Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases

Biosensors (Basel). 2021 Feb 24;11(3):59. doi: 10.3390/bios11030059.


Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases' sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green's function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.

Keywords: 2D material; DFT; DNA/RNA nucleobases; biosensor; germanene; silicene.

MeSH terms

  • Adenine / chemistry
  • Adsorption
  • Biosensing Techniques*
  • Computer Simulation*
  • Cytosine / chemistry
  • DNA / chemistry*
  • Germanium / chemistry*
  • Guanine / chemistry
  • RNA / chemistry*
  • Silicon / chemistry*
  • Thymine / chemistry
  • Uracil / chemistry


  • Germanium
  • Uracil
  • Guanine
  • RNA
  • Cytosine
  • DNA
  • Adenine
  • Thymine
  • Silicon