Investigating Conformations of Single Polysaccharides and Nucleic Acids by Force Spectroscopy

通过力谱研究单多糖和核酸的构象

• 批准号: 0717770
• 负责人: Piotr Marszalek
• 金额: $ 51.01万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0717770&HistoricalAwards=false
• 关键词: Investigating; Conformations; Single; Polysaccharides; Nucleic

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.

该项目的重点是研究强迫构象转变多糖和单链DNA使用原子力显微镜（AFM）技术。其目标是：1）使用力钳原子力显微镜监测海藻酸盐中的差向异构化反应; 2）改进和扩展糖弹性的计算机建模; 3）使用力谱法检查单链核酸的弹性及其碱基堆积相互作用。为了实现这些目标，藻酸盐前体将在C-5差向异构酶的存在下在AFM中拉伸，并且甘露糖醛酸向古洛糖醛酸的构象转化将通过力钳AFM监测。糖的弹性将通过开发计算方法来建模，以解决两个重要问题：糖中原子相互作用能的准确性以及模拟和AFM实验之间的时间间隔。单个同源多核苷酸的弹性将通过AFM测量，并且碱基之间的堆叠相互作用的特征将在各种溶剂条件下建立。该项目将推进单分子生物物理学研究，并将增加对多糖和单链DNA的机械化学的理解。该项目还将开发新的方法来建模应变糖。碱基堆积相互作用中作用力的测量对于理解DNA和RNA的结构和功能具有重要意义。 这个项目将为两个研究生和两个本科生提供一个令人兴奋的教育和研究机会，并将有利于研究人员建模碳水化合物。外展活动将涉及本科生，K12学生和他们的老师。该项目由生物科学理事会分子和细胞生物科学部的分子生物物理学和数学和物理科学理事会化学部的实验物理化学计划共同支持。