Comparing ion distributions around RNA and DNA helical and loop-loop motifs
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Comparing ion distributions around RNA and DNA helical and loop-loop motifs Andrey V. Semichaevsky, Ashley E. Marlowe and Yaroslava G. Yingling Materials Science and Engineering Department, North Carolina State University, Raleigh, NC, 27695, U.S.A. ABSTRACT Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this paper we use explicit molecular dynamics simulations to examine the variations in cationic distributions around DNA and RNA helices and loop-loop interactions with identical sequence except for Thymine to Uracil substitution. Our simulations show that the ionic distributions are different around RNA and DNA motifs which could be related to the discrepancy in stability of loop-loop complexes. INTRODUCTION The ionic environment plays an important role in nucleic acids structural stability, conformational transitions, intermolecular interactions, and binding [1]. The formation of the tertiary structure requires highly negatively charged nucleic acids to overcome the repulsion which is usually accomplished by the presence of positively charged ions. It has been shown that the ionic environment around DNA is strongly dependent on conformation, sequence, and salt concentration [2]. The distribution of the majority of the cations is dynamic and nonspecific; however, some ions are specifically bind to RNA. Folding of RNA into a specific tertiary structure is highly sensitive to the concentration and types of cations [3, 4]. For example, the loop-loop motifs which associate through complementary Watson-Crick base pairing are stabilized via presence of excess cations. The selective binding properties of these loop-loop motifs are used to induced self-assembly of nucleic acids into regular patterns [5-10], such as nanopatterns with mixed DNA/RNA architectures [10], nanorings and nanotubes [7], large macromolecular assemblies [6, 9] and to serve as a platform for the autonomous DNA computation [5]. Thus understanding of the role of ions and ionic distributions around nucleic acids is critical for control over the self-assembly of nucleic acids into effective nanostructures and devices. The RNA and DNA molecules have similar structures and consist of the phosphate backbones, pentose sugars, and purine or pyrimidine nucleobases. The differences in their physico-chemical properties are mainly due to the fact that: (1) DNA molecules contain 2’deoxyribose sugar which lacks the OH- group as compared to the RNA sugar, and (2) DNA molecules contain Thymine (T) nucleobases instead of the Uracil (U) which is present in RNA. RNA-RNA helices have been shown experimentally to exhibit higher stability compared to the DNA helices [11]. It is also known that a lower conformational energy in the phosphate backbone is assumed by the DNA sugar as compared to the RNA sugar [12] which makes backbone of a single DNA str
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