Abstract
DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.
Similar content being viewed by others
Data availability
The data that support the findings of this study are available upon reasonable request from the authors.
References
M. Löwe, M. Kalacheva, A.J. Boersma, A. Kedrov, FEBS J. 287(23), 5039 (2020)
S.L. Speer, C.J. Stewart, L. Sapir, D. Harries, G.J. Pielak, Annu. Rev. Biophys. 51, 267 (2022)
G. Rivas, A.P. Minton, Biophys. Rev. 10(2), 241 (2018)
J. Kim, C. Jeon, H. Jeong, Y. Jung, B.Y. Ha, Soft Matter 11(10), 1877 (2015)
D. Miyoshi, N. Sugimoto, Biochimie 90(7), 1040 (2008)
G. Nettesheim, I. Nabti, C.U. Murade, G.R. Jaffe, S.J. King, G.T. Shubeita, Nat. Phys. 16(11), 1144 (2020)
T.P. Silverstein, K. Slade, J. Chem. Educ. 96(11), 2476 (2019)
P. Dey, A. Bhattacherjee, Soft Matter 15(9), 1960 (2019)
C.A. Mirkin, R.L. Letsinger, R.C. Mucic, J.J. Storhoff, Nature 382(1476–4687), 607 (1996)
S.Y. Park, J.S. Lee, D. Georganopoulou, C.A. Mirkin, G.C. Schatz, J. Phys. Chem. B 110, 12673 (2006)
R. Jin, G. Wu, Z. Li, C.A. Mirkin, G.C. Schatz, J. Am. Chem. Soc. 125(6), 1643 (2003). https://doi.org/10.1021/ja021096v. (PMID: 12568626)
J.M. Gibbs, S.J. Park, D.R. Anderson, K.J. Watson, C.A. Mirkin, S.T. Nguyen, J. Am. Chem. Soc. 127, 1170 (2005)
T.R. Prytkova, I. Eryazici, B. Stepp, S.B. Nguyen, G.C. Schatz, J. Phys. Chem. B 114, 2627 (2010)
B.R. Stepp, J.M. Gibbs-Davis, D.L.F. Koh, S.T. Nguyen, J. Am. Chem. Soc. 130, 9628 (2008)
S.Y. Park, D. Stroud, Phys. Rev. B 67, 212202 (2003)
H. Long, A. Kudlay, G.C. Schatz, J. Phys. Chem. B 110, 2918 (2006)
S.B. Zimmerman, L.D. Murphy, FEBS Lett. 390(3), 245 (1996)
S. Hormeno, B. Ibarra, J.M. Valpuesta, J.L. Carrascosa, J. Ricardo Arias-Gonzalez Biopolymers 97(4) 2012
I. Khimji, J. Shin, J. Liu, Chem. Commun. 49(13), 1306 (2013). https://doi.org/10.1039/C2CC38627E
A.B. Menhaj, B.D. Smith, J. Liu, Chem. Sci. 3(11), 3216 (2012)
S. Dutta, in Gold and Silver Nanoparticles (Elsevier), pp. 411–434 (2023)
A.K.R. Lytton-Jean, J.M. Gibbs-Davis, H. Long, G.C. Schatz, C.A. Mirkin, S.T. Nguyen, Adv. Mater. 21(6), 706 (2009). https://doi.org/10.1002/adma.200801724
E. Grueso, R.M. Giráldez-Pérez, P. Perez-Tejeda, E. Roldán, R. Prado-Gotor, Phys. Chem. Chem. Phys. 21, 11019 (2019). https://doi.org/10.1039/C9CP01162E
C. Lu, S. Zhou, F. Gao, J. Lin, J. Liu, J. Zheng, TrAC Trend Anal Chem 148 116533 (2022)
O.S. Lee, T.R. Prytkova, G.C. Schatz, J. Phys. Chem. Lett. 1(12), 1781 (2010). https://doi.org/10.1021/jz100435a. (PMID: 20606716)
H. Wang, R. Yang, L. Yang, W. Tan, ACS Nano 3(9), 2451 (2009)
K. Saha, S.S. Agasti, C. Kim, X. Li, V.M. Rotello, Chem. Rev. 112(5), 2739 (2012). https://doi.org/10.1021/cr2001178. (PMID: 22295941)
H. Karimata, S.i. Nakano, T. Ohmichi, J. Kawakami, N. Sugimoto, Nucleic Acids Symposium Series, 48(1), 107 (2004)
M. Peyrard, A.R. Bishop, Phys. Rev. Lett. 62(23), 2755 (1989). https://doi.org/10.1103/PhysRevLett.62.2755
T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E 47(1), R44 (1993). https://doi.org/10.1103/PhysRevE.47.R44
S. Cocco, R. Monasson, Phys. Rev. Lett. 83(24), 5178 (1999). https://doi.org/10.1103/PhysRevLett.83.5178
N. Singh, Y. Singh, Eur. Phys. J. E 17(1), 7 (2005). https://doi.org/10.1140/epje/i2004-10100-7
M. Zoli, Phys. Chem. Chem. Phys. 22, 26901 (2020). https://doi.org/10.1039/D0CP04046K
M. Zoli, J. Theor. Biol. 354, 95 (2014). https://doi.org/10.1016/j.jtbi.2014.03.031
Y.l. Zhang, W.M. Zheng, J.X. Liu, Y.Z. Chen, Phys. Rev. E 56(6), 7100 (1997). https://doi.org/10.1103/PhysRevE.56.7100
T.S. van Erp, S. Cuesta-Lopez, M. Peyrard, Eur. Phys. J. E 20(4), 421 (2006). https://doi.org/10.1140/epje/i2006-10032-2
A. Singh, N. Singh, Phys. Rev. E 92, 032703 (2015). https://doi.org/10.1103/PhysRevE.92.032703
M. Zoli, Phys. Chem. Chem. Phys. 21, 12566 (2019). https://doi.org/10.1039/C9CP01098J
M. Zoli, J. Chem. Phys. 154(19), 194102 (2021). https://doi.org/10.1063/5.0046891
A. Singh, A. Maity, N. Singh, Entropy 24(11) (2022). https://doi.org/10.3390/e24111587. https://www.mdpi.com/1099-4300/24/11/1587
A. Campa, A. Giansanti, Phys. Rev. E 58(3), 3585 (1998). https://doi.org/10.1103/PhysRevE.58.3585
N. Singh, Y. Singh, Phys. Rev. E 64(4), 042901 (2001). https://doi.org/10.1103/PhysRevE.64.042901
A. Campa, A. Giansanti, J. Biol. Phys. 24, 14 (1999)
D. Mohanta, D. Giri, S. Kumar, Phys.: Stat. Mech. Appl. 562, 125379 (2021). https://doi.org/10.1016/j.physa.2020.125379
Acknowledgements
We acknowledge the financial support from the Science and Engineering Research Board (SERB), New Delhi.
Author information
Authors and Affiliations
Contributions
All authors contributed equally to the paper.
Corresponding author
Ethics declarations
Conflicts of interest
There are no conflicts to declare.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Mathur, N., Singh, N. Melting of dsDNA attached with AuNPs. Eur. Phys. J. E 46, 58 (2023). https://doi.org/10.1140/epje/s10189-023-00318-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1140/epje/s10189-023-00318-2