Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies

Author
Abstract
<p>Amino acid and nucleic acid interactions are central in biology and may have played a role in the evolutionary development of protein-based life from an early \textquotedblleftRNA Universe.\textquotedblright To explore the possible role of single amino acids in promoting nucleic acid folding, single-molecule Förster resonance energy transfer experiments have been implemented with a DNA hairpin construct (7 nucleotide double strand with a 40A loop) as a simple model for secondary structure formation. Exposure to positively charged amino acids (arginine and lysine) is found to clearly stabilize the secondary structure. Kinetically, each amino acid promotes folding by generating a large increase in the folding rate with little change in the unfolding rate. From analysis as a function of temperature, arginine and lysine are found to significantly increase the overall exothermicity of folding while imposing only a small entropic penalty on the folding process. Detailed investigations into the kinetics and thermodynamics of this amino acid-induced folding stability reveal arginine and lysine to interact with nucleic acids in a manner reminiscent of monovalent cations. Specifically, these observations are interpreted in the context of an ion atmosphere surrounding the nucleic acid, in which amino acid salts stabilize folding qualitatively like small monovalent cations but also exhibit differences because of the composition of their side chains.</p>
Year of Publication
2018
Journal
The Journal of Physical Chemistry B
Volume
122
Number of Pages
9869-9876
Date Published
2018-10
URL
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.8b06872
DOI
10.1021/acs.jpcb.8b06872
JILA PI
Journal Article