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- W2914970143 abstract "Single-stranded domains destabilize nucleic acid helical structure; however, their presence can also enhance the functional and architectural capabilities of helical structure. These domains serve critical roles in structured nucleic acids, such as catalytic centers, tertiary contacts, ligand-binding sites, and positioning of helical junctions. Developing predictive tools for their biophysical properties supports the rational design of functional DNA and RNA nanostructures. Here, DNA constructs containing centrally positioned, poly(dA) internal loops of varying size (1 to 20 nt) and strand asymmetry have been systematically investigated to quantify the energetics and conformational behavior of homologous single-stranded domains. For optical melting studies, loop constructs were designed with a specific number of unpaired adenines in each strand (N1 and N2), and three loop categories were examined: symmetric (N1 = N2), asymmetric (N2 ≠ N1 and N1, N2 ≠ 0), and bulge (N1 = 0, N2 > 0). The enthalpic and entropic components were extracted by fitting the melting curves to a multiparametric, two-state model based on the van’t Hoff equation. We present an improved, energetic prediction model for DNA internal loops that incorporates the poly(dA) results and our previous data for poly(dT) loops. The new model accounts for the destabilizing effect of DNA loops based on size, intrastrand stacking, strand asymmetry, and interstrand interactions. Comparison of experimental data with the energetic model show excellent agreement. In addition, single-molecule FRET experiments were conducted with dye-labeled constructs containing an equivalent loop size but different strand asymmetries. These experiments provide a direct measurement of the conformational entropy associated with the loop domains that complements the optical melting studies and reveal distinct differences in the geometry and dynamics of the flanking helical regions as a consequence of strand asymmetry in the internal loops." @default.
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- W2914970143 date "2019-02-01" @default.
- W2914970143 modified "2023-10-18" @default.
- W2914970143 title "The Effect of Intrastrand Base-Stacking Interactions on the Energetics and Structural Dynamics of DNA Internal Loops" @default.
- W2914970143 doi "https://doi.org/10.1016/j.bpj.2018.11.1941" @default.
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