DNA imaged on a HOPG electrode surface by AFM with controlled potential.

TLDR: In this article, single-molecule AFM imaging of singlestranded and double-stranded DNA molecules self-assembled from solution onto a HOPG electrode surface is reported, where the interaction of DNA with the hydrophobic surface induced DNA aggregation, overlapping, intra- and intermolecular interactions.

About: This article is published in Bioelectrochemistry.The article was published on 2005-04-01 and is currently open access. It has received 39 citations till now. The article focuses on the topics: Electrode potential.

Figures

Fig. 4. (A, B, C) MAC Mode AFM topographical images in air of ssDNA prepare during 3 min to the electrode immersed into 1 Ag/ml ssDNA solution pH 7.0 0.1 M the topographic image C. (E) Three-dimensional representation of image C. (F) C

Fig. 5. (A, B) MAC Mode AFM topographical images in air of dsDNA prepared onto HOPG by applying a deposition potential of +300 mV (vs. AgQRE) during 3 min to the electrode immersed into 1 Ag/ml dsDNA solution pH 7.0 0.1 M phosphate buffer electrolyte. (C) Phase image recorded simultaneously with the topographic image B. (D) Cross-section profiles through white lines 1 and 2 in the image B.

Fig. 1. (A) MAC Mode AFM topographical image in air of ssDNA prepared onto H M phosphate buffer electrolyte. (B) Amplitude image (feedback error) and (C) pha images (1) marks an ssDNA aggregate and (2) marks an HOPG step.

Fig. 2. (A, C) MAC Mode AFM topographical images in air of dsDNA prepared on 0.1 M phosphate buffer electrolyte. (B, D) Phase images recorded simultaneously an dsDNA aggregate and (2) marks an HOPG step. (E) Three-dimensional represe the image C.

Fig. 3. (A) MAC Mode AFM topographical image in air of ssDNA prepared onto H M phosphate buffer electrolyte. (B) Amplitude image (feedback error) and (C) pha images, the arrows mark the trajectory traces of ssDNA fragments moved by the

Frequently asked questions

Q1. What are the contributions mentioned in the paper "Dna imaged on a hopg electrode surface by afm with controlled potential" ?

In this paper, a single-molecule image of DNA self-assembly on a HOPG electrode surface is reported. 

Q2. What are the future works mentioned in the paper "Dna imaged on a hopg electrode surface by afm with controlled potential" ?

The AFM images MAC Mode AFM offers the possibility of overcoming the difficulties in STM imaging of DNA related to the HOPG grain boundaries and imaging isolated DNA molecules attached to defect-free HOPG surface terraces. 

Q3. What is the effect of oxidation on the surface of the gold electrodes?

the oxidation of the gold electrodes occurs at potentials of approximately +0.8 V, [10,11] and the gold surface becomes covered with gold oxides. 

Q4. What is the effect of dsDNA on the surface of a HOPG?

The interaction of dsDNA with the HOPG surface can induce overlapping and superposition of the molecules, sticky-ended cohesion and conformation changes, leading to DNA–DNA interactions and to formation of alternative DNA structures [2,3,23]. 

Q5. What is the way to visualize a single-molecule?

Magnetic AC mode AFM (MAC Mode AFM) permits the visualization of the molecules weakly bound to the substrate material and it can be very helpful in the investigation of single-molecules loosely attached to the conducting surface of electrochemical transducers. 

Q6. What is the main challenge in the area of direct visualization of DNA molecules?

A major challenge in the area of direct visualization of DNA molecules is to extend the capability of AFM imaging to other conducting substrates required in electrochemical applications. 

Q7. What is the way to obtain high-resolution images of DNA?

Atomic force microscopy (AFM) has proved to be a powerful tool for obtaining high-resolution images of DNA in air and in solution. 

Q8. What is the mechanism of stabilization of dsDNA at the surface?

The stabilization of dsDNA at the surface may occur through interaction between the hydrophobic HOPG surface and several hydrophobic bases at the dsDNA ends. 

Q9. Why did the dsDNA have a higher value of heights than free a?

Due to stronger adsorption of the molecules on the HOPG substrate, the condensed molecules were less compressible by the AFM tip, which explains the higher values of DNA heights compared with free adsorption. 

Q10. What was the main disadvantage of the AFM tip during the experiments?

It was observed during the experiments that the AFM tip could easily move fragments of DNA molecules condensed by free adsorption. 

Q11. How many dsDNA molecules were applied to a HOPG surface?

The dsDNA had a large number of intramoleculard onto HOPG by applying a deposition potential of +300 mV (vs. AgQRE) phosphate buffer electrolyte. 

Q12. What software was used to visualize the images?

All images were visualized in three-dimensions using the Scanning Probe Image Processor, SPIP version 2.3011, Image Metrology ApS. Section analysis over DNA molecules and films was performed with PicoScan software version 6.0, Molecular Imaging. 

Q13. What is the effect of the AFM tip on the HOPG surface?

The friction caused by the AFM tip during scanning the surface is frequently superior to the adhesion to the surface and the AFM tip easily sweeps away and drags the DNA molecules adsorbed on the HOPG surface. 

Q14. What was the method used for AFM?

AFM was performed with a Pico SPM controlled by a MAC Mode (Magnetic AC Mode) module and interfaced with a PicoScan controller from Molecular Imaging, USA. 

Q15. What is the ssDNA structure on the HOPG surface?

The ssDNA molecules are stabilized on the HOPG surface by hydrophobic interactions between the hydrophobic aromatic rings of the bases and the hydrophobic carbon surface. 

Q16. What is the typical procedure used for imaging dry nucleic acid molecules in air?

The excess of DNA was gently cleaned with a jet of Milli Q water and the HOPG with adsorbed DNAwas then dried with nitrogen, which is a typical procedure used for imaging dry nucleic acid molecules in air [6]. 

Q17. What is the reason for the formation of dsDNA?

It is also very probable that many parts of the ssDNA molecules contain complementary bases leading to local hybridizationand the formation of portions of dsDNA. 

Q18. What are the different structures and conformations that DNA molecules can adopt at the electrode surface?

Different structures and conformations that DNA molecules can adopt at the electrode surface lead to different interactions with other molecules, such as modifications of the accessibility of different drugs to the DNA grooves and modifications in DNA hybridization efficiency. 

Q19. What is the effect of a positive potential on dsDNA?

During the controlled potential adsorption process, dsDNA adsorbs electrostatically at a given number of points along its length. 

Q20. What are the main differences in phase contrast between a HOPG and a molecule?

During scanning of the sample, the changes in phase contrast depend not only on topography changes, but also on the adhesion, elasticity and viscoelastic properties of the surface.