Temperature-Controlled Assembly of High Ordered/Disordered Dodecylamine Layers on HOPG: Consequences for DNA Patterning

Adamčík, Jozef; Tobenas, Susana; Santo, Giovanni Di; Klinov, Dmitry V.; Dietler, Giovanni

doi:10.1021/la803308j

Cited by 28 publications

(42 citation statements)

References 34 publications

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“…The AFM results of this study indicated that circular DNA tends to form hexagonal patterns on bare HOPG surfaces. It should be pointed out that the DNA patterns obtained in this study are similar to those formed on the alkylamines modified HOPG (Severin et al , ; Adamcik et al , ; Dubrovin et al , ). However, the interactions of DNA and bare HOPG surface have not been well addressed in these studies.…”

Section: Resultssupporting

confidence: 83%

“…Therefore, direct adsorption of DNA onto HOPG surfaces seemed impossible from this point of view. An immobilization method have been developed in the recent studies, in which DNA molecules can be immobilized on alkylamines‐modified HOPG surfaces (Severin et al , ; Adamcik et al , , ; Klinov et al , ; Dubrovin et al , ). In the meantime, Oliveira‐Brett and Lin have demonstrated that DNA molecules can be freely adsorbed on HOPG surface (Brett and Chiorcea, ; Jiang and Lin, ; Chiorcea‐Paquim et al , ).…”

Section: Resultsmentioning

confidence: 99%

“…Atomic force microscopy (AFM) is a powerful tool for observation of DNA molecules and protein immobilized on a solid substrate since it has been invented (Rippe et al , '; Pope et al , '; Liu et al , , ). Recently, DNA structures formed on the alkylamines and a graphite modifier‐modified HOPG surface have been observed by AFM (Severin et al , ; Adamcik et al , , ; Klinov et al , ; Dubrovin et al , ).…”

Section: Introductionmentioning

confidence: 99%

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Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Zhao

Liu

et al. 2011

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Adsorption of circular DNA onto bare highly oriented pyrolytic graphite (HOPG) surfaces by the addition of Mg²⁺, Ni²⁺, and Cu²⁺ has been investigated by atomic force microscopy (AFM). AFM results revealed that the topography and height of DNA on HOPG surface by the addition of different metal ions are quite different. After the addition of Mg²⁺ for incubation, DNA molecules tend to form many loops on HOPG surfaces, which are derived from the crossover of intramolecular and intermolecular chains. After the addition of Ni²⁺, DNA molecules can form network on HOPG surfaces, and the density of DNA network was significantly increased with increasing DNA concentration. Consequently, dense DNA network can be obtained by using relatively low concentration of DNA and Ni²⁺. As for the addition of Cu²⁺, angular DNA loops composed of flat chains were observed. The observed flat DNA chains with an average height of 0.52 nm can be ascribed to Cu²⁺ insert into the site between bases and phosphate group of DNA inducing denaturation of DNA molecules. This study is very helpful for understanding the interactions of metal ions and DNA molecules, and for constructing various DNA structures on the carbonaceous surfaces.

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Section: Resultssupporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Zhao

Liu

et al. 2011

Scanning

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“…Recently, a simplified procedure for modifying HOPG was proposed [30]. The authors used a graphite modifier composed of a hydrocarbon–peptide pair terminating with an amine group: (CH 2 ) n -(NCRH 2 CO) m -NH 2 [30,75,76]. The application of this graphite modifier to the hydrophobic HOPG surface results in the formation of a thin (0.7 nm) monolayer of positively charged polymer on the graphite surface, which promotes DNA binding.…”

Section: Experimental Designmentioning

confidence: 99%

Imaging of nucleic acids with atomic force microscopy

Lyubchenko

Shlyakhtenko

Ando

2011

Methods

145

135

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Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM.

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“…For better observation of λ-DNA molecules and its stable arrangement on the HOPG substrate, here we used an amphilphilic dodecylamine (DA) layer which has two functional groups at its both ends; an alkyl chain for graphite and an amine group for DNA affinity. 13 A set of data illustrating the release of λ-DNA molecule from the DA-HOPG was recorded in Fig. 4.…”

Section: Resultsmentioning

confidence: 99%

Controlling a Single DNA Molecule in an Electric Field by Means of In Situ Atomic Force Microscopy

Jeong

Dietler

2012

J. Electrochem. Soc.

Self Cite

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DNA is the bio-polymer containing the genetic information needed for the development and functioning for all living organisms. It has a polymeric structure consisting of units called nucleotides, each consisting of a non-polar, hydrophobic interior (the base pairs) and polar, hydrophilic exterior which is negatively charged due to the phosphate groups along the backbone of the DNA. Its heterogeneous properties permit DNA molecule to interact with other molecules and different types of substrates at the same time.It is important to understand the DNA morphology on flat surface that serves as a template for DNA based sensors and microarray applications, particularly under an electric field. Taken together, the ability to deposit a single DNA molecule on the electrode is essential to increase its specificity. In our study, we optimize the conditions in order to control a single DNA molecule adsorbing and desorbing to/from the electrode. Atomic force microscopy (AFM) is a powerful single molecule imaging technique for biomolecules which enables exploration of the detailed topography at molecular level. Moreover, coupled with the ability to characterize living bio-materials under physiological conditions, the AFM data provide information for statistical analysis of the biomolecule's conformation from AFM images. In recent studies, an electrochemical cell combined with an AFM (EC-AFM) has been used to visualize the surface conformation of DNA with nano-meter size resolution under electric field in-situ (AFM imaging in solution during electrochemical reaction).1,2 This technical development allows us to visualize the dynamic movement of DNA molecule in an electric field without perturbing its bio-functionality. There are many reports regarding DNA network film adsorption on a highly oriented pyrolytic graphite (HOPG) electrode under controlled potential with an ex-situ AFM.3-5 However, until now there is no report of in-situ single DNA molecule immobilization or release by applying potential through EC-AFM.In our study, we optimize the conditions for immobilization/release of a single DNA molecule to/from a HOPG electrode in an electric field. The electrode, by the applied potential, enables the negatively charged phosphate backbone group of DNA molecule to be attracted toward electrode, or repel DNA molecule from negatively charged electrode by electrostatic interaction. Then the morphological changes of DNA molecules on the electrode depending on the applied potential were investigated using in-situ EC-AFM. Commonly, it is not easy to obtain a stable conformation of DNA molecules in aqueous condition because of the thermal agitation that allows DNA molecules to move in electrolyte solution. However the electrostatic interaction force between molecules and electrode was reinforced during the DNA immobilization process by an applied potential, yielding the increased stability. [3][4][5] It is critical to understand the morphological and electrochemical properties of DNA molecules in order to construct the DNA based ele...

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Temperature-Controlled Assembly of High Ordered/Disordered Dodecylamine Layers on HOPG: Consequences for DNA Patterning

Cited by 28 publications

References 34 publications

Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Imaging of nucleic acids with atomic force microscopy

Controlling a Single DNA Molecule in an Electric Field by Means of In Situ Atomic Force Microscopy

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Temperature-Controlled Assembly of High Ordered/Disordered Dodecylamine Layers on HOPG: Consequences for DNA Patterning

Cited by 28 publications

References 34 publications

Influence of Mg2+, Ni2+, and Cu2+ on DNA assembly on HOPG surfaces: atomic force microscopy study

Influence of Mg2+, Ni2+, and Cu2+ on DNA assembly on HOPG surfaces: atomic force microscopy study

Imaging of nucleic acids with atomic force microscopy

Controlling a Single DNA Molecule in an Electric Field by Means of In Situ Atomic Force Microscopy

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Product

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Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study

Influence of Mg²⁺, Ni²⁺, and Cu²⁺ on DNA assembly on HOPG surfaces: atomic force microscopy study