Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Dorey, Adam; Howorka, Stefan

doi:10.1038/s41557-023-01322-x

Cited by 10 publications

(3 citation statements)

References 234 publications

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“…These sequencing platforms improved the resolution of complex genomic regions, structural variations, and repetitive sequences. Nanopores can test nucleic acids, including both native DNA and RNA molecules, and have the advantages of rapid readout, high accuracy, low cost, and portability ( Dorey and Howorka, 2024 ). It has been reported that nanopore sequences are promising for polypeptide identification and sequencing, capturing folded proteins, and achieving peptide threading ( Dorey and Howorka, 2024 ).…”

Section: Methods For Identifying the Microbiota In Humansmentioning

confidence: 99%

“…Nanopores can test nucleic acids, including both native DNA and RNA molecules, and have the advantages of rapid readout, high accuracy, low cost, and portability ( Dorey and Howorka, 2024 ). It has been reported that nanopore sequences are promising for polypeptide identification and sequencing, capturing folded proteins, and achieving peptide threading ( Dorey and Howorka, 2024 ). With the progress of sequencing technologies, we will learn more about the gut microbiota and epilepsy.…”

Section: Methods For Identifying the Microbiota In Humansmentioning

confidence: 99%

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A long journey to treat epilepsy with the gut microbiota

Li,

Gu,

Liang

et al. 2024

Front. Cell. Neurosci.

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Epilepsy is a common neurological disorder that affects approximately 10.5 million children worldwide. Approximately 33% of affected patients exhibit resistance to all available antiseizure medications, but the underlying mechanisms are unknown and there is no effective treatment. Increasing evidence has shown that an abnormal gut microbiota may be associated with epilepsy. The gut microbiota can influence the function of the brain through multiple pathways, including the neuroendocrine, neuroimmune, and autonomic nervous systems. This review discusses the interactions between the central nervous system and the gastrointestinal tract (the brain–gut axis) and the role of the gut microbiota in the pathogenesis of epilepsy. However, the exact gut microbiota involved in epileptogenesis is unknown, and no consistent results have been obtained based on current research. Moreover, the target that should be further explored to identify a novel antiseizure drug is unclear. The role of the gut microbiota in epilepsy will most likely be uncovered with the development of genomics technology.

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Section: Methods For Identifying the Microbiota In Humansmentioning

confidence: 99%

Section: Methods For Identifying the Microbiota In Humansmentioning

confidence: 99%

A long journey to treat epilepsy with the gut microbiota

Li,

Gu,

Liang

et al. 2024

Front. Cell. Neurosci.

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“…Nanopore sequencing is a new generation of gene sequencing technology, which is characterized by fast sequencing speed, long sequencing reads, real-time monitoring of sequencing data, and portable equipment [ 15 ]. So far, nanopore sequencing is relatively expensive compared to other tests and requires good laboratory conditions, but these are not worth mentioning compared to its benefits [ 16 ]. Nanopore sequencing is now showing its advantages in the field of infectious disease diagnosis, which can effectively improve the detection efficiency of pathogenic bacteria [ 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Diagnostic accuracy of nanopore sequencing for the rapid diagnosis of pulmonary tuberculosis: A protocol for a systematic review and meta-analysis

Yu,

Xu,

Shen

et al. 2024

PLoS ONE

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Background Pulmonary tuberculosis (PTB) is the most common type of tuberculosis (TB). Rapid diagnosis of PTB can help in TB control. Although the use of molecular tests (such as the GeneXpert MTB/RIF) has improved the ability to rapidly diagnose PTB, there is still room for improvement. Nanopore sequencing is a novel means of rapid TB detection. The purpose of this study was to establish a systematic review and meta-analysis protocol for evaluating the accuracy of nanopore sequencing for the rapid diagnosis of PTB. Methods We completed this protocol according to the Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) statement and registered on the PROSPERO platform. We will screen studies related to nanopore sequencing for diagnosis of PTB by searching through PubMed, EMBASE, the Cochrane Library using English, and Wanfang database, CNKI (China National Knowledge Infrastructure) using Chinese. Eligible studies will be screened according to the inclusion and exclusion criteria established in the study protocol. We will evaluate the methodological quality of the individual included studies using Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). We will use Stata (version 15.0) with the midas command and RevMan (version 5.3) for meta-analysis and forest plots and SROC curves generation. A p < 0.05 was treated as a statistically significant difference. When significant heterogeneity exists between studies, we will explore sources of heterogeneity through meta-regression analysis and subgroup analysis. Conclusion To the best of our knowledge, this will be the first systematic review and meta-analysis of nanopore sequencing for the diagnosis of PTB. We hope that this study will find a new and effective tool for the early diagnosis of PTB. PROSPERO Registration number CRD42023495593.

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Compliant DNA Origami Nanoactuators as Size‐Selective Nanopores

Yu,

Baptist,

Reinhardt

et al. 2024

Advanced Materials

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Biological nanopores crucially control the import and export of biomolecules across lipid membranes in cells. They have found widespread use in biophysics and biotechnology, where their typically narrow, fixed diameters enable selective transport of ions and small molecules, as well as DNA and peptides for sequencing applications. Yet, due to their small channel sizes, they preclude the passage of large macromolecules, e.g., therapeutics. Here, the unique combined properties of DNA origami nanotechnology, machine‐inspired design, and synthetic biology are harnessed, to present a structurally reconfigurable DNA origami MechanoPore (MP) that features a lumen that is tuneable in size through molecular triggers. Controllable switching of MPs between 3 stable states is confirmed by 3D‐DNA‐PAINT super‐resolution imaging and through dye‐influx assays, after reconstitution of the large MPs in the membrane of liposomes via an inverted‐emulsion cDICE technique. Confocal imaging of transmembrane transport shows size‐selective behavior with adjustable thresholds. Importantly, the conformational changes are fully reversible, attesting to the robust mechanical switching that overcomes pressure from the surrounding lipid molecules. These MPs advance nanopore technology, offering functional nanostructures that can be tuned on‐demand – thereby impacting fields as diverse as drug delivery, biomolecule sorting, and sensing, as well as bottom‐up synthetic biology.

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Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Cited by 10 publications

References 234 publications

A long journey to treat epilepsy with the gut microbiota

A long journey to treat epilepsy with the gut microbiota

Diagnostic accuracy of nanopore sequencing for the rapid diagnosis of pulmonary tuberculosis: A protocol for a systematic review and meta-analysis

Compliant DNA Origami Nanoactuators as Size‐Selective Nanopores

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