Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

Shankla, Manish; Aksimentiev, Aleksei

doi:10.1038/ncomms6171

Cited by 103 publications

(99 citation statements)

References 49 publications

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“…On the other hand, a ssDNA molecule can easily orient along the graphene surface and enter the nanopore through a 2D diffusion process which would significantly slow down DNA translocations as confirmed by our results. [38,39] …”

Section: Resultsmentioning

confidence: 99%

“…[37] Recently, the potential for DNA–graphene hydrophobic interactions to induce ssDNA translocations in single-nucleotide steps was discussed. [38,39] ssDNA translocation experiments with standalone graphene membranes have been demonstrated by coating the graphene surface with a hydrophilic layer [40] or by performing the experiments at highly alkaline pH, which significantly reduce DNA–graphene interactions. [19] Our experiments are performed at a lower pH value (pH = 7.6) which enhances DNA adsorption on graphene [41] and is the first demonstration of the effect of DNA–graphene interactions on DNA translocation.…”

Section: Introductionmentioning

confidence: 99%

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Slowing DNA Transport Using Graphene–DNA Interactions

Banerjee

Wilson

Shim

et al. 2014

Adv Funct Materials

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108

106

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Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 dielectric layers in stacked membrane structures are fabricated. Slow translocations of ssDNA in nanopores drilled in membranes with layers of graphene are reported. The increased hydrophobic interactions between the ssDNA and the graphene layers could explain this phenomenon. Further confirmation of the hydrophobic origins of these interactions is obtained through reporting significantly faster translocations of dsDNA through these graphene layered membranes. Molecular dynamics simulations confirm the preferential interactions of DNA with the graphene layers as compared to the dielectric layer verifying the experimental findings. Based on our findings, we propose that the integration of multiple stacked graphene layers could slow down DNA enough to enable the identification of nucleobases.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Slowing DNA Transport Using Graphene–DNA Interactions

Banerjee

Wilson

Shim

et al. 2014

Adv Funct Materials

Self Cite

108

106

View full text Add to dashboard Cite

show abstract

“…Moreover, the device sensitivity will be influenced by the nucleobase adsorption angle that modulates the strength of the adsorbed molecular dipoles, potentially resulting in a significant difference between free nucleobases compared with attached nucleobase in a DNA strand. The charge state of graphene may provide an effective tool for electrical control of the nucleobase-graphene angle and the conformation of the DNA strand 55 .…”

Section: Discussionmentioning

confidence: 99%

A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases

et al. 2015

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Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene.

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“…It is even possible to observe the conformational change when nucleotide is methylated, a tiny chemical change can turn a gene on or off. It is obvious that such a DNA (reversible) performance can be used in DNA sequencing for personalized medicine [64]. …”

Section: Prospectsmentioning

confidence: 99%

“…15 [53][54][55] and [56,57]), new computers, and for a time being, unreachable quantum computers, makes unthinkable possibilities (Fig. 17) [63,64]. Graphene, DNA chips or biosensors are on the way to revolutionize almost all aspects of our lives.…”

Section: Prospectsmentioning

confidence: 99%

A century of X-ray crystallography and 2014 international year of X-ray crystallography

Kojić‐Prodić

2015

Maced. J. Chem. Chem. Eng.

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The 100 th anniversary of the Nobel prize awarded to Max von Laue in 1914 for his discovery of diffraction of X-rays on a crystal marked the beginning of a new branch of science -X-ray crystallography. The experimental evidence of von Laue's discovery was provided by physicists W. Friedrich and P. Knipping in 1912. In the same year, W. L. Bragg described the analogy between X-rays and visible light and formulated the Bragg's law, a fundamental relation that connected the wave nature of X-rays and fine structure of a crystal at atomic level. In 1913 the first simple diffractometer was constructed and structure determination started by the Braggs, father and son. In 1915 their discoveries were acknowledged by a Nobel Prize in physics. Since then, X-ray diffraction has been the basic method for determination of three-dimensional structures of synthetic and natural compounds. The three-dimensional structure of a substances defines its physical, chemical, and biological properties. Over the past century the significance of X-ray crystallography has been recognized by about forty Nobel prizes. X-ray structure analysis of simple crystals of rock salt, diamond and graphite, and later of complex biomolecules such as B12-vitamin, penicillin, haemoglobin/myoglobin, DNA, and biomolecular complexes such as viruses, chromatin, ribozyme, and other molecular machines have illustrated the development of the method. Among these big discoveries the double helix DNA structure was an epochal achievement of the 20 th century. These discoveries, together with many others of the X-ray crystallography, have completely changed our views and helped to develop other new fields of science such as molecular genetics, biophysics, structural molecular biology, material science, and many others. During the last decade, the implementation of free electron X-ray lasers, a new experimental tool, has opened up femtosecond dynamic crystallography. This highly advanced methodology enables to solve the structures and dynamics of the most complex biological assemblies involved in a cell metabolism. The advancements of science and technology over the 20 th and 21 st centuries are of great influence on our views in almost all human activities. The importance of Xray crystallography for science and technology advocates for its high impact on a wide area of research and declares it as a highly interdisciplinary science. In short, crystallography has defined the shape of the modern world.Focusing on single crystal diffraction, this essay tackles only one field of crystallography; the comprehensive review on X-ray crystallography can hardly be fitted into a single article. The aim with this review was to highlight the most striking examples illustrating some of the milestones over the past century.Keywords: centennial anniversary of X-ray crystallography; discovery of X-ray crystallography -dazzling history; highlights; X-ray structure analysis and its prospect Тридимензионалната структура на супстанците ги дефинира нивните физички, хемиски и биолошки својс...

show abstract

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

Cited by 103 publications

References 49 publications

Slowing DNA Transport Using Graphene–DNA Interactions

Slowing DNA Transport Using Graphene–DNA Interactions

A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases

A century of X-ray crystallography and 2014 international year of X-ray crystallography

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