Selective Detection and Quantification of Modified DNA with Solid-State Nanopores

Carlsen, Autumn; Zahid, Osama K.; Růžička, Jan; Taylor, Ethan Will; Hall, Adam R.

doi:10.1021/nl501340d

Cited by 70 publications

(84 citation statements)

References 43 publications

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“…Voltage-driven dsDNA translocation through 5-15 nm diameter pores in thin (20-50 nm) solid-state materials proceeds with mean velocities of 10-100 ns/bp, and often in large pores multiple DNA strands enter simultaneously (17,19,32,33), which complicates single-file readout of information that is encoded in the linear sequence. Proteins such as RecA from Escherichia coli form filaments around the DNA that slows DNA transport and prevents its folding (26,34,35), although this approach inherently masks chemical information contained within the DNA, such as the presence of DNA chemical modifications (7,36) or small bound drug/reporter molecules (37)(38)(39)(40). Explorations of the effects of parameters such as the electrolyte viscosity (41,42), salt type (43,44), membrane material (45,46), applied pressure (47,48), and chemical composition inside (49)(50)(51)(52) and outside (53) the pore have yielded only moderate DNA retardation factors.…”

Section: Introductionmentioning

confidence: 99%

Smooth DNA Transport through a Narrowed Pore Geometry

Carson

Wilson

Aksimentiev

et al. 2014

Biophysical Journal

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Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.

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Section: Introductionmentioning

confidence: 99%

Smooth DNA Transport through a Narrowed Pore Geometry

Carson

Wilson

Aksimentiev

et al. 2014

Biophysical Journal

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“…Key to this is the creation of a point-mutated SA construct that is incapable of binding biotin 18 . MonoSA is used in structural biology 19,20 , nanobiotechnology 21,22 and in vivo detection 23,24 . Similarly, applications for monovalent ST (monoST) arise, for example, in vivo, where biotin labelling is not always an option and working with genetically encoded SII is convenient.…”

mentioning

confidence: 99%

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

Baumann¹,

Bauer²,

Milles³

et al. 2015

Nature Nanotech

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Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.

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“…They used an α-Haemolysin protein pore to detect miR-155 at the single-molecule level in the serum of lung cancer patients. Carlsen et al (2014) demonstrated the detection of the detection of nucleic acids of the order of 100 NTs at nM concentrations using a silicon nitride solid-state nanopore. However, this method involved the modification of the analyte-capture probe duplex with biotin.…”

Section: Nanoporesmentioning

confidence: 99%

Micro- and nano-structure based oligonucleotide sensors

Ferrier

Shaver

Hands

2015

Biosensors and Bioelectronics

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This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.

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Selective Detection and Quantification of Modified DNA with Solid-State Nanopores

Cited by 70 publications

References 43 publications

Smooth DNA Transport through a Narrowed Pore Geometry

Smooth DNA Transport through a Narrowed Pore Geometry

Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy

Micro- and nano-structure based oligonucleotide sensors

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