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1.
Nano Lett ; 24(33): 10388-10395, 2024 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-39116280

RESUMEN

Biomaterials in nature form hierarchical structures and functions across various length scales through binding and assembly processes. Inspired by nature, we developed hierarchically organized tissue engineering materials through evolutionary screening and self-templating assembly. Leveraging the M13 bacteriophage (phage), we employed an evolutionary selection process against hydroxyapatite (HA) to isolate HA-binding phage (HAPh). The newly discovered phage exhibits a bimodal length, comprising 950 nm and 240 nm, where the synergistic effect of these dual lengths promotes the formation of supramolecular fibrils with periodic banded structures. The assembled HAPh fibrils show the capability of HA mineralization and the directional growth of osteoblast cells. When applied to a dentin surface, it induces the regeneration of dentin-like tissue structures, showcasing its potential applications as a scaffold in tissue engineering. The integration of evolutionary screening and self-templating assembly holds promise for the future development of hierarchically organized tissue engineering materials.


Asunto(s)
Bacteriófago M13 , Durapatita , Ingeniería de Tejidos , Ingeniería de Tejidos/métodos , Bacteriófago M13/química , Bacteriófago M13/genética , Durapatita/química , Osteoblastos/citología , Humanos , Materiales Biocompatibles/química , Andamios del Tejido/química , Dentina/química
2.
Nano Lett ; 24(32): 9946-9952, 2024 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-39101944

RESUMEN

The utilization of biomaterials for the separation of rare earth elements (REEs) has attracted considerable interest due to their inherent advantages, including diverse molecular structures for selective binding and the use of eco-friendly materials for sustainable systems. We present a pioneering methodology for developing a safe virus to selectively bind REEs and facilitate their release through pH modulation. We engineered the major coat protein of M13 bacteriophage (phage) to incorporate a lanthanide-binding peptide. The engineered lanthanide-binding phage (LBPh), presenting ∼3300 copies of the peptide, serves as an effective biological template for REE separation. Our findings demonstrate the LBPh's preferential binding for heavy REEs over light REEs. Moreover, the LBPh exhibits remarkable robustness with excellent recyclability and stability across multiple cycles of separations. This study underscores the potential of genetically integrating virus templates with selective binding motifs for REE separation, offering a promising avenue for environmentally friendly and energy-efficient separation processes.


Asunto(s)
Bacteriófago M13 , Metales de Tierras Raras , Metales de Tierras Raras/química , Metales de Tierras Raras/aislamiento & purificación , Bacteriófago M13/química , Bacteriófago M13/genética , Elementos de la Serie de los Lantanoides/química , Proteínas de la Cápside/química , Proteínas de la Cápside/aislamiento & purificación , Proteínas de la Cápside/genética , Péptidos/química , Concentración de Iones de Hidrógeno
3.
Phys Chem Chem Phys ; 26(31): 20760-20769, 2024 Aug 07.
Artículo en Inglés | MEDLINE | ID: mdl-39046426

RESUMEN

M13 bacteriophages serve as a versatile foundation for nanobiotechnology due to their unique biological and chemical properties. The polypeptides that comprise their coat proteins, specifically pVIII, can be precisely tailored through genetic engineering. This enables the customized integration of various functional elements through specific interactions, leading to the development of innovative hybrid materials for applications such as energy storage, biosensing, and catalysis. Notably, a certain genetically engineered M13 bacteriophage variant, referred to as DSPH, features a pVIII with a repeating DSPHTELP peptide sequence. This sequence facilitates specific adhesion to single-walled carbon nanotubes (SWCNTs), primarily through π-π and hydrophobic interactions, though the exact mechanism remains unconfirmed. In this study, we synthesized the DSPHTELP peptide (an 8-mer peptide) and analyzed its interaction forces with different functional groups across various pH levels using surface forces apparatus (SFA). Our findings indicate that the 8-mer peptide binds most strongly to CH3 groups (Wad = 13.74 ± 1.04 mJ m-2 at pH 3.0), suggesting that hydrophobic interactions are indeed the predominant mechanism. These insights offer both quantitative and qualitative understanding of the molecular interaction mechanisms of the 8-mer peptide and clarify the basis of its specific interaction with SWCNTs through the DSPHTELP M13 bacteriophage.


Asunto(s)
Bacteriófago M13 , Interacciones Hidrofóbicas e Hidrofílicas , Nanotubos de Carbono , Péptidos , Nanotubos de Carbono/química , Bacteriófago M13/química , Bacteriófago M13/genética , Bacteriófago M13/metabolismo , Péptidos/química , Péptidos/metabolismo , Concentración de Iones de Hidrógeno , Proteínas de la Cápside/química , Proteínas de la Cápside/metabolismo
4.
J Nanobiotechnology ; 22(1): 599, 2024 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-39363262

RESUMEN

BACKGROUND: The urgent need for affordable and rapid detection methodologies for foodborne pathogens, particularly Escherichia coli (E. coli), highlights the importance of developing efficient and widely accessible diagnostic systems. Dark field microscopy, although effective, requires specific isolation of the target bacteria which can be hindered by the high cost of producing specialized antibodies. Alternatively, M13 bacteriophage, which naturally targets E. coli, offers a cost-efficient option with well-established techniques for its display and modification. Nevertheless, its filamentous structure with a large length-diameter ratio contributes to nonspecific binding and low separation efficiency, posing significant challenges. Consequently, refining M13 phage methodologies and their integration with advanced microscopy techniques stands as a critical pathway to improve detection specificity and efficiency in food safety diagnostics. METHODS: We employed a dual-plasmid strategy to generate a truncated M13 phage (tM13). This engineered tM13 incorporates two key genetic modifications: a partial mutation at the N-terminus of pIII and biotinylation at the hydrophobic end of pVIII. These alterations enable efficient attachment of tM13 to diverse E. coli strains, facilitating rapid magnetic separation. For detection, we additionally implemented a convolutional neural network (CNN)-based algorithm for precise identification and quantification of bacterial cells using dark field microscopy. RESULTS: The results obtained from spike-in and clinical sample analyses demonstrated the accuracy, high sensitivity (with a detection limit of 10 CFU/µL), and time-saving nature (30 min) of our tM13-based immunomagnetic enrichment approach combined with AI-enabled analytics, thereby supporting its potential to facilitate the identification of diverse E. coli strains in complex samples. CONCLUSION: The study established a rapid and accurate detection strategy for E. coli utilizing truncated M13 phages as capture probes, along with a dark field microscopy detection platform that integrates an image processing model and convolutional neural network.


Asunto(s)
Bacteriófago M13 , Escherichia coli , Bacteriófago M13/química , Bacteriófago M13/genética , Escherichia coli/virología , Escherichia coli/genética , Microscopía/métodos , Redes Neurales de la Computación , Humanos , Microbiología de Alimentos/métodos , Plásmidos/genética
5.
J Am Chem Soc ; 145(1): 300-310, 2023 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-36542094

RESUMEN

F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via magic-angle spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.


Asunto(s)
Bacteriófago M13 , ADN de Cadena Simple , Bacteriófago M13/química , Bacteriófago M13/metabolismo , ADN de Cadena Simple/metabolismo , Resonancia Magnética Nuclear Biomolecular , Espectroscopía de Resonancia Magnética , Proteínas de la Cápside/genética , Proteínas de la Cápside/metabolismo , ADN Viral/genética
6.
Nat Chem Biol ; 17(7): 806-816, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33958792

RESUMEN

The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA 'barcoded' M13 virions that display 30-1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, such as CD22, on cells in vitro and immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identify the glycoconjugates with optimal avidity necessary for binding to lectins on living cells in vitro and in vivo.


Asunto(s)
Bacteriófago M13/química , Análisis por Micromatrices , Polisacáridos/química , Animales , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bacteriófago M13/genética , Bacteriófago M13/metabolismo , Ratones , Polisacáridos/genética , Polisacáridos/metabolismo
7.
Sensors (Basel) ; 23(13)2023 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-37447860

RESUMEN

The dynamic and surface manipulation of the M13 bacteriophage via the meeting application demands the creation of a pathway to design efficient applications with high selectivity and responsivity rates. Here, we report the role of the M13 bacteriophage thin film layer that is deposited on an optical nanostructure involving gold nanoparticles/SiO2/Si, as well as its influence on optical and geometrical properties. The thickness of the M13 bacteriophage layer was controlled by varying either the concentration or humidity exposure levels, and optical studies were conducted. We designed a standard and dynamic model based upon three-dimensional finite-difference time-domain (3D FDTD) simulations that distinguished the respective necessity of each model under variable conditions. As seen in the experiments, the origin of respective peak wavelength positions was addressed in detail with the help of simulations. The importance of the dynamic model was noted when humidity-based experiments were conducted. Upon introducing varied humidity levels, the dynamic model predicted changes in plasmonic properties as a function of changes in NP positioning, gap size, and effective index (this approach agreed with the experiments and simulated results). We believe that this work will provide fundamental insight into understanding and interpreting the geometrical and optical properties of the nanostructures that involve the M13 bacteriophage. By combining such significant plasmonic properties with the numerous benefits of M13 bacteriophage (like low-cost fabrication, multi-wavelength optical characteristics devised from a single structure, reproducibility, reversible characteristics, and surface modification to suit application requirements), it is possible to develop highly efficient integrated plasmonic biomaterial-based sensor nanostructures.


Asunto(s)
Bacteriófagos , Nanopartículas del Metal , Nanoestructuras , Oro , Dióxido de Silicio , Reproducibilidad de los Resultados , Nanoestructuras/química , Bacteriófago M13/química
8.
Nucleic Acids Res ; 48(21): 12407-12414, 2020 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-33152066

RESUMEN

The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force-displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.


Asunto(s)
ADN Cruciforme/química , ADN de Cadena Simple/química , ADN Viral/química , Nanoestructuras/química , Bacteriófago M13/química , Bacteriófago M13/genética , Fenómenos Biomecánicos , ADN Cruciforme/genética , ADN Cruciforme/metabolismo , ADN de Cadena Simple/genética , ADN de Cadena Simple/metabolismo , ADN Viral/genética , ADN Viral/metabolismo , Elasticidad , Polinucleótido 5'-Hidroxil-Quinasa/química , Termodinámica
9.
Acc Chem Res ; 53(10): 2384-2394, 2020 10 20.
Artículo en Inglés | MEDLINE | ID: mdl-33001632

RESUMEN

The 2018 Nobel Prize in Chemistry recognized in vitro evolution, including the development by George Smith and Gregory Winter of phage display, a technology for engineering the functional capabilities of antibodies into viruses. Such bacteriophages solve inherent problems with antibodies, including their high cost, thermal lability, and propensity to aggregate. While phage display accelerated the discovery of peptide and protein motifs for recognition and binding to proteins in a variety of applications, the development of biosensors using intact phage particles was largely unexplored in the early 2000s. Virus particles, 16.5 MDa in size and assembled from thousands of proteins, could not simply be substituted for antibodies in any existing biosensor architectures.Incorporating viruses into biosensors required us to answer several questions: What process will allow the incorporation of viruses into a functional bioaffinity layer? How can the binding of a protein disease marker to a virus particle be electrically transduced to produce a signal? Will the variable salt concentration of a bodily fluid interfere with electrical transduction? A completely new biosensor architecture and a new scheme for electrical transduction of the binding of molecules to viruses were required.This Account describes the highlights of a research program launched in 2006 that answered these questions. These efforts culminated in 2018 in the invention of a biosensor specifically designed to interface with virus particles: the Virus BioResistor (VBR). The VBR is a resistor consisting of a conductive polymer matrix in which M13 virus particles are entrained. The electrical impedance of this resistor, measured across 4 orders of magnitude in frequency, simultaneously measures the concentration of a target protein and the ionic conductivity of the medium in which the resistor is immersed. Large signal amplitudes coupled with the inherent simplicity of the VBR sensor design result in high signal-to-noise ratio (S/N > 100) and excellent sensor-to-sensor reproducibility. Using this new device, we have measured the urinary bladder cancer biomarker nucleic acid deglycase (DJ-1) in urine samples. This optimized VBR is characterized by extremely low sensor-to-sensor coefficients of variation in the range of 3-7% across the DJ-1 binding curve down to a limit of quantitation of 30 pM, encompassing 4 orders of magnitude in concentration.


Asunto(s)
Bacteriófago M13/aislamiento & purificación , Técnicas Biosensibles/métodos , Anticuerpos/inmunología , Bacteriófago M13/química , Bacteriófago M13/inmunología , Bacteriófago M13/metabolismo , Biomarcadores de Tumor/orina , Técnicas Biosensibles/instrumentación , Compuestos Bicíclicos Heterocíclicos con Puentes/química , Electrodos , Humanos , Límite de Detección , Nanocables/química , Neoplasias/diagnóstico , Biblioteca de Péptidos , Polímeros/química , Proteína Desglicasa DJ-1/orina , Tecnicas de Microbalanza del Cristal de Cuarzo , Reproducibilidad de los Resultados , Relación Señal-Ruido
10.
Int J Mol Sci ; 22(7)2021 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-33810266

RESUMEN

The conformational variation of the viral capsid structure plays an essential role both for the environmental resistance and acid nuclear release during cellular infection. The aim of this study was to evaluate how capsid rearrangement in engineered phages of M13 protects viral DNA and peptide bonds from damage induced by UV-C radiation. From in silico 3D modelling analysis, two M13 engineered phage clones, namely P9b and 12III1, were chosen for (i) chemical features of amino acids sequences, (ii) rearrangements in the secondary structure of their pVIII proteins and (iii) in turn the interactions involved in phage capsid. Then, their resistance to UV-C radiation and hydrogen peroxide (H2O2) was compared to M13 wild-type vector (pC89) without peptide insert. Results showed that both the phage clones acquired an advantage against direct radiation damage, due to a reorganization of interactions in the capsid for an increase of H-bond and steric interactions. However, only P9b had an increase in resistance against H2O2. These results could help to understand the molecular mechanisms involved in the stability of new virus variants, also providing quick and necessary information to develop effective protocols in the virus inactivation for human activities, such as safety foods and animal-derived materials.


Asunto(s)
Bacteriófago M13/efectos de la radiación , Proteínas de la Cápside/química , Tolerancia a Radiación , Rayos Ultravioleta , Bacteriófago M13/química , Bacteriófago M13/efectos de los fármacos , Farmacorresistencia Viral , Peróxido de Hidrógeno/toxicidad , Dominios Proteicos
11.
Anal Chem ; 92(9): 6654-6666, 2020 05 05.
Artículo en Inglés | MEDLINE | ID: mdl-32252524

RESUMEN

DJ-1, a 20.7 kDa protein, is overexpressed in people who have bladder cancer (BC). Its elevated concentration in urine allows it to serve as a marker for BC. However, no biosensor for the detection of DJ-1 has been demonstrated. Here, we describe a virus bioresistor (VBR) capable of detecting DJ-1 in urine at a concentration of 10 pM in 1 min. The VBR consists of a pair of millimeter-scale gold electrodes that measure the electrical impedance of an ultrathin (≈ 150-200 nm), two-layer polymeric channel. The top layer of this channel (90-105 nm in thickness) consists of an electrodeposited virus-PEDOT (PEDOT is poly(3,4-ethylenedioxythiophene)) composite containing embedded M13 virus particles that are engineered to recognize and bind to the target protein of interest, DJ-1. The bottom layer consists of spin-coated PEDOT-PSS (poly(styrenesulfonate)). Together, these two layers constitute a current divider. We demonstrate here that reducing the thickness of the bottom PEDOT-PSS layer increases its resistance and concentrates the resistance drop of the channel in the top virus-PEDOT layer, thereby increasing the sensitivity of the VBR and enabling the detection of DJ-1. Large signal amplitudes coupled with the inherent simplicity of the VBR sensor design result in high signal-to-noise (S/N > 100) and excellent sensor-to-sensor reproducibility characterized by coefficients of variation in the range of 3-7% across the DJ-1 binding curve down to a concentration of 30 pM, near the 10 pM limit of detection (LOD), encompassing four orders of magnitude in concentration.


Asunto(s)
Bacteriófago M13/química , Biomarcadores de Tumor/orina , Técnicas Biosensibles , Proteína Desglicasa DJ-1/orina , Neoplasias de la Vejiga Urinaria/orina , Humanos , Factores de Tiempo
12.
Nano Lett ; 19(3): 1467-1478, 2019 03 13.
Artículo en Inglés | MEDLINE | ID: mdl-30730145

RESUMEN

Sustaining blood retention for theranostic nanoparticles is a big challenge. Various approaches have been attempted and have demonstrated some success but limitations remain. We hypothesized that peptides capable of increasing blood residence time for M13 bacteriophage, a rod-shaped nanoparticle self-assembled from proteins and nucleic acids, should also prolong blood circulation for engineered nanoparticles. Here we demonstrate the feasibility of this approach by identifying a series of blood circulation-prolonging (BCP) peptides through in vivo screening of an M13 peptide phage display library. Intriguingly, the majority of the identified BCP peptides contained an arginine-glycine-aspartic acid (RGD) motif, which was necessary but insufficient for the circulation-prolonging activity. We further demonstrated that the RGD-mediated specific binding to platelets was primarily responsible for the enhanced blood retention of BCP1. The utility of the BCP1 peptide was demonstrated by fusion of the peptide to human heavy-chain ferritin (HFn), leading to significantly improved pharmacokinetic profile, enhanced tumor cell uptake and optimum anticancer efficacy for doxorubicin encapsulated in the HFn nanocage. Our results provided a proof-of-concept for an innovative yet simple strategy, which utilizes phage display to discover novel peptides with the capability of substantially prolonging blood circulation for engineered theranostic nanoparticles.


Asunto(s)
Doxorrubicina/farmacología , Ferritinas/química , Nanopartículas/química , Péptidos/química , Secuencia de Aminoácidos/genética , Arginina/química , Ácido Aspártico/química , Bacteriófago M13/química , Transporte Biológico/genética , Técnicas de Visualización de Superficie Celular , Doxorrubicina/química , Glicina/química , Humanos , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Neoplasias/patología , Biblioteca de Péptidos , Péptidos/sangre
13.
Molecules ; 25(15)2020 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-32722650

RESUMEN

DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage's circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design-allowing for increasing structural complexity-and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.


Asunto(s)
ADN/biosíntesis , Nanoestructuras/química , Nanotecnología , Oligonucleótidos/biosíntesis , Bacteriófago M13/química , Bacteriófago M13/genética , ADN/química , ADN/genética , ADN de Cadena Simple/biosíntesis , Conformación de Ácido Nucleico , Oligonucleótidos/química , Oligonucleótidos/genética
14.
J Biol Chem ; 293(39): 15033-15042, 2018 09 28.
Artículo en Inglés | MEDLINE | ID: mdl-30068548

RESUMEN

Environmental exposure and cellular metabolism can give rise to DNA alkylation, which can occur on the nitrogen and oxygen atoms of nucleobases, as well as on the phosphate backbone. Although O6-alkyl-2'-deoxyguanosine (O6-alkyl-dG) lesions are known to be associated with cancer, not much is known about how the alkyl group structures in these lesions affect their repair and replicative bypass in vivo or how translesion synthesis DNA polymerases influence the latter process. To answer these questions, here we synthesized oligodeoxyribonucleotides harboring seven O6-alkyl-dG lesions, with the alkyl group being Me, Et, nPr, iPr, nBu, iBu, or sBu, and examined the impact of these lesions on DNA replication in Escherichia coli cells. We found that replication past all the O6-alkyl-dG lesions was highly efficient and that SOS-induced DNA polymerases play redundant roles in bypassing these lesions. Moreover, these lesions directed exclusively the G → A mutation, the frequency of which increased with the size of the alkyl group on the DNA. This could be attributed to the varied repair efficiencies of these lesions by O6-alkylguanine DNA alkyltransferase (MGMT) in cells, which involve the MGMT Ogt and, to a lesser extent, Ada. In conclusion, our study provides important new knowledge about the repair of the O6-alkyl-dG lesions and their recognition by the E. coli DNA replication machinery. Our results suggest that the lesions' carcinogenic potentials may be attributed, at least in part, to their strong mutagenic potential and their efficient bypass by the DNA replication machinery.


Asunto(s)
Transferasas Alquil y Aril/genética , Alquilación/genética , Desoxiguanosina/química , Proteínas de Escherichia coli/genética , O(6)-Metilguanina-ADN Metiltransferasa/genética , Factores de Transcripción/genética , Transferasas Alquil y Aril/química , Bacteriófago M13/química , Bacteriófago M13/efectos de los fármacos , Bacteriófago M13/genética , Daño del ADN/genética , Reparación del ADN/genética , Replicación del ADN/genética , ADN Polimerasa Dirigida por ADN/química , ADN Polimerasa Dirigida por ADN/genética , Desoxiguanosina/análogos & derivados , Desoxiguanosina/síntesis química , Desoxiguanosina/farmacología , Escherichia coli/genética , Proteínas de Escherichia coli/química , Humanos , Mutagénesis/genética , Mutágenos/química , Mutación , O(6)-Metilguanina-ADN Metiltransferasa/química , Factores de Transcripción/química
15.
Anal Biochem ; 570: 21-26, 2019 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-30735666

RESUMEN

Urinary tract infections (UTIs) are a common problem worldwide. The most prevalent causative pathogen of UTI is Escherichia coli, focus of this study. The current golden standard for detecting UTI is bacterial culture, creating a major workload for hospital laboratories - cost-effective and rapid mass screening of patient samples is needed. Here we present an alternative approach to screen patient samples with a single-step assay utilising time-resolved luminescence and luminescence modulating biosensing phages. Filamentous phage M13 was biopanned for binding luminescence quenching metal (copper) and further E. coli. The screening assay luminescence modulation was further enhanced by selecting right chemical environment for the functioning phage clones. Semi-specific interaction between phage, target bacteria and metal was detected by modulation in the signal of a weakly chelating, easily quenchable lanthanide complex. In the presence of the target pathogen, the phages collected quenching metal from solution to the bacterial surface changing the quenching effect on the lanthanide label and thus modulating the signal. Our method was compared with the bacterial culture data obtained from 70 patient samples. The developed proof-of-principle screening assay showed sensitivity and a specificity at the 90% mark when compared to culture method although some samples had high turbidity and even blood. The detection limit of E. coli was in the range of 1000-10 000 colony forming units/mL. Untreated urine sample was screened and time-resolved luminescence signal result was achieved within 10 min in a single incubation step.


Asunto(s)
Bacteriófago M13/química , Técnicas Biosensibles/métodos , Escherichia coli/aislamiento & purificación , Orina/microbiología , Bacteriófago M13/metabolismo , Cobre/química , Humanos , Elementos de la Serie de los Lantanoides/química , Mediciones Luminiscentes , Infecciones Urinarias/diagnóstico , Infecciones Urinarias/microbiología
16.
Biomacromolecules ; 20(10): 3658-3671, 2019 10 14.
Artículo en Inglés | MEDLINE | ID: mdl-31430134

RESUMEN

Instructive tissue engineering biomaterials provide a vascular niche and protect oxidative stress in injured tissue. In this study, we exploited bioinspired bacteriophage nanofibers, previously recognized by their biochemical and structural cues inducing angiogenesis, as an antioxidant tissue engineering material. We demonstrated that topological cues of Arg-Gly-Asp (RGD)-engineered bacteriophage nanofibers provide angiogenic niches and cytoprotective functions against cellular oxidative stress with increased expression of antioxidant enzymes heme oxygenase-1 (HO-1) and NAD(P)H-quinone oxidoreductase 1 (NQO1) via the extracellular-signal-regulated kinase (ERK)-nuclear factor erythroid 2-related factor2 (Nrf2)-mediated signaling pathway, where a high density of RGD cues on the phage body support efficient interaction of cells with phage cues. These bioinspired RGD-engineered bacteriophage nanofibers can serve as a novel therapeutic platform for curing ischemic diseases.


Asunto(s)
Bacteriófago M13/química , Nanofibras/química , Oligopéptidos/química , Estrés Oxidativo , Polímeros de Estímulo Receptivo/química , Células HeLa , Hemo Oxigenasa (Desciclizante)/metabolismo , Células Endoteliales de la Vena Umbilical Humana/metabolismo , Células Endoteliales de la Vena Umbilical Humana/fisiología , Humanos , Proteína Quinasa 1 Activada por Mitógenos/metabolismo , Proteína Quinasa 3 Activada por Mitógenos/metabolismo , NAD(P)H Deshidrogenasa (Quinona)/metabolismo , Factor 2 Relacionado con NF-E2/metabolismo , Neovascularización Fisiológica
17.
Nano Lett ; 18(6): 3623-3629, 2018 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-29718676

RESUMEN

The virus bioresistor (VBR) is a chemiresistor that directly transfers information from virus particles to an electrical circuit. Specifically, the VBR enables the label-free detection of a target protein that is recognized and bound by filamentous M13 virus particles, each with dimensions of 6 nm ( w) × 1 µm ( l), entrained in an ultrathin (∼250 nm) composite virus-polymer resistor. Signal produced by the specific binding of virus to target molecules is monitored using the electrical impedance of the VBR: The VBR presents a complex impedance that is modeled by an equivalent circuit containing just three circuit elements: a solution resistance ( Rsoln), a channel resistance ( RVBR), and an interfacial capacitance ( CVBR). The value of RVBR, measured across 5 orders of magnitude in frequency, is increased by the specific recognition and binding of a target protein to the virus particles in the resistor, producing a signal Δ RVBR. The VBR concept is demonstrated using a model system in which human serum albumin (HSA, 66 kDa) is detected in a phosphate buffer solution. The VBR cleanly discriminates between a change in the electrical resistance of the buffer, measured by Rsoln, and selective binding of HSA to virus particles, measured by RVBR. The Δ RVBR induced by HSA binding is as high as 200 Ω, contributing to low sensor-to-sensor coefficients-of-variation (<15%) across the entire calibration curve for HSA from 7.5 nM to 900 nM. The response time for the VBR is 3-30 s.


Asunto(s)
Bacteriófago M13/química , Técnicas Biosensibles/instrumentación , Albúmina Sérica Humana/análisis , Virión/química , Técnicas Biosensibles/métodos , Impedancia Eléctrica , Diseño de Equipo , Humanos , Límite de Detección
18.
J Biomol NMR ; 72(1-2): 55-67, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-30141148

RESUMEN

Determination of chemical shift anisotropy (CSA) in immobilized proteins and protein assemblies is one of several tools to determine protein dynamics on the timescales of microseconds and faster. The large CSA values of C=O groups in the rigid limit makes them in particular attractive for measurements of large amplitude motions, or their absence. In this study, we implement a 3D R-symmetry-based sequence that recouples the second spatial component of the 13C CSA with the corresponding isotropic 13C'-13C cross-peaks in order to probe backbone and sidechain dynamics in an intact fd-y21m filamentous phage viral capsid. The assignment of the isotropic cross-peaks and the analysis were conducted automatically using a new software named 'Raven'. The software can be utilized to auto-assign any 2D 13C-13C or 15N-13C spectrum given a previously-determined assignment table and generates simultaneously all intensity curves acquired in the third dimension. Here, all CSA spectra were automatically generated, and subsequently matched against a simulated set of CSA curves to yield their values. For the multi-copy, 50-residue-long protein capsid of fd-y21m, the backbone of the helical region is rigid, with reduced CSA values of ~ 12.5 kHz (~ 83 ppm). The N-terminus shows motionally-averaged CSA lineshapes and the carboxylic sidechain groups of four residues indicate large amplitude motions for D4, D5, D12 and E20. The current results further strengthen our previous studies of 15N CSA values and are in agreement with qualitative analysis of 13C-13C dipolar build-up curves, which were automatically obtained using our software. Our automated analysis technique is general and can be applied to study protein structure and dynamics, with data resulting from experiments that probe different variables such as relaxation rates and scaled anisotropic interactions.


Asunto(s)
Anisotropía , Bacteriófago M13/química , Resonancia Magnética Nuclear Biomolecular/métodos , Proteínas/química , Isótopos de Carbono , Simulación de Dinámica Molecular , Movimiento (Física) , Conformación Proteica , Programas Informáticos , Factores de Tiempo
19.
Bioconjug Chem ; 29(11): 3705-3714, 2018 11 21.
Artículo en Inglés | MEDLINE | ID: mdl-30347978

RESUMEN

One of the central themes of biomolecular engineering is the challenge of exploiting the properties of biological materials. Part of this challenge has been uncovering and harnessing properties of biological components that only emerge following their ordered self-assembly. One biomolecular building block that has received significant interest in the past decade is the M13 bacteriophage. There have been a number of recent attempts to trigger the ordered assembly of M13 bacteriophage into multivirion structures, relying on the innate tendency of M13 to form liquid crystals at high concentrations. These, in general, yield planar two-dimensional materials. Presented here is the production of multivirion assemblies of M13 bacteriophage via the chemical modification of its surface by the covalent attachment of the xanthene-based dye tetramethylrhodamine (TMR) isothiocyanate (TRITC). We show that TMR induces the formation of three-dimensional aster-like assemblies of M13 by providing "adhesive" action between bacteriophage particles through the formation of H-aggregates (face-to-face stacking of dye molecules). We also show that the H-aggregation of TMR is greatly enhanced by covalent attachment to M13 and is enhanced further still upon the ordered self-assembly of M13, leading to the suggestion that M13 could be used to promote the self-assembly of dyes that form J-aggregates, a desirable arrangement of fluorescent dye, which has interesting optical properties and potential applications in the fields of medicine and light harvesting technology.


Asunto(s)
Bacteriófago M13/química , Colorantes Fluorescentes/química , Cristales Líquidos/química , Sulfato de Amonio/química , Bacteriófago M13/ultraestructura , Dimerización , Polarización de Fluorescencia , Rodaminas/química
20.
Bioconjug Chem ; 29(6): 1872-1875, 2018 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-29800521

RESUMEN

Over the past ten years there has been increasing interest in the conjugation of exogenous compounds to the surface of the M13 bacteriophage. M13 offers a convenient scaffold for the development of nanoassemblies with useful functions, such as highly specific drug delivery and pathogen detection. However, the progress of these technologies has been hindered by the limited efficiency of conjugation to the bacteriophage. Here we generate a mutant version of M13 with an additional lysine residue expressed on the outer surface of the M13 major coat protein, pVIII. We show that this mutation is accommodated by the bacteriophage and that up to an additional 520 exogenous groups can be attached to the bacteriophage surface via amine-directed conjugation. These results could aid the development of high payload drug delivery nanoassemblies and pathogen detection systems with increased sensitivity.


Asunto(s)
Aminas/química , Bacteriófago M13/química , Bacteriófago M13/genética , Proteínas de la Cápside/química , Proteínas de la Cápside/genética , Aminación , Secuencia de Aminoácidos , Técnicas de Química Sintética , Lisina/química , Lisina/genética , Mutación
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