity of Chiral Poly( p-Aryltriazole) Foldamers. ACS OMEGA 2021; 6:33231-33237. [PMID: 34901675 PMCID: PMC8656205 DOI: 10.1021/acsomega.1c06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 05/04/2023]
Abstract
Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.
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Affiliation(s)
- Jake G. Carter
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Rueben Pfukwa
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
| | - Liam Riley
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Bert Klumperman
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
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Krell K, Wagenknecht HA. Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry. Biomolecules 2020; 10:biom10030480. [PMID: 32245224 PMCID: PMC7175119 DOI: 10.3390/biom10030480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/27/2022] Open
Abstract
A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows "photoclick"-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells.
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Kim WG, Zueger C, Kim C, Wong W, Devaraj V, Yoo HW, Hwang S, Oh JW, Lee SW. Experimental and numerical evaluation of a genetically engineered M13 bacteriophage with high sensitivity and selectivity for 2,4,6-trinitrotoluene. Org Biomol Chem 2020; 17:5666-5670. [PMID: 30973549 DOI: 10.1039/c8ob03075h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Selective and sensitive detection of desired targets is very critical in sensor design. Here, we report a genetically engineered M13 bacteriophage-based sensor system evaluated by quantum mechanics (QM) calculations. Phage display is a facile way to develop the desired peptide sequences, but the resulting sequences can be imperfect peptides for binding of target molecules. A TNT binding peptide (WHW) carrying phage was self-assembled to fabricate thin films and tested for the sensitive and selective surface plasmon resonance-based detection of TNT molecules at the 500 femtomole level. SPR studies performed with the WHW peptide and control peptides (WAW, WHA, AHW) were well-matched with those of the QM calculations. Our combined method between phage engineering and QM calculation will significantly enhance our ability to design selective and sensitive sensors.
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Affiliation(s)
- Won-Geun Kim
- Department of Nano Fusion Technology, Pusan National University, Busan, 609-735, South Korea.
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Ali A, Little HA, Carter JG, Douglas C, Hicks MR, Kenyon DM, Lacomme C, Logan RT, Dafforn TR, Tucker JHR. Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay. RSC Chem Biol 2020; 1:449-454. [PMID: 34458772 PMCID: PMC8341927 DOI: 10.1039/d0cb00135j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
Nucleic acid detection is an important part of our bio-detection arsenal, with the COVID-19 pandemic clearly demonstrating the importance to healthcare of rapid and efficient detection of specific pathogenic sequences. As part of the drive to establish new DNA detection methodologies and signal read-outs, here we show how linear dichroism (LD) spectroscopy can be used to produce a rapid and modular detection system for detecting quantities of DNA from both bacterial and viral pathogens. The LD sensing method exploits changes in fluid alignment of bionanoparticles (bacteriophage M13) engineered with DNA stands covalently attached to their surfaces, with the read-out signal induced by the formation of complementary duplexes between DNA targets and two M13 bionanoparticles. This new sandwich assay can detect pathogenic material down to picomolar levels in under 1 minute without amplification, as demonstrated by the successful sensing of DNA sequences from a plant virus (Potato virus Y) and an ampicillin resistance gene, ampR. A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.![]()
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Affiliation(s)
- Aysha Ali
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
- School of Biosciences
| | - Haydn A. Little
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
| | - Jake G. Carter
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT
- UK
| | | | | | | | | | - Richard T. Logan
- School of Biosciences
- University of Birmingham
- Birmingham B15 2TT
- UK
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