Thermodynamic Analysis of Short Single-Stranded DNA (ssDNA) for Advancing DNA-Based Biosensor-biocatalyst Development

Subject Areas :

Mohammad Reza Bozorgmehr ¹ , Maryam Ghanbari-Ghanbarlo ² , Ali Morsali ³

1 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
2 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
3 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

Received: 2023-10-30 Accepted : 2023-11-11 Published : 2023-11-22

Keywords: catalyst, Biosensor, molecular dynamics, nanodevice,

Abstract :

This study aimed to enhance our understanding of short single-stranded DNA (ssDNA) to facilitate the development of novel DNA-based biosensors-biocatalyst. A 10-base ssDNA model was constructed based on the 130-145 codon sequence of the p53 gene, a key tumor suppressor gene. By employing molecular dynamics (MD) simulations, we delved into the thermodynamic properties and equilibrium states of the ssDNA system, unveiling crucial insights into its behavior. Various macroscopic observables were investigated during the MD simulations, including temperature, energy distributions, and the root mean square deviation (RMSD) of the ssDNA's nucleic acid backbone. The structural model of the ssDNA was meticulously constructed using the AMBER program, ensuring accuracy and reliability. Subsequently, atomistic MD simulations were conducted in three different ensembles utilizing the Gromacs program. The microcanonical, canonical, and isobaric-isothermal ensembles were employed to compare and contrast the equilibrium characteristics of the ssDNA in aqueous solutions. The choice of ensemble played a decisive role in capturing the dynamic equilibrium and conformational behavior of the ssDNA system. The distribution of energy, encompassing both kinetic and potential energy, provided valuable insights into the establishment of thermodynamic equilibrium. Fluctuations in temperature and total energy underscored the finite nature of the system, while the average kinetic energy confirmed the attainment of physiological temperature. Furthermore, the RMSD analysis shed light on the conformational stability of the ssDNA, with both NVT and NPT ensembles exhibiting stable conformational states under their respective thermodynamic conditions. These findings emphasize the intricate interplay between thermodynamic conditions and the conformational flexibility of ssDNA.

References:

[1] C. M. Niemeyer, Angew. Chem. Int. 40 (2001) 4128.
[2] N. L. Rosi, C. A. Mirkin, Chem Rev. 105 (2005) 1547.
[3] V. V. Demidov, M. D. Frank-Kamenetskii, Trends Biochem Sci. 29 (2004) 62.
[4] B. Samori, G. Zuccheri, Angew. Chem. Int. 44 (2005) 1166
[5] I. Yeh, G. Hummer, Proc. Nat. Acad. Sci. 10 (2004) 12177.
[6] D. Roxbury, J. Mittal, A. Jagota, Nano Lett. 12 (2012) 1464.
[7] S. Gowtham, RH. Scheicher, R. Pandey, SP. Karna, R. Ahuja, Nanotech. 19 (2008) 125701.
[8] WL. Delano, San. Carl. 1 (2004) 68.
[9] H. Berendsen, D. Spoel, R. Drunen, Comp. Phys. Comm. 91 (1995) 43.
[10] RM Betz, RC. Walker, J. Comp. Chem. 36 (2023) 79.
[11] P. Mark, L. Nilsson, J. Phys. Chem. 105 (2001) 9954.
[12] Y. Fanbfei, F. Fan, C. Zhu, Q. Li, View 2 (2021) 202.