טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentKuchuk Kfir
SubjectDNA Hydration and Structure Revealed by High Resolution
FM-AFM
DepartmentDepartment of Physics
Supervisor Professor Uri Sivan


Abstract

Studies of the solid-liquid interface have been greatly empowered in the passing decade by dramatic improvements in atomic force microscopy (AFM). Atomic resolution images and 3D force maps can now be routinely acquired in liquid environment at room temperature, revealing interfacial phenomena with unprecedented detail. These capabilities, while particularly germane for biomolecular structure and hydration studies, have hitherto been demonstrated exclusively with flat, stable and uniform surfaces such as mica. Biomolecules pose a significantly greater experimental challenge, being typically bulky, soft, and heterogeneous.

Here, I report multiple advancements in the characterization of DNA molecules by high resolution frequency-modulation AFM (FM-AFM). Additionally, I describe the development of an FM-AFM feedback optimization algorithm, which enables delicate low-noise scanning, a perquisite for biomolecular imaging. Our efforts culminated in several major milestones. We obtained the highest-resolution images of DNA to date, revealing individual phosphates along the DNA backbone. We revealed and characterized the hydration structure of individual DNA molecules. We developed a framework for analysis of DNA structure from AFM images, showed significant deviations of constrained DNA from canonical models, and characterized sequence-specific variations in DNA structure induced by strain. Our results establish FM-AFM as a singular technique capable of characterizing biomolecular structure and hydration at near-physiological conditions, at room temperature and at the single molecule level.