Single molecule based SNP detection using designed DNA carriers and solid-state nanopores

Kong, Jinglin; Zhu, Jinbo; Keyser, Ulrich F.

doi:10.1039/c6cc08621g

Cited by 68 publications

(66 citation statements)

References 29 publications

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“…It has to be noted that the ATP occupied fraction (0.25) is higher than the lower limit (0.08), as the displacement reaction was probably not fully complete. Although higher concentration ratios between DNA circuits and carriers could help to reach a more complete reaction, the background signal increases in parallel . We use the concentration ratio of 10 in all the measurements to balance between high response with low background.…”

Section: Resultsmentioning

confidence: 99%

“…For other target systems, 60 × 10 −9 m Thrombin (Haematologic Technologies) and 29 × 10 −6 m lysozyme (Sigma‐Aldrich) were used in the incubations. Quantitative concentration measurements were not carried out in this work, however the feasibility of measuring concentrations was demonstrated in a previous work . Gel electrophoresis was used as reference assay to validate the structural changes in the DNA circuit (Figure S4, Supporting Information).…”

Section: Methodsmentioning

confidence: 99%

“…Specific features in the ionic current signal confirm the presence of the target when the DNA carrier with the corresponding binding site passes through the nanopore. In previous studies, basic sensing functions including target identification, concentration quantification in the nanomolar range, and real‐time kinetics screening have been demonstrated, and multiplexed detection of high affinity antibodies was achieved …”

Section: Introductionmentioning

confidence: 99%

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Specific Biosensing Using DNA Aptamers and Nanopores

Kong

Zhu

Chen

et al. 2018

Adv Funct Materials

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The multiplexed biosensing of target molecules with high specificity and accuracy is of fundamental importance in both biological research and medical diagnostics. In this paper, the working range of the recent nanopore-DNA carrier based method is extended by introducing a two-step assay using specific DNA aptamers. A signal translation step allows for binding of the target in physiological conditions before the nanopore measurements. Using protein encoded DNA carriers, the simultaneous detection of three targets spanning several orders of magnitude in molecular weight is demonstrated. The single-molecule method may be integrated into nanopore sensing devices for future applied research and point-of-care applications.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Specific Biosensing Using DNA Aptamers and Nanopores

Kong

Zhu

Chen

et al. 2018

Adv Funct Materials

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“…(13) A biotinylated DNA-MSA approach was also used to identify base modifications (14) and to quantify nanomolar levels of MSA bound to 7.2 kb dsDNA. (15) More recently, MSA acted as a critical component in a scheme to detect single nucleotide polymorphism, (16) and to map the positions of short sequences in longer dsDNA. (17) Despite the growing body of applied nanopore research into streptavidin-based complexes, no studies have compared the characteristics of passage and capture of the protein itself or the protein-DNA complex under widely varying conditions (i.e.…”

Section: Introductionmentioning

confidence: 99%

Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation

Carlsen

Tabard‐Cossa

2020

Preprint

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Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals. STATEMENT OF SIGNIFICANCENanopore sensing allows investigation of biomolecular structure in aqueous solution, including electricfield-induced changes in protein conformation. This nanopore-based study probes the tetramer-dimer transition of streptavidin, observing the effects of increasing voltage with varying salt type and concentration. Binding of biotinylated DNA to streptavidin boosts the complex's structural integrity, while complicating signal analysis. We describe a broadly applicable geometric approach that maps stepwise changes in the nanopore signal to real-time conformational transitions. These results represent important progress toward accurate interpretation of nanopore signals generated by macromolecular complexes.

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“…These randomized modifications in DNA bases cause alterations in protein sequence residues of amino acids, thus altering their functions which lead to different disease conditions in individuals (1) . Several of these SNPs have been identified as disease-related genetic markers that have been used to recognize genes responsible for a particular disease in humans (2) .…”

Section: Introductionmentioning

confidence: 99%

SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence

Habib¹,

Alsamman²,

Shereif³

et al. 2019

Preprint

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Due to the ability to diagnose diseases early and evaluate the effectiveness of medicinal drugs, single nucleotide polymorphism (SNP) identification receives significant interest. Detection and diagnosis of genetic variation through skill-less computational tools would help researchers reducing the severity of such health complications and improving the well-tailored therapies using discovered and previously known information. We introduce SNPector, which is a standalone SNP inspection software could be used to diagnose gene pathogenicity and drug reaction in naked genomic sequences. It identifies and extracts gene-related SNPs, and reports their genomic position, associated phenotype disorder, associated diseases, linkage disequilibrium, in addition to various drug reaction information. SNPector detects and verifies the existence of an SNP in a given DNA sequence based on different clinically relevant SNP databases such as NCBI Clinvar database, Awesome database, and PharmGKB and generates highly informative visualizations of the recovered information.

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Single molecule based SNP detection using designed DNA carriers and solid-state nanopores

Cited by 68 publications

References 29 publications

Specific Biosensing Using DNA Aptamers and Nanopores

Specific Biosensing Using DNA Aptamers and Nanopores

Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation

SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence

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