Progress and challenges in bacterial whole-cell-components Aptamer advanced screening and site identification

Su, Yuan; Zhu, Longjiao; Wu, Yifan; Liu, Zihong; Xu, Wentao

doi:10.1016/j.trac.2022.116731

Cited by 14 publications

(6 citation statements)

References 85 publications

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“…The epitopes involved in aptamer−bacteria interactions are often proteins. 26 In particular, the capture aptamer in the study by Zhou et al was shown to target amino acids in the α-helix of the B. cereus epiprotein. 19 For this reason, we decided to use nanosome suspensions with a constant protein concentration to compare the affinity of the aptamers with the study's different nanosomes.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…It is also often necessary to perfect their performance by truncating the selected aptamers and then ensuring that the latter maintain a stable conformation in complex matrices when grafted onto a substrate. 2 Various techniques can be used to characterize the affinity and specificity of aptamers. 3 However, when SELEX is applied to cells like bacteria (cell-SELEX), most of these affinity characterization methods are actually unsuitable, primarily due to the large size of bacteria.…”

Section: ■ Introductionmentioning

confidence: 99%

“…3 However, when SELEX is applied to cells like bacteria (cell-SELEX), most of these affinity characterization methods are actually unsuitable, primarily due to the large size of bacteria. The most commonly used methods are fluorescence spectrophotometry and flow cytometry, 2 but both require a fluorescent label and cannot be used for multiplexed analyses.…”

Section: ■ Introductionmentioning

confidence: 99%

“…After several rounds, this technique yields a range of potential candidates that must be further characterized to determine their binding affinities and specificities. It is also often necessary to perfect their performance by truncating the selected aptamers and then ensuring that the latter maintain a stable conformation in complex matrices when grafted onto a substrate . Various techniques can be used to characterize the affinity and specificity of aptamers .…”

Section: Introductionmentioning

confidence: 99%

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Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes

Manceau,

Farre,

Lagarde

et al. 2024

ACS Appl. Mater. Interfaces

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The cell-SELEX method enables efficient selection of aptamers that bind whole bacterial cells. However, after selection, it is difficult to determine their binding affinities using common screening methods because of the large size of the bacteria. Here we propose a simple surface plasmon resonance imaging method (SPRi) for aptamer characterization using bacterial membrane vesicles, called nanosomes, instead of whole cells. Nanosomes were obtained from membrane fragments after mechanical cell disruption in order to preserve the external surface epitopes of the bacterium used for their production. The study was conducted on Bacillus cereus (B. cereus), a Gram-positive bacterium commonly found in soil, rice, vegetables, and dairy products. Four aptamers and one negative control were initially grafted onto a biochip. The binding of B. cereus cells and nanosomes to immobilized aptamers was then compared. The use of nanosomes instead of cells provided a 30-fold amplification of the SPRi signal, thus allowing the selection of aptamers with higher affinities. Aptamer SP15 was found to be the most sensitive and selective for B. cereus ATCC14579 nanosomes. It was then truncated into three new sequences (SP15M, SP15S1, and SP15S2) to reduce its size while preserving the binding site. Fitting the results of the SPRi signal for B. cereus nanosomes showed a similar trend for SP15 and SP15M, and a slightly higher apparent association rate constant k on for SP15S2, which is the truncation with a high probability of a G-quadruplex structure. These observations were confirmed on nanosomes from B. cereus ATCC14579 grown in milk and from the clinical strain B. cereus J066. The developed method was validated using fluorescence microscopy on whole B. cereus cells and the SP15M aptamer labeled with a rhodamine. This study showed that nanosomes can successfully mimic the bacterial membrane with great potential for facilitating the screening of specific ligands for bacteria.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes

Manceau,

Farre,

Lagarde

et al. 2024

ACS Appl. Mater. Interfaces

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“…Aptamer refers to DNA or RNA sequences that can specifically bind to macromolecular proteins, inorganic ions, organic molecules, cells, and microorganisms, and has the advantages of good affinity, high sensitivity, and low cost. [116,117] Aptamer can bind with nanozymes to form aptamer-functionalized nanoprobes for the clearance of bacteria through targeting and catalytic properties. The bacterial targeting of aptamer and the antibacterial properties of nanozymes can enhance the antibacterial performance.…”

Section: Aptamermentioning

confidence: 99%

Tailoring the Surface and Composition of Nanozymes for Enhanced Bacterial Binding and Antibacterial Activity

Hou

Xianyu

2023

Small

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With the advantages of diverse structures, tunable enzymatic activity, and high stability, nanozymes are widely used in medicine, chemistry, food, environment, and other fields. As an alternative to traditional antibiotics, nanozymes attract more and more attention from the scientific researchers in recent years. Developing nanozymes‐based antibacterial materials opens up a new avenue for the bacterial disinfection and sterilization. In this review, the classification of nanozymes and their antibacterial mechanisms are discussed. The surface and composition of nanozymes are critical for the antibacterial efficacy, which can be tailored to enhance both the bacterial binding and the antibacterial activity. On the one hand, the surface modification of nanozymes enables binding and targeting of bacteria that improves the antibacterial performance of nanozymes including the biochemical recognition, the surface charge, and the surface topography. On the other hand, the composition of nanozymes can be modulated to achieve enhanced antibacterial performance including the single nanozyme‐mediated synergistic and multiple nanozymes‐mediated cascade catalytic antibacterial applications. In addition, the current challenges and future prospects of tailoring nanozymes for antibacterial applications are discussed. This review can provide insights into the design of future nanozymes‐based materials for the antibacterial treatments.

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Intratumoral Microbiota as a Target for Advanced Cancer Therapeutics

Peng,

Hu,

et al. 2024

Advanced Materials

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In recent years, advancements in microbial sequencing technology have sparked an increasing interest in the bacteria residing within solid tumors and its distribution and functions in various tumors. Intratumoral bacteria critically modulate tumor oncogenesis and development through DNA damage induction, chronic inflammation, epigenetic alterations, and metabolic and immune regulation, while also influencing cancer treatment efficacy by affecting drug metabolism. In response to these discoveries, a variety of anti‐cancer therapies targeting these microorganisms have emerged. These approaches encompass oncolytic therapy utilizing tumor‐associated bacteria, the design of biomaterials based on intratumoral bacteria, the use of intratumoral bacterial components for drug delivery systems, and comprehensive strategies aimed at the eradication of tumor‐promoting bacteria. Herein, this review article summarizes the distribution patterns of bacteria in different solid tumors, examines their impact on tumors, and evaluates current therapeutic strategies centered on tumor‐associated bacteria. Furthermore, the challenges and prospects for developing drugs that target these bacterial communities are also explored, promising new directions for cancer treatment.

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Progress and challenges in bacterial whole-cell-components Aptamer advanced screening and site identification

Cited by 14 publications

References 85 publications

Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes

Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes

Tailoring the Surface and Composition of Nanozymes for Enhanced Bacterial Binding and Antibacterial Activity

Intratumoral Microbiota as a Target for Advanced Cancer Therapeutics

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