Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse-grained molecular simulation study

A Prhashanna and A Jayaraman, JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 57, 1196-1208 (2019).

DOI: 10.1002/polb.24780

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T-m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse-grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8-mer ONAs (e.g., DNA) and neutral and flexible 8-mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G-C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G-C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. (c) 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 1196-1208

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