Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions
Source abstract
Abstract
Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Advanced biosensing and bioanalysis techniques · Graphene and Nanomaterials Applications · Graphene research and applications
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
Computer Science Department and Engineering, Faculty of Automatic Control and Computers, University Politehnica of Bucharest, 060042 Bucharest, Romania
Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41121 Modena, Italy
Funding
Ministry of Research and Innovation, Operational Program Competitiveness Axis 1 - Section E, Program co-financed from European Regional Development Fund
References (33)
Show source-provided references
1. Modelling of graphene functionalization10.1039/C5CP03599F ↗
2. The rise of graphene10.1038/nmat1849 ↗
3. Graphene: The new two-dimensional nanomaterial10.1002/anie.200901678 ↗
4. Graphene-based materials: Synthesis, characterization, properties, and applications10.1002/smll.201002009 ↗
5. Wafer scale fabrication of graphene microelectrode arrays for the detection of DNA hybridization10.1016/j.mee.2017.12.015 ↗
6. Suvarnaphaet, P., and Pechprasarn, S. (2017). Graphene-Based Materials for Biosensors: A Review. Sensors, 17.10.3390/s17102161 ↗
7. The Worldwide Graphene Flake Production10.1002/adma.201803784 ↗
8. Perspective of graphene-based electronic devices: Graphene synthesis and diverse applications10.1063/1.5054823 ↗
9. Molecular dynamics simulations of the adsorption of DNA segments onto graphene oxide10.1088/0022-3727/47/50/505401 ↗
10. Exploration on the mechanism of DNA adsorption on graphene and graphene oxide via molecular simulations10.1088/0022-3727/48/27/275402 ↗
11. Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide10.1002/chem.201701733 ↗
12. Becheru, D., Vlăsceanu, G., Banciu, A., Vasile, E., Ioniţă, M., and Burns, J. (2018). Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength. Int. J. Mol., 19.10.3390/ijms19103230 ↗
13. Effect of pH and Salt on Adsorption of Double-Stranded DNA on Graphene Oxide10.1166/jnn.2015.11217 ↗
14. Structure of a B-DNA dodecamer: Conformation and dynamics10.1073/pnas.78.4.2179 ↗
15. Long-timescale dynamics of the Drew-Dickerson dodecamer10.1093/nar/gkw264 ↗
16. The Amber biomolecular simulation programs10.1002/jcc.20290 ↗
17. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers10.1016/j.softx.2015.06.001 ↗
18. VMD: Visual molecular dynamics10.1016/0263-7855(96)00018-5 ↗
19. Hydrogen Bond Networks in Graphene Oxide Composite Paper: Structure and Mechanical Properties10.1021/nn901934u ↗
20. Tunning of graphene oxide composition by multiple oxidations for carbon dioxide storage and capture of toxic metals
21. (2020, March 05). Aminated Graphene Amino-PEG covalently linked. Available online: https://www.acsmaterial.com/aminated-graphene-amino-peg-covalently-linked.html.
22. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations10.1021/ja00051a040 ↗
23. Parmbsc1: A refined force field for DNA simulations10.1038/nmeth.3658 ↗
24. An improved DNA force field for ssDNA interactions with gold nanoparticles10.1063/1.4882657 ↗
25. Gowers, R.J., Linke, M., Barnoud, J., Reddy, T.J.E., Melo, M.N., Seyler, S.L., Domański, J., Dotson, D.L., Buchoux, S., and Kenney, I.M. (2016, January 11–17). MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Proceedings of the 15th Python in Science Conference, Austin, TX, USA.10.25080/Majora-629e541a-00e ↗
26. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations10.1002/jcc.21787 ↗
27. Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment10.1021/ct501170h ↗
28. Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: A molecular dynamics study10.1039/c2cp23540d ↗
29. Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions10.1016/S0006-3495(01)75770-0 ↗
30. On the T-shaped structures of the benzene dimer10.1016/j.cplett.2007.02.034 ↗
31. Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature10.1007/s11224-017-0954-7 ↗
32. New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions10.1039/C7CP08185E ↗
33. ReaxFF: A Reactive Force Field for Hydrocarbons10.1021/jp004368u ↗