Optimization of porous silicon conditions for DNA-based biosensing via reflectometric interference spectroscopy
Creators: name: Shafiekhani, Azizollah
name: Rahimi, Fereshteh
name: Somayeh Fardindoost
name: Ansari-Pour, Naser
name: Sepehri, Fatemeh
name: Makiyan, Farideh
name: Rezayan, Ali Hossein
Publisher: name: figshare
Year: 2020
Subjects: subject: 20301 Acoustics and Acoustical Devices; Waves
subject: FOS: Physical sciences
subject: FOS: Physical sciences
subject: Applied Physics
subject: Atomic Physics
subject: 20201 Atomic and Molecular Physics
subject: 20299 Atomic, Molecular, Nuclear, Particle and Plasma Physics not elsewhere classified
subject: 29901 Biological Physics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Computational Physics
subject: 20401 Condensed Matter Characterisation Technique Development
subject: 20402 Condensed Matter Imaging
subject: 20403 Condensed Matter Modelling and Density Functional Theory
subject: Condensed Matter Physics
subject: 20499 Condensed Matter Physics not elsewhere classified
subject: 20601 Degenerate Quantum Gases and Atom Optics
subject: 20404 Electronic and Magnetic Properties of Condensed Matter; Superconductivity
subject: 20302 Electrostatics and Electrodynamics
subject: Entropy
subject: General Relativity
subject: 29903 Medical Physics
subject: 20503 Nonlinear Optics and Spectroscopy
subject: 20202 Nuclear Physics
subject: 20599 Optical Physics not elsewhere classified
subject: 20203 Particle Physics
subject: 20504 Photonics, Optoelectronics and Optical Communications
subject: 29999 Physical Sciences not elsewhere classified
subject: 20405 Soft Condensed Matter
subject: Special Relativity
subject: 29904 Synchrotrons; Accelerators; Instruments and Techniques
subject: Thermodynamics
subject: 20304 Thermodynamics and Statistical Physics
subject: FOS: Mechanical engineering
subject: FOS: Mechanical engineering

description: Objective: Substantial effort has been put into designing DNA-based biosensors, which are commonly used to detect presence of known sequences including the quantification of gene expression. Porous silicon (PSi), as a nanostructured base, has been commonly used in the fabrication of optimally transducing biosensors. Given that the function of any PSi-based biosensor is highly dependent on its nanomorphology, we systematically optimized a PSi biosensor based on reflectometric interference spectroscopy (RIS) detecting the high penetrance breast cancer susceptibility gene, BRCA1. Materials and Methods: In this experimental study, PSi pore sizes on the PSi surface were controlled for optimum filling with DNA oligonucleotides and surface roughness was optimized for obtaining higher resolution RIS patterns. In addition, the influence of two different organic electrolyte mixtures on the formation and morphology of the pores, based on various current densities and etching times on doped p-type silicon, were examined. Moreover, we introduce two cleaning processes which can efficiently remove the undesirable outer parasitic layer created during PSi formation. Results of all the optimization steps were observed by field emission scanning electron microscopy (FE-SEM). Results: DNA sensing reached its optimum when PSi was formed in a two-step process in the ethanol electrolyte accompanied by removal of the parasitic layer in NaOH solution. These optimal conditions, which result in pore sizes of approximately 20 nm as well as a low surface roughness, provide a considerable RIS shift upon complementary sequence hybridization, suggesting efficient detectability. Conclusion: We demonstrate that the optimal conditions identified here makes PSi an attractive solid-phase DNA-based biosensing method and may be used to not only detect full complementary DNA sequences, but it may also be used for detecting point mutations such as single nucleotide substitutions and indels