نانوحسگرهای زیستی مولکولی پایه گرافین برای تشخیص مولفه‌های مولکول DNA

نوع مقاله : مقاله پژوهشی

نویسندگان

گروه فیزیک، دانشکده مهندسی انرژی و فیزیک، دانشگاه صنعتی امیرکبیر، تهران، ایران

چکیده

در این پژوهش، ویژگی های زیست حسگری گرافین های مولکولی از جمله کرونین، سیرکوم-کرونین و سیرکوم سیرکوم-کرونین از نظر اندازه، ساختار مولکولی و ویژگی‌های شیمیایی مورد بررسی قرار گرفته‌است. شبیه‌سازی ها با نرم افزار گوسین به روش نظریه‌ی تابعی چگالی تحت تابعی و توابع پایه ی B3LYP/6-31G(d,p) انجام شده است. نتایج محاسبات نشان می دهد که از ساختارهای مورد بررسی، دو ساختارهای کرونین و سیرکوم-کرونین به لحاظ ویژگی‌های فیزیکی همچون انرژی بستگی، و ویژگی‌های شیمیایی همچون سختی شیمیایی بالا، برای توالی یابی مولکول زیستی DNA پیشنهاد می شود و می‌توان از این ساختارها حسگرهایی ساخت که قابلیت تشخیص هر چهار نوکلئوبازهای مولکول DNA را داشته باشند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Graphene based molecular bio-nanosensors to identify the components of DNA

نویسندگان [English]

  • Mohammad Ajmal Khishki
  • Mohammad Qasemnahznd
  • Farah Marsusi
Amirkabir University of Technology
چکیده [English]

Trying to discover the different characteristics of biosensor systems is the most important part of research development in various fields, especially in the field of biomolecular science. In this research, the biosensor properties of molecular graphene (Coronene, Circumcoronene and Circumcircumcoronene) have been investigated for their molecular size and chemical properties. Among the three mentioned structures, two of them (coronene and Circumcoronene) have been selected based on their properties for sequencing DNA molecules. Calculations were performed with the B3LYP hybrid function and 6-31G(d,p) basis set. After performing the necessary simulations and calculations, the results show that these graphene molecular structures can be used as biosensors.

کلیدواژه‌ها [English]

  • Biosenso
  • Coronene
  • DNA
  • Density Functional Theory
  • Binding Energy
[1] M. L. Metzker, “Emerging technologies in DNA sequencing,” Genome research, 15, 1767-1776, 2005.
[2] K. K. Murray, “DNA sequencing by mass spectrometry,” Journal of Mass Spectrometry, 31, 1203-1215, 1996.
[3] L. Sastre, “New DNA sequencing technologies open a promising era for cancer research and treatment,” Clinical and Translational Oncology, 13, 301-306, 2011.
[4] M. Xu, D. Fujita, N. Hanagata, “Perspectives and challenges of emerging single‐molecule DNA sequencing technologies,” Small, 5, 2638-2649, 2009.
[5] M. Morey, A. Fernandez-Marmiesse, D. Castineiras, J. M. Fraga, M. L. Couce, J. A. Cocho, “A glimpse into past, present, and future DNA sequencing,” Molecular genetics and metabolism, 110, 3-24, 2013.
[6] K. Neveling, R.W. Collin, C. Gilissen, R.A. van Huet, L. Visser, M.P. Kwint, S.J. Gijsen, M.N. Zonneveld, N. Wieskamp, J. de Ligt, A.M. Siemiatkowska, “Next‐generation genetic testing for retinitis pigmentosa,” Human mutation, 33, 963-972, 2012.
[7] D. Pushkarev, N. F. Neff, S. R. Quake, “Single-molecule sequencing of an individual human genome,” Nature biotechnology, 27, 847-852, 2009.
[8] P. Kapranov, L. Chen, D. Dederich, B. Dong, J. He, K.E. Steinmann, A.R. Moore, J.F. Thompson, P.M. Milos, W. Xiao, “Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing,” Human gene therapy, 23, 46-55, 2011.
[9] F. Marsusi, M. Qasemnazhand, “Opto-Electronic Properties of Novel Structures: Sila-Fulleranes,” 18th International Conference on Materials and Structural Integrity; Vancouver, Canada, 2016.
[10] K.S. Novoselov, V.I. Fal, L. Colombo, P.R. Gellert, M.G. Schwab, K. Kim, “A roadmap for graphene,” nature, 490, 192-200, 2012.
[11] M. Qasemnazhand, F. Khoeini, and F. Marsusi, “Photoluminescence in a Glucose-coated Sila-fullerane and Its Nanomedicine Applications,” 2021.
[12] Y.H. Yun, E. Eteshola, A. Bhattacharya, Z. Dong, J.S. Shim, L. Conforti, D. Kim, M.J. Schulz, C.H. Ahn, N. Watts, “Tiny medicine: nanomaterial-based biosensors,” Sensors, 9, 9275-9299, 2009.
[13] M. Qasemnazhand, F. Khoeini, “Theoretical study of structural and electronic properties of sila-dodecahedrane as an optical-chemical sensor by density functional theory method,” Nanoscale, 8, 4, 32-41, 2021.
[14] A. Srivastava, I. Kumar, S. Anusiewicz, W. Velickovic, and N. Misra. “Atomic clusters: theory & experiments,” Frontiers in Chemistry, 9, 2021.
[15] M. N. Velasco-Garcia, “Optical biosensors for probing at the cellular level: a review of recent progress and future prospects,” Seminars in cell & developmental biology, 20, 27–33, 2009.
[16] M. Qasemnazhand, F. Khoeini, and F. Marsusi, “Optical response of sila-fulleranes in interaction with glycoproteins for environmental monitoring,” Frontiers in Physics, 340, 2021.
[17] M. Sharifi, M., H. Pashaei Adl, H. Tajalli, and A. Bahrampour, “Design of surface plasmon resonance biosensor with one dimensional photonic crystal for detection of cancer,” Iranian Journal of Physics Research, 16, 133-138, 2019.
[18] M. Qasemnazhand, F. Khoeini, and M. Badakhshan, “Investigation of electron transport properties in Fullerene and Fullerane nanocages,” Iranian Journal of Physics Research, 21, 441-448, 2021.
[19] S. M. Monavari, F. Marsusi, N. Memarian, M. Qasemnazhand, “Biosensors based on carbon nanotubes and carbon
nano-rings: A DFT study,” Research Square, 2022.
 
[20] E. V. Basiuk, M. Martínez-Herrera, E. Álvarez-Zauco, L. V. Henao-Holguín, I. Puente-Lee, V. A. Basiuk, “Noncovalent functionalization of graphene with a Ni (II) tetraaza,” Dalton Transactions, 43 7413-7428, 2014.
[21] M. Qasemnazhand, F. Khoeini, and F. Marsusi, “Fullerene, fullerane and the fulleryne: A comparative thermodynamic study for a new member of the carbon cage family,” Results in Physics, 106066, 2022.
[22] P.V. Medeiros, G.K. Gueorguiev, S. Stafström, “Benzene coronene and circumcoronene adsorbed on gold, and a gold cluster adsorbed on graphene: Structural and electronic properties,” Physical Review B, 85, 205423-205429, 2012.
[23] M. Qasemnazhand, F. Marsusi, “Theoretical Study of Opto-Electronic properties of Silafulleranes Using Density Functional Theory,” journal of research on many body systems, 7, 77-87, 2017.
[24] M. Qasemnazhand, F. Khoeini, F. Marsusi, “Predicting the new carbon nanocages, fullerynes: a DFT study,” Scientific reports 11, 1, 1-14, 2021.
[25] M. Qasemnazhand, F. Khoeini, F. Marsusi, “Fulleryne, a new member of the carbon cages family,” arXiv preprint arXiv, 2003, 09835, 2020.
[26] F. Marsusi, M. Qasemnazhand, “Sila-fulleranes: promising chemically active fullerene analogs,” Nanotechnology, 27, 275704-275714, 2016.
[27] M. Qasemnazhand, F. Khoeini, S. Shekarforush, “Electronic transport properties in stability phase of cumulene/B7/cumulene molecular bridge by Density functional theory and tight binding method,” New Journal of Chemistry, 43, 42, 16515-16523, 2019.
[28] A. K. Srivastava, I. Anusiewicz, S. Velickovic, W. M. Sun, N. Misra. “Atomic Clusters: Theory & Experiments,” Frontiers in Chemistry, 9, 2021.
[29] G. Sivaraman, M. Fyta, “Chemically modified diamondoids as biosensors for DNA,” Nanoscale, 6, 4225-4232, 2014.