Study Nucleic Acid Interaction Using Atomic Force Microscopy

To study the structure and nature of the material on the atom or the molecule level has been the goal that the scientist has made great efforts to pursue all the time. The development of scientific research needs correct theoretical instruction and also there should be suitable research tools, the invention of scanning probe microscope has offered the opportunity for people to know the microworld on nanometer and molecule level. As one of the most important member in scanning probe microscopy family, atomic force microscope (AFM) has been extensively applied to many disciplines. It is a kind of important research tool, especially in the research of life sciences. Because AFM not only can obtain surface topography of biomolecules on nanometer and molecule level, but also can study interactions between biomolecules under the near physiological condition.This thesis uses the atomic force microscope to study the nucleic acid interactions involved in the important life process, such as nucleic acid hybridization and nucleic acid ligation. The high recongnization specificity of molecular beacon (MB) for target DNA was investigated by AFM force measurements. From the results obtained in force measurements, we can confirm that the recongnization specificity of MB is higher than that of linear DNA probe. A novel method was developed to study the interaction between MB and target DNA on-line and realtime in flow system. The effects of medium on the MB-target DNA interaction have been realtime investigated in flow system based on the technological platform here. Some important life processes, such as nucleic acid hybridization and nucleic acid ligation, have been directly revealed by AFM imaging on nanometer level by use of colloidal gold labeling technology.The main researches included in this dissertation are presented as following:1. For the first time, the specific interactions between MB and target DNA have been successfully measured by atomic force microscopy. The hybridization specificities of both a molecular beacon and a linear DNA probe have been investigated by rupture force measurements. Experimental results showed that the difference of mean rupture force for MB with different target DNA is larger than that of linear DNA probe. These results reveal that the MB is much more specific than linear DNA to base mismatch in the target DNA. Therefore the high recongnization...