Label‐Free Detection of DNA Hybridization at the Nanoscale: A Highly Sensitive and Selective Approach Using Atomic‐Force Microscopy

Zhou, Dejian; Sinniah, Kumar; Abell, Chris; Rayment, Trevor

doi:10.1002/anie.200352178

Cited by 61 publications

(65 citation statements)

References 30 publications

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“…The motion of its free terminus is then a random rotation confined on the surface of a hemisphere of radius r = L = 15 nm. From the data in Figure 1g and from other data in literature 20,25,26,28,32 , it is evident that, for the rod-like dsDNAs, the maximum tilt is limited by the crowding of the DNA as a function of density when an AFM tip contacts the topmost interface of the matrices. Hence, it is likely that the crowding in the matrices limits the rotational diffusion of the dsDNA also in the absence of a contacting object on top, as already derived for a rigid-rod macromolecule in concentrated solution 30,31 .…”

Section: Resultssupporting

confidence: 56%

“…By simply changing the number of times the tip is overwriting the same area during the nanolithography process, we can fine-tune the molecular density in that area 25 . The topographic height of such dsDNA matrices increases with the dsDNA packing and saturates to the length of dsDNA molecules (~15 nm) as they stand vertically in crowded monolayers 25,26,28 . The dsDNA sequences are designed such that they are cut at half height by a restriction enzyme (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Two-dimensional enzyme diffusion in laterally confined DNA monolayers

et al. 2011

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Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DnA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDnAs from the topmatrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top-and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.

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Section: Resultssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

et al. 2011

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“…8,9 AFM imaging has also been used to address the height of the self-assemblies primarily based on the scratch-and-height determination technique. 29,30 These types of experiments have been used to detect DNA hybridization by comparing various surface parameters, e.g., smoothness, 31 height, 32,33 and density. 34 We have also reported single-molecule imaging of a molecular-beacon DNA self-assembly to achieve target DNA detection through visualizaton.…”

Section: Afm Imaging Of E37 Molecular Aggregates and Surface Topologimentioning

confidence: 99%

A Pivot-Hinge-Style DNA Immobilization Method with Adaptable Surface Concentration Based on Oligodeoxynucleotide-Phosphorothioate Chemisorption on Gold Surfaces

et al. 2012

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The chemisorption of oligodeoxynucleotide phosphorothioate (s-oligo) is reported. A series of s-oligo DNAs was designed for use as capture probe DNA molecules. The s-oligo DNAs consist of the K-ras gene (5′-GGA GCT GGT GGC-3′) and a dodecamer deoxyriboadenosine, both of which lie on either side of an s-oligo DNA sequence. By primarily focusing on the capture probe DNA having five-successive s-oligo sequences, e37, the immobilization chemistry of e37 was examined; atomic force microscopy achieved the direct visualization of individual molecules on Au (111) substrates, while a series of surface analyses, including IR, ellipsometry, and microgravimetry, showed that the s-oligo functional groups played a pivotal role in the surface-adlayer through the gold-thiol interaction. Interestingly, the amount of immobilization showed a definite relationship with the number of s-oligo linkages introduced, which should be important to regulate the concentration of the capture probe DNA molecules on the surface. Some preliminary studies using ferrocene-modified complementary sequences indicated that electrochemical labeling and readouts were possible.

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“…Different detection techniques have been evaluated for DNA hybridization sensing such as optical [5,6], fluorescent [7,8], chemiluminescent [9,10], radiochemical [11], electrochemical [12 -14], acoustic wave [15], quartz crystal microbalance [16,17], atomic force microscopy [18,19] and surface plasmon resonance [20,21]. Electrochemical DNA sensors are of great interest since they provide the direct, rapid, simple and low cost detection of DNA while at the same time they allow for the microfabrication of DNA assays.…”

Section: Introductionmentioning

confidence: 99%

DNA Stabilization and Hybridization Detection on Porous Silicon Surface by EIS and Total Reflection FT‐IR Spectroscopy

Vamvakaki

Chaniotakis

2008

Electroanalysis

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Electrochemically etched porous silicon (PSi) is formed and employed as a substrate for the entrapment of oligonucleotides and the subsequent development of stable DNA biosensors. The controlled potential anodic etching of p-type silicon wafers is optimized in order to obtain a surface layer with pore diameters which are close to those of the adsorbed DNA helix. The stabilization and hybridization of DNA inside the PSi layer is confirmed using ATR-FTIR. Moreover hybridization is verified by the large and reproducible impedance changes at the interface layer. The developed PSi DNA sensor paves the way for the label-free detection of oligonucleotide sequences in DNA microarrays and microfabricated PSi field-effect sensors.

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Label‐Free Detection of DNA Hybridization at the Nanoscale: A Highly Sensitive and Selective Approach Using Atomic‐Force Microscopy

Cited by 61 publications

References 30 publications

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

A Pivot-Hinge-Style DNA Immobilization Method with Adaptable Surface Concentration Based on Oligodeoxynucleotide-Phosphorothioate Chemisorption on Gold Surfaces

DNA Stabilization and Hybridization Detection on Porous Silicon Surface by EIS and Total Reflection FT‐IR Spectroscopy

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