1
|
Xiong X, Han J, Chen Y, Li S, Xiao W, Shi Q. DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment. NANOTECHNOLOGY 2021; 32:055601. [PMID: 33179606 DOI: 10.1088/1361-6528/abb507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The evolution of single-stranded DNA (ssDNA) assembly on octadecylamine (ODA) modified highly oriented pyrolytic graphite (HOPG) surface by heating and ultrasonic treatment has been studied for the first time. We have observed that DNA on the ODA coated HOPG surface underwent dramatic morphological changes as a function of heating and ultrasonic treatment. Ordered DNA firstly changed to random aggregates by heating and then changed to three-dimensional (3D) networks by ultrasonic treatment. This finding points to previously unknown factors that impact graphite-DNA interaction and opens new opportunities to control the deposition of DNA onto graphitic substrates. In this way, we built a cost-effective method to produce large-scale 3D ssDNA networks. All of these studies pave the way to understand the properties of DNA-solid interface, design novel nanomaterials, and improve the sensitivity of DNA biosensors.
Collapse
Affiliation(s)
- Xiaolu Xiong
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Junfeng Han
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yu Chen
- Institute of High Energy Physics, CAS. 19B Yuquan Road, Shijingshan District, Beijing 100081, People's Republic of China
| | - Shanshan Li
- Department of Rheumatology, China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Wende Xiao
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Qingfan Shi
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| |
Collapse
|
2
|
Qian W, Doi K, Uehara S, Morita K, Kawano S. Theoretical study of the transpore velocity control of single-stranded DNA. Int J Mol Sci 2014; 15:13817-32. [PMID: 25116683 PMCID: PMC4159826 DOI: 10.3390/ijms150813817] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/17/2022] Open
Abstract
The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.
Collapse
Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoshi Uehara
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kaito Morita
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| |
Collapse
|
3
|
Doi K, Takeuchi H, Nii R, Akamatsu S, Kakizaki T, Kawano S. Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation. J Chem Phys 2014; 139:085102. [PMID: 24007039 DOI: 10.1063/1.4818595] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This study has investigated the formation patterns resulting from the self-assembly of deoxyribonucleic acid (DNA) on highly oriented pyrolytic graphite (HOPG), using both experimental and molecular dynamics approaches. Under optimized conditions based on pretreatment of HOPG surface and specific solution concentrations, DNA is found to self-assemble to form various patterned networks. The associated self-assembly mechanism is elucidated using coarse-grained molecular dynamics simulations and fractal dimension analysis. The results of this work demonstrate an effective technique allowing the formation of arrays of negatively charged biomacromolecules on negatively charged HOPG surfaces.
Collapse
Affiliation(s)
- Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | | | | | | | | |
Collapse
|
4
|
Doi K, Nishioka Y, Kawano S. Theoretical study of electric current in DNA base molecules trapped between nanogap electrodes. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.08.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|