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Bacteriophage M13

Bacteriophage M13 is a filamentous bacteriophage that infects the bacterium Escherichia coli.
It is a commonly used model system for studying viral biology, protein engineering, and biotechnology applications.
Bacteriophage M13 has a single-stranded DNA genome and a rod-shaped capsid structure.
Its small size, ease of manipulation, and ability to display foreign peptides on its surface make it a versatile tool for research.
Optimized protocols and methods for working with Bacteriaphage M13 can enhance reproducibility, accuracy, and efficiency in your research endeavors.

Most cited protocols related to «Bacteriophage M13»

1
Identification of LPS Peptide Mimics using Phage Display
Identification of the LPS peptide mimics was performed by using a 7-mer Phage display peptide library referred to as Ph.D.-7 (New England BioLabs, Ipswich, MA). Panning was performed according to manufactures specifications using a LPS specific antibody as the target. The LPS antibody (Abcam, Cambridge, MA, CAT# ab35654) used for the panning was a monoclonal antibody, which was produced by vaccinating mice with whole Escherichia coli O111B4J5 cells. Although it is not known by the manufacturer as to which structural component of LPS is recognized by the antibody, it is specific to LPS and has been used in various publications [31] (link), [32] (link). Briefly, 1 µg of the LPS antibody was absorbed to one well of a 96 well plate in a total volume of 100 µl of PBS overnight at 4°C. Phages (2×1011) were added to the well and allowed to adhere at room temperature after which non-binding phages were washed away and bound phages eluted. Eluted phages were subsequently amplified and used for further panning so as to enrich for LPS antibody specific phages. The panning procedure described was repeated three times. Lastly, twelve random phage clones were selected from three rounds of panning and specificity to LPS antibody (black bars) was confirmed by ELISA using HSP70 antibody (ENZO life sciences, Farmingdale, NY) (white bars) as a negative control. The species for both the anti-LPS and anti-HSP70 antibodies used were mouse. Bound phages were detected by using a HRP labeled anti-M13 phage antibody (Abcam) followed by adding the HRP substrate SIGMAFAST™ OPD (Sigma, St. Louis, MO) and absorbance measured at 490 nm using a microplate reader (Bio-Rad, Hercules, CA). The panning, titer determination, and ELISA experiments were performed according to the manufacture's protocol. Once their reactivity was determined, the DNA encoding the peptide sequence from each positively reacting phage clone was purified using QIAprep Spin M13 Kit (Qiagen, Valencia, CA) and were sequenced by Genewiz (Genewiz, South Plainfield, NJ) using the primers supplied in the kit (New England BioLabs). The LPS peptide mimics sequenced were synthesized by Genemed Synthesis and their purity was greater than 95% (Genemed Synthesis, San Antonio, TX).
Shanmugam A., Rajoria S., George A.L., Mittelman A., Suriano R, & Tiwari R.K. (2012). Synthetic Toll Like Receptor-4 (TLR-4) Agonist Peptides as a Novel Class of Adjuvants. PLoS ONE, 7(2), e30839.
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Publication 2012
Anabolism Anti-Antibodies Antibodies, Anti-Idiotypic Antibody Specificity Bacteriophage M13 Bacteriophages Cells Clone Cells Enzyme-Linked Immunosorbent Assay Escherichia coli Heat-Shock Proteins 70 Immunoglobulins Monoclonal Antibodies Mus Oligonucleotide Primers Peptides Phage Display Peptide Library
2
CRISPR Cassette Expansion Monitoring in E. coli
The E. coli KD263 strain is a derivative of BW40119 strain described earlier (28 (link)). It contains the cas3 gene under the control of the lacUV5 promoter and the casABCDE12 operon under the araBp8 promoter control. The KD263 strains harbors a single genetically modified CRISPR cassette with two repeats and a single g8 spacer described earlier (14 (link)). KD263 was transformed with a pG8_C1T plasmid, a derivative of the pT7blue cloning vector harboring a 209-bp fragment of the M13 bacteriophage DNA containing the g8 protospacer (28 (link)). The protospacer sequence harbors a C to T change at the position of +1 that renders CRISPR interference by the g8 spacer containing crRNA ineffective (14 (link)). KD263 cells transformed with pG8_C1T were grown overnight at 37°C in Luria-Bertani (LB) broth supplemented with 100 μg/ml ampicillin. Aliquots of the culture were diluted 200-fold into six individual tubes with fresh LB broth without ampicillin and supplemented with IPTG (isopropyl β-D-1 thiogalactopyranoside) and arabinose to the final concentration 1 mM each. The cultures were grown at 37°C overnight. The six individual cultures were mixed and genomic DNA was isolated from the pooled cultures. The cells were lyzed by 2-min incubation with 1 mg/ml lysozyme and DNA was purified by phenol, phenol/chloroform, chloroform extractions followed by ethanol precipitation. CRISPR expansion was monitored by polymerase chain reaction (PCR) in 20 μl reactions containing 20–50 ng genomic DNA with primers matched the CRISPR leader sequence and g8 spacer: Ec_LDR-F (5′-AAGGTTGGTGGGTTGTTTTTATGG-3′) and M13g8 (5′-GGATCGTCACCCTCAGCAGCG-3′) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). Six independent amplification reactions were pooled, PCR products corresponding to expanded CRISPR cassette were gel purified using QIAquick Gel Extraction Kit (QIAGEN) and sequenced with MySeq Illumina System at Moscow State University Genomics facility as described (31 (link)).
Shmakov S., Savitskaya E., Semenova E., Logacheva M.D., Datsenko K.A, & Severinov K. (2014). Pervasive generation of oppositely oriented spacers during CRISPR adaptation. Nucleic Acids Research, 42(9), 5907-5916.
Publication 2014
Ampicillin Arabinose Bacteriophage M13 Cells Chloroform Cloning Vectors Clustered Regularly Interspaced Short Palindromic Repeats CRISPR Spacers DNA, A-Form DNA-Directed DNA Polymerase DNA Primers Escherichia coli Ethanol Gene Expression Regulation Genome Isopropyl Thiogalactoside Muramidase Operon Phenol Plasmids Polymerase Chain Reaction RNA, CRISPR Guide Strains
3
Antibody Fragment Expression Protocols
Artificial gene synthesis (Mr Gene, GmbH, Germany) composed of a 6His-Tag and a triple c-myc Tag was inserted into the pHEN2 phagemid vector (Griffin 1. library) between NotI and BamHI sites. CcdB gene from pENTR4 vector (Invitrogen - ThermoFisher Scientific, France) was inserted into the pHEN2 vector between NcoI and NotI sites. This vector allows to express antibody fragments in fusion, upstream, with the pelB leader to drive secretion in the periplasm and downstream with the PIII protein of M13 phages. An amber stop codon is present between the antibody and the pIII. This stop codon is partially suppressed in SupE E. coli. For expression and purification of dimeric antibodies, hs2dAb were inserted in vectors derived from pFuse (Invivogen, France) as described in Moutel et al. (2009) (link). For intrabody expression in mammalian cells, hs2dAb were digested by NcoI and NotI and ligated into the pIb-mEGFP, pEGFP or the pmCherry vectors (Clontech - Takara, USA). (See the Appendix for more details).
Moutel S., Bery N., Bernard V., Keller L., Lemesre E., de Marco A., Ligat L., Rain J.C., Favre G., Olichon A, & Perez F. (2016). NaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodies. eLife, 5, e16228.
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Publication 2016
Amber Stop Codon Anabolism Antibodies Bacteriophage M13 Cells Cloning Vectors Codon, Terminator DNA Library Escherichia coli Genes Genetic Vectors Immunoglobulins Mammals Periplasm Proteins secretion Synthetic Genes
4
Fabrication of DNA Nanostructures
The design-specific staple strands were purchased from IDT Technologies in 250 μM scale. The sequence of the staple strands and the design is reported in the Supplementary Information. The p7308 scaffold strand was produced from M13 phage replication in Escherichia coli and was endotoxin-purified using Triton X-114 as described previously13 (link).
For the synthesis of DNs, 10 nM p7308 scaffold was mixed with tenfold excess of staples in TE buffer (5 mM Tris and 1 mM EDTA) containing 10–20 mM MgCl2. The amount of MgCl2 varied with the structure: DN1 (10 mM), DN2 (6 mM), DN3 (10 mM), DN4 (10 mM), DN5 (10 mM), DN6 (12 mM), DN7 (14 mM), DN8 (12 mM) and DN9 (6 mM). The solutions were subjected to a thermal annealing ramp on a Tetrad 2 Peltier thermal cycler (Bio-Rad) according to the following schedule: incubate at 65 °C for 15 min, decrease to 50 °C, incubate at 50 °C for 6 h 30 min and decrease to 40 °C at 6 h 30 min °C−1. The quality of folding was analysed by AGE. Solutions of folded DN were concentrated tenfold using a 30k MWCO Amicon Ultra centrifugal filter device (Millipore) and then purified by glycerol gradient ultracentrifugation30 (link). The 45% and 15% glycerol solutions were made in 1 × TE buffer containing the same levels of MgCl2 as required for folding. The glycerol fractions containing nanostructures was concentrated and buffer exchanged to remove glycerol using a 30k MWCO Amicon Ultra centrifugal filter device. Following purification, the stock solution was diluted appropriately for TEM imaging to verify quality. The stock concentration was determined by ultraviolet absorbance at 260 nm on a Nanodrop spectrophotometer (Thermo Scientific), assuming that A260=1 for 50 μg ml−1 DNs. Stock solutions were stored at 4 °C until use.
Ponnuswamy N., Bastings M.M., Nathwani B., Ryu J.H., Chou L.Y., Vinther M., Li W.A., Anastassacos F.M., Mooney D.J, & Shih W.M. (2017). Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nature Communications, 8, 15654.
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Publication 2017
Anabolism Bacteriophage M13 Buffers DNA Replication Edetic Acid Endotoxins Escherichia coli Glycerin Magnesium Chloride Medical Devices Staple, Surgical Triton X-114 Tromethamine
5
Phage Display ELISA Protocol

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Publication 2012
Ampicillin Antibodies, Anti-Idiotypic Bacteriophage M13 Bacteriophages Binding Sites Biotin Buffers Cardiac Arrest Clone Cells Enzyme-Linked Immunosorbent Assay Epiphyseal Cartilage neutravidin Phocidae Proteins Technique, Dilution Tweens

Most recents protocols related to «Bacteriophage M13»

1
PHESELECTOR Assay for Thiol Reactivity Evaluation
Not available on PMC !

Example 2

Bovine serum albumin (BSA), erbB2 extracellular domain (HER2) and streptavidin (100 μl of 2 μg/ml) were separately coated on Maxisorp 96 well plates. After blocking with 0.5% Tween-20 (in PBS), biotinylated and non-biotinylated hu4D5Fabv8-ThioFab-Phage (2×1010 phage particles) were incubated for 1 hour at room temperature followed by incubation with horseradish peroxidase (HRP) labeled secondary antibody (anti-M13 phage coat protein, pVIII protein antibody). FIG. 8 illustrates the PHESELECTOR Assay by a schematic representation depicting the binding of Fab or ThioFab to HER2 (top) and biotinylated ThioFab to streptavidin (bottom).

Standard HRP reaction was carried out and the absorbance was measured at 450 nm. Thiol reactivity was measured by calculating the ratio between OD450 for streptavidin/OD450 for HER2. A thiol reactivity value of 1 indicates complete biotinylation of the cysteine thiol. In the case of Fab protein binding measurements, hu4D5Fabv8 (2-20 ng) was used followed by incubation with HRP labeled goat polyclonal anti-Fab antibodies.

US11873330B2. Cysteine engineered antibodies and conjugates (2024-01-16). Genentech, Inc. [None]. Inventors: Sunil Bhakta [US], Jagath R. Junutula [US].
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Patent 2024
Anti-Antibodies Bacteriophage M13 Bacteriophages Biological Assay Biotinylation Cardiac Arrest Cysteine ERBB2 protein, human Goat herstatin protein, human Horseradish Peroxidase Immunoglobulins Proteins Serum Albumin, Bovine Streptavidin Sulfhydryl Compounds Tween 20
2
FACS Screening of GPRC5D Phage Clones
Not available on PMC !

Example 4

FACS Screening: FIG. 24 shows FACS analysis of GPRC5D-specific phage antibody clones (ET150-1, ET150-2, ET150-5, ET150-8, ET150-18). Phage clones were incubated with 3T3-GPRC5D cell line, then with anti-M13 mouse antibody. Finally APC-labeled anti-mouse IgG 2nd antibody was added to the reaction after washing again. The binding was measured by FACS and expressed as mean fluorescence intensity (MFI). Cells incubated with M13 K07 helper phage and cells only were used as negative controls.

US11866478B2. Nucleic acid molecules encoding chimeric antigen receptors targeting G-protein coupled receptor (2024-01-09). MEMORIAL SLOAN KETTERING CANCER CENTER [US], EUREKA THERAPEUTICS, INC. [US]. Inventors: Renier J. Brentjens [US], Eric L Smith [US], Cheng Liu [US].
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Patent 2024
3T3 Cells Anti-Antibodies Antibodies, Anti-Idiotypic Bacteriophage M13 Bacteriophages Cell Lines Cells Clone Cells Fluorescence GPRC5D protein, human Immunoglobulin G Immunoglobulins Mus
3
Virus-Like Models for SARS-CoV-2 Spike Protein Detection
Sandwich ELISA was applied for the expression verification of the spike protein. Rabbit anti-SARS-CoV-2 S protein polyclonal antibody was used to coat a 96-well plate. Then, the produced Model-S was placed with different diluted ratios after washing and blocking the plates. After that, the Rabbit anti-M13 pAb-HRP was added and aimed to form a sandwich structure. Followed by the reaction with the TMB substrate, OD values at 450 nm were collected and analyzed to decide whether the Model-S could express the spike protein of SARS-CoV-2.
In order to estimate the infection ability of the virus-like model, the plaque assay was used to determine the titer of the produced Model-S since it is the gold standard for titer measurement. The displayed phages Model-S from different dilution ratios were employed to infect E. coli TG1. After that, LB solid culture media with kanamycin was applied to provide a space for cultivation. Moreover, the mixtures were cultivated at 37 °C overnight. The plates were collected, and all the plaques were counted to obtain the titer of Model-S the following day.
The molecular interaction instrument ForteBio Octet K2 (SARTORIUS, Göttingen, Germany) was used to assess the combination between the produced Model-S and the corresponding anti-SARS-CoV-2 spike protein antibody (Rabbit pAb). The interaction between these biomolecules could be monitored and collected through the shift of the probe surface reflection interference spectrum following the thin film interferometry technology. The process, including association, dissociation, and regeneration, was performed repeatedly according to the preprogramming. After the measurement, the association constant (ka) and dissociation constant (kd) were obtained. Moreover, the affinity constant could be calculated.
After production and verification, the two virus-like models: Model-N [45 (link)] and Model-S, were prepared. Accompanied by these two models (as biothreats), M13 phage, bovine serum albumin (BSA), ovalbumin (OVA), commercial N protein, commercial S1 protein, commercial S2 protein, and E. coli TG1 were used as control samples for further study. All selected samples are related to the actual SARS-CoV-2 virus. The produced Model-S and Model-N are the substitutions of SARS-CoV-2 in this research, which could be regarded as the combination of M13 phage (main body) and N/S protein (p3 site). The M13 phage used in the phage display to synthesize the models is a kind of virus that belongs to the virus family, as SARS-CoV-2 does. BSA and OVA are common proteins for scientific research. In addition, the N protein, S1 protein, and S2 protein are the structural proteins of SARS-CoV-2. Furthermore, as common pathogen types, both bacteria and viruses can cause the outbreak of large-scale infectious diseases. Thus, E. coli TG1 was also included for identification research since one of the hosts of the M13 phage is E. coli TG1, and it was also used to produce the models. Therefore, the nine selected samples are more or less related to the SARS-CoV-2 virus. The higher the relation between the sample and the SARS-CoV-2 virus (or its substitution), the more difficult it might be to distinguish. In general, the nine selected samples, including viruses, proteins, and bacteria, might be representative of the research. The recognition of the Model-S and Model-N among those related samples could provide a possibility for the nondestructive detection and identification of targeted biothreats. Therefore, the nine samples were prepared for spectroscopy analysis.
Wu Y., Liu Z., Mao S., Liu B, & Tong Z. (2023). Identify the Virus-like Models for COVID-19 as Bio-Threats: Combining Phage Display, Spectral Detection and Algorithms Analysis. International Journal of Molecular Sciences, 24(4), 3209.
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Publication 2023
Antibodies, Anti-Idiotypic Bacteria Bacteriophage M13 Bacteriophages Biological Assay Culture Media Disease Outbreaks Enzyme-Linked Immunosorbent Assay Escherichia coli Gold Human Body Interferometry Kanamycin M protein, multiple myeloma nucleoprotein, Measles virus Ovalbumin Pathogenicity Proteins Rabbits Regeneration SARS-CoV-2 Senile Plaques Serum Albumin, Bovine Spectrum Analysis spike protein, SARS-CoV-2 Technique, Dilution Virus Virus Diseases
4
Production of SARS-CoV-2 Spike Protein Model
In our previous work, the nucleocapsid (N) protein of SARS-CoV-2 was focused on synthesizing the Model-N by phage display. Similarly, in this study, the spike (S) protein was targeted and used to produce the Model-S following the same protocol. The S protein of SARS-CoV-2 has a molecular weight of about 180–200 kDa. Figure 6 illustrates the processing for the synthesis of Model-S.
After searching the gene corresponding to the S protein of SARS-CoV-2 at the National Center for Biotechnology Information (NCBI) website (Gene ID: 43740568), it was modified by adding SfiI and NotI restriction digest sites on both sides. After the regular PCR amplification and double endonuclease digestion by SfiI/NotI enzyme, the inserted fragment was prepared. The dosage and duration conditions were in accordance with the previous work, as shown in Table 8 (a) and (b) [45 (link)].
When the vector pHB was digested by the same enzymes as well, the two parts were constructed and combined with recombinant vector pHB-S produced. The experimental conditions followed the same protocol preparing pHB-N, as presented in Table 9 [45 (link)].
Then, it was transformed into the competent E. coli TG1. After cultivation, M13 phages were added to infect TG1, and the synthesized Model-S was finally produced after filtrations. The specific cultivation process was described before [45 (link)].
Wu Y., Liu Z., Mao S., Liu B, & Tong Z. (2023). Identify the Virus-like Models for COVID-19 as Bio-Threats: Combining Phage Display, Spectral Detection and Algorithms Analysis. International Journal of Molecular Sciences, 24(4), 3209.
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Publication 2023
Anabolism Bacteriophage M13 Cloning Vectors Digestion endodeoxyribonuclease NotI Enzymes Escherichia coli Filtration Genes Nucleocapsid nucleocapsid phosphoprotein, SARS-CoV-2 Phage Display Techniques spike protein, SARS-CoV-2
5
Comparative Genomics of Bacteriophages
Forty-one bacteriophage genome sequences listed in Table 1 were aligned using the CLC whole genome analysis tool by default parameters (Min. initial seed length = 15; Allow mismatches = yes; Min. alignment block = 100; Min. similarity (0.8); Min. length (0.8)). Average nucleotide identity (ANI) and alignment percentage (AP) were calculated based on the aligned genomes. A heat map was computed based on the previous alignment using the heat-map tool with default parameters (Euclidean distance method and complete cluster linkages). Closely related bacteriophage genomes were selected for further comparative synteny analysis. Dot plots were generated to represent homologous regions, orthologs, genome gaps (GGs), and inversions within the genomes. The evolutionary analyses of the whole genome of the phage fp01 were conducted using MEGAX. The Neighbor-Joining method [35 (link)] with a bootstrap test of 1000 replicates and the Jukes–cantor method [36 ] was utilized to determine the evolutionary distances. The Enterobacteria bacteriophage M13 genome was used as out group for the analysis.
Vasquez I., Retamales J., Parra B., Machimbirike V., Robeson J, & Santander J. (2023). Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor. Viruses, 15(2), 379.
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Publication 2023
Bacteriophage M13 Bacteriophages Biological Evolution Cantor Genome Inversion, Chromosome Nucleotides Synteny

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1
96 well plate by Thermo Fisher Scientific
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96-well plates are a common laboratory tool used for a variety of applications. They are typically made of plastic and contain 96 individual wells arranged in a 8x12 grid format. The plates provide a standardized platform for conducting small-scale experiments, assays, or sample preparation. Each well can hold a small volume of liquid or sample. 96-well plates are widely used in fields such as biochemistry, cell biology, and high-throughput screening.
2
M13 phage by New England Biolabs
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M13 phages are a type of bacteriophage, a virus that infects bacterial cells. They have a circular, single-stranded DNA genome and are commonly used in molecular biology and biotechnology applications.
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M13ke by New England Biolabs
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M13KE is a bacteriophage vector used for DNA cloning and sequencing. It functions as a single-stranded DNA template for in vitro synthesis of complementary DNA strands.
4
M13ko7 helper phage by New England Biolabs
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M13KO7 helper phage is a DNA vector used in molecular biology laboratories. It serves as a helper phage to facilitate the production of single-stranded DNA from phagemid vectors, which are commonly used for DNA sequencing and protein display applications.
5
E coli clone n 29664 by Addgene
E.coli clone n 29664 is a bacterial strain that can be used for various molecular biology applications. It is a non-pathogenic strain of Escherichia coli, a commonly used model organism in research. The strain can be used for the propagation and maintenance of plasmid DNA.
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T4 DNA ligase is an enzyme that catalyzes the formation of phosphodiester bonds between adjacent 3'-hydroxyl and 5'-phosphate termini in DNA. It is commonly used in molecular biology for the joining of DNA fragments.
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Anti m13 bacteriophage antibody by Abcam
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Anti-M13 bacteriophage antibody is a laboratory reagent used to detect and quantify the presence of M13 bacteriophage, a type of virus that infects bacteria. It functions by binding specifically to the protein coat of the M13 bacteriophage, allowing its identification and measurement in various experimental settings.
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Anti mouse igg r antibody by Santa Cruz Biotechnology
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Tmb substrate by Thermo Fisher Scientific
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More about "Bacteriophage M13"

Bacteriophage M13, a filamentous viral particle, has become a widely used model system in various fields of research, including viral biology, protein engineering, and biotechnology applications.
This single-stranded DNA (ssDNA) phage is known for its ability to infect the common bacterium Escherichia coli (E. coli), making it a valuable tool for scientists.
One of the key advantages of Bacteriophage M13 is its small size and ease of manipulation, which allows for efficient genetic engineering and display of foreign peptides on its surface.
This feature has led to its widespread use in applications such as phage display, where the phage's surface is modified to present a diverse library of peptides or proteins for screening and selection purposes.
The M13 phage is often used in conjunction with other laboratory tools and reagents, such as 96-well plates, which provide a convenient format for high-throughput experiments.
Additionally, the M13KE and M13KO7 helper phages are commonly utilized to assist in the production and purification of recombinant M13 phage particles.
Researchers working with Bacteriophage M13 may also encounter the use of E. coli clone n 29664, a specific bacterial strain commonly used as a host for M13 phage propagation.
Other related materials, such as TMB (3,3',5,5'-Tetramethylbenzidine) for colorimetric assays, T4 DNA ligase for genetic manipulations, and antibodies like Anti-M13 bacteriophage antibody and Anti-mouse IgG-R antibody, are often employed in experiments involving the M13 phage system.
By leveraging the insights and techniques associated with Bacteriophage M13, researchers can enhance the reproducibility, accuracy, and efficiency of their research endeavors, leading to valuable advancements in fields ranging from viral biology to biotechnology applications.