An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids.

Lorenzo Rovigatti,Emanuele Locatelli

doi:10.3390/polym10040447

Lorenzo Rovigatti, Emanuele Locatelli

Open Access

https://doi.org/10.3390/polym10040447

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Journal: Polymers	Publication Date: Apr 16, 2018
Citations: 3	License type: CC BY 4.0

Affiliation: Sapienza University of Rome, University of Vienna

Abstract

We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.

Highlights

The most prominent function of DNA is to store the genetic information of all living organisms.the main biophysical features that allow DNA to fulfil its role, namely, the extremely regular structure of its double-stranded form and the outstanding specificity of its single-stranded form, make it a great addition to the toolboxes of nanotechnology and materials science [1,2]
We find that Larm depends on the salt concentration only, as we obtain Larm = 9.70 nm for S = 0.05 M, Larm = 8.93 nm for S = 0.2 M, and Larm = 8.72 nm for S = 0.5 M, regardless of temperature and functionality
This was done by employing the hybrid theoretical/numerical approach introduced in [31], where numerical simulations were used to calculate the inputs required by the Wertheim thermodynamic perturbation theory (WTPT) to evaluate the system free energy

Summary

Introduction

The most prominent function of DNA is to store the genetic information of all living organisms.the main biophysical features that allow DNA to fulfil its role, namely, the extremely regular structure of its double-stranded form and the outstanding specificity of its single-stranded form, make it a great addition to the toolboxes of nanotechnology and materials science [1,2]. The usage of DNA in the latter field is extremely variegated, as it can be used as a link to connect nano- or micro-particles [3,4], and to synthesize all-DNA materials. In both cases, the resulting materials can be made either ordered or disordered [5,6,7,8]. An important factor that contributes to the complexity of DNA self-assembly is its polymeric nature [9,10,11,12,13,14]. DNA has been used to synthesize polymeric materials such as dendrimers [23,24] or hydrogels [25,26]

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Results

Conclusion