“Effect of Single-stranded Domains on the Energetics and Structural Flexibility of DNA Structure”
Single-stranded domains within structured nucleic acids disrupt local base-stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities for structured nucleic acids. Using a combination of optical melting and single-molecule FRET microscopy, we investigated the influence of variations in the number, relative distribution, and sequence of unpaired nucleotides within opposing DNA strands on their biophysical properties. A thermodynamic prediction model is described for the energetic penalty of these domains. The findings provide a framework for understanding the thermodynamic and conformational effects of these domains for the rational design of functional DNA nanostructures.
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