Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations

Bullard, Kaitlin; Okyere, Deborah; Foster, Shelbi J.; Sadoon, Asmaa A.; Li, Jiali; Chen, Jingyi; Wang, Yong

doi:10.3390/bios15050272

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Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations

by

Kaitlin Bullard

¹,

Deborah Okyere

^2,3,

Shelbi J. Foster

¹,

Asmaa A. Sadoon

^1,2,4,

Jiali Li

^1,2,5,

Jingyi Chen

^2,3

and

Yong Wang

^1,2,5,*

¹

Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA

²

Materials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USA

³

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA

⁴

Department of Physics, University of Thi-Qar, Nassiriya 64001, Iraq

⁵

Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA

^*

Author to whom correspondence should be addressed.

Biosensors 2025, 15(5), 272; https://doi.org/10.3390/bios15050272 (registering DOI)

Submission received: 26 March 2025 / Revised: 20 April 2025 / Accepted: 23 April 2025 / Published: 26 April 2025

(This article belongs to the Special Issue DNA Molecular Engineering-Based Biosensors)

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Abstract

Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg²⁺ ions at different concentrations. The simulations show that Mg²⁺ ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules.

Keywords: DNA bows; melting curve; FRET; NAMD; VMD

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MDPI and ACS Style

Bullard, K.; Okyere, D.; Foster, S.J.; Sadoon, A.A.; Li, J.; Chen, J.; Wang, Y. Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations. Biosensors 2025, 15, 272. https://doi.org/10.3390/bios15050272

AMA Style

Bullard K, Okyere D, Foster SJ, Sadoon AA, Li J, Chen J, Wang Y. Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations. Biosensors. 2025; 15(5):272. https://doi.org/10.3390/bios15050272

Chicago/Turabian Style

Bullard, Kaitlin, Deborah Okyere, Shelbi J. Foster, Asmaa A. Sadoon, Jiali Li, Jingyi Chen, and Yong Wang. 2025. "Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations" Biosensors 15, no. 5: 272. https://doi.org/10.3390/bios15050272

APA Style

Bullard, K., Okyere, D., Foster, S. J., Sadoon, A. A., Li, J., Chen, J., & Wang, Y. (2025). Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations. Biosensors, 15(5), 272. https://doi.org/10.3390/bios15050272

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Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations

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