Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

Rahong, Sakon; Yasui, Takahiro; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Guodong; He, Yabai; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

doi:10.1038/srep05252

Cited by 57 publications

(67 citation statements)

References 49 publications

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“…According to our previous work, 17 we prepared the nanowire embedded in the microchannel by varying the number of nanowire growth cycles from 1, 3 and 5 and the detection points were 1 and 3 mm from the junction. In this work, we increased the number of nanowire growth cycles to 7 times as illustrated in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, the microchannel was sealed using a fused silica cover glass (130 μm thick) according to the method described in literature. 10,16,17 …”

Section: Fabrication Of the Self-assembled Nanowire Arrays Embedded Imentioning

confidence: 99%

“…Recently, we presented bottom-up self-assembled nanowire structures as a sieving material embedded in a microfluidic channel for manipulation of long DNA molecules 16 and for ultrafast DNA separation of a wide range of molecule sizes. 17 Here we report an ultrafast DNA filtration by using self-assembled nanowire arrays embedded in a microfluidic channel as a sieving material. The self-assembled nanowire arrays can be fabricated by a vapor-liquid-solid (VLS) technique, which can prepare nanowire in nanoscale (10 -50 nm) with high aspect ratio (>100) in microchannel, while the smallest diameter by the top down method is about 100 nm with an aspect ratio of about 10.…”

Section: Introductionmentioning

confidence: 99%

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Self-assembled Nanowire Arrays as Three-dimensional Nanopores for Filtration of DNA Molecules

et al. 2015

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Molecular filtration and purification play important roles for biomolecule analysis. However, it is still necessary to improve efficiency and reduce the filtration time. Here, we show self-assembled nanowire arrays as three-dimensional (3D) nanopores embedded in a microfluidic channel for ultrafast DNA filtration. The 3D nanopore structure was formed by a vapor-liquid-solid (VLS) nanowire growth technique, which allowed us to control pore size of the filtration material by varying the number of growth cycles. λ DNA molecules (48.5 kbp) were filtrated from a mixture of T4 DNA (166 kbp) at the entrance of the 3D nanopore structure within 1 s under an applied electric field. Moreover, we observed single DNA molecule migration of T4 and λ DNA molecules to clarify the filtration mechanism. The 3D nanopore structure has simplicity of fabrication, flexibility of pore size control and reusability for biomolecule filtration. Consequently it is an excellent material for biomolecular filtration.

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Section: Resultsmentioning

confidence: 99%

“…Finally, the microchannel was sealed using a fused silica cover glass (130 μm thick) according to the method described in literature. 10,16,17 …”

Section: Fabrication Of the Self-assembled Nanowire Arrays Embedded Imentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Self-assembled Nanowire Arrays as Three-dimensional Nanopores for Filtration of DNA Molecules

et al. 2015

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“…We can therefore use this simplified model to predict the moderate field mobility and the shape of the electrophoretic arcs of DNA knots in gels of variable pore size, e.g., tuned via agarose concentration (36) or nanowire growth cycle (37). The plots presented in Fig.…”

Section: Random Walk Model With Topology-dependent Rates Captures Thementioning

confidence: 99%

Topological patterns in two-dimensional gel electrophoresis of DNA knots

Michieletto

Marenduzzo

Orlandini

2015

Proc. Natl. Acad. Sci. U.S.A.

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Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number" and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.DNA knots | topology | gel electrophoresis T opology plays a key role in the biophysics of DNA and is intimately related to its functioning. For instance, transcription of a gene redistributes twist locally to create what is known as supercoiling, whereas catenanes or knots can prevent cell division; hence they need to be quickly and accurately removed by specialized enzymes known as topoisomerases. How can one establish experimentally the topological state of a given DNA molecule? By far the most successful and widely used technique to do so is gel electrophoresis (1, 2). This method exploits the empirical observation that the mobility of a charged DNA molecule under an electric field depends on its size, shape, and topology (2). Gel electrophoresis is so reliable that it can be used, for instance, to map replication origins and stalled replication forks (3), to separate plasmids with different amount of supercoiling (3, 4), and to identify DNA knots (5, 6). The most widely used variant of this technique nowadays is 2D gel electrophoresis, where a DNA molecule is subjected to a sequence of two fields, applied along orthogonal directions (2). The two runs are characterized by different field strengths and sometimes also gel concentrations (4); with suitable choices, the joint responses lead to increased sensitivity.Although gel electrophoresis is used very often, and is extremely well characterized empirically, there is still no comprehensive theory to quantitatively understand, or predict, what results will be observed in a particular experiment. Some aspects are reasonably well established. For instance, it is now widely accepted that the physics of the size-dependent migration of linear polymers can be explained by the theory of biased polymer reptation (7-12). Likewise, the behavior of, for example, nicked, torsionally relaxed, DNA knots in a sparse gel and under a weak field is analogous to that of molecules sedimenting under gravity (13-15). The terminal velocity can be estimated via a balance between the applied force and the fr...

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“…4, but it is hard to fabricate nanopillar less than 100-nm diameter, which is required to separate smaller molecules, including protein, sugar chain, lipid, and microRNA. Vapor-liquid-solid methods were utilized to fabricate nanowire structures, which are less than 100-nm diameter, inside microfabricated channels [28,29,33]. Even three-dimensional nanowire structures are possible to fabricate inside a microchannel as shown in Fig.…”

Section: Nanowire Devicesmentioning

confidence: 99%

Nano- and Microbiodevices for High-Performance Separation of Biomolecules

Baba

2015

Chromatography

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Nano-and microbiodevices were developed for the high-performance separation of DNA, RNA, protein, sugar chain, and other biomolecules. We describe numerous advantages of nano-and microbiodevices as the separation technologies, including HPLC and capillary electrophoretic separation of DNA, nanopillar devices for the ultra-fast separation of DNA and proteins, nanoball materials for the fast separation of wide range of DNA fragments, nanowire devices for ultra-fast separation of DNA, RNA, and proteins. Because of the high efficiency of nano-and microbiodevices for the separation of biomolecules in the clinical blood and urea samples, numerous types of nano-and microbiodevices were developed and applied to the diagnosis of diseases, including cancer, diabetes, hypertension, infectious diseases, and other noncommunicable diseases.

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Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

Cited by 57 publications

References 49 publications

Self-assembled Nanowire Arrays as Three-dimensional Nanopores for Filtration of DNA Molecules

Self-assembled Nanowire Arrays as Three-dimensional Nanopores for Filtration of DNA Molecules

Topological patterns in two-dimensional gel electrophoresis of DNA knots

Nano- and Microbiodevices for High-Performance Separation of Biomolecules

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