Investigating Conformations of Single Polysaccharides and Nucleic Acids by Force Spectroscopy

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The project focuses on investigating forced conformational transitions in polysaccharides and single-stranded DNA using atomic force microscopy (AFM) techniques. The objectives are: 1) Use force-clamp AFM to monitor the epimerization reaction in alginates; 2) Improve and expand computer modeling of sugars' elasticity; 3) Use force spectroscopy to examine the elasticity of single stranded nucleic acids and their base stacking interactions. To achieve these objectives alginate precursors will be stretched in an AFM in the presence of C-5 epimerase enzyme and the conformational conversion of the mannuronic acid to guluronic acid will be monitored by force-clamp AFM. Sugars' elasticity will be modeled with computational methods developed to address two important issues: the accuracy of the atomic interaction energy in sugars and the time gap between simulations and AFM experiments. The elasticity of individual homo-polynucleotides will be measured by AFM and the signatures of stacking interactions among the bases will be established under various solvent conditions. The project will advance single-molecule biophysics research and will increase the understanding of the mechanochemistry of polysaccharides and single-stranded DNA. The project will also develop novel approaches to modeling strained sugars. Measurements of forces involved in base stacking interactions are of a fundamental significance to the understanding of DNA and RNA structure and function. This project will provide an exciting education and research opportunity for two graduate and two undergraduate students and will benefit researchers modeling carbohydrates. Outreach activities will involve undergraduate students, K12 students and their teachers. This project is jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Experimental Physical Chemistry Program in the Division of Chemistry in the Mathematical and Physical Sciences Directorate.