Allison Stuart A, Pei Hongxia, Xin Yao
Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA.
Biopolymers. 2007;87(2-3):102-14. doi: 10.1002/bip.20809.
Free solution and gel electrophoresis is an extremely useful tool in the separation of biopolymers. The complex nature of biopolymers, coupled with the usefulness of electrophoretic methods, has stimulated the development of theoretical modeling over the last 30 years. In this work, these developments are first reviewed with emphasis on Boundary Element and bead methodologies that enable the investigator to design realistic models of biopolymers. In the present work, the bead methodology is generalized to include the presence of a gel through the Effective Medium model. The biopolymer is represented as a bead array. A peptide, for example, made up of N amino acids is modeled as 2N beads. Duplex DNA is modeled as a discrete wormlike chain consisting of touching beads. The technical details of the method are placed in three Appendices. To illustrate the accuracy and effectiveness of the approach, two applications are considered. Model studies on both the free solution mobility of 73 peptides ranging in size from 2 to 42 amino acids, and the mobility of short duplex DNA in dilute agarose gels are discussed.
自由溶液和凝胶电泳是分离生物聚合物的一种极其有用的工具。生物聚合物的复杂性质，再加上电泳方法的实用性，在过去30年里推动了理论模型的发展。在这项工作中，首先回顾这些进展，重点是边界元法和珠子方法，这些方法使研究人员能够设计出生物聚合物的实际模型。在目前的工作中，通过有效介质模型将珠子方法推广到包括凝胶的存在。生物聚合物被表示为珠子阵列。例如，由N个氨基酸组成的肽被建模为2N个珠子。双链DNA被建模为一个由相互接触的珠子组成的离散蠕虫状链。该方法的技术细节放在三个附录中。为了说明该方法的准确性和有效性，考虑了两个应用。讨论了对73种大小从2到42个氨基酸的肽在自由溶液中的迁移率以及短双链DNA在稀琼脂糖凝胶中的迁移率的模型研究。
