Scanning probe microscopy of nucleic acids and thin organic films

TL;DR

This paper presents models, algorithms, and experimental AFM techniques to analyze the morphology, elastic properties, and molecular structures of nucleic acids and organic thin films, revealing detailed insights into their physical behavior.

Contribution

It introduces new models and algorithms for AFM artefact correction, visualizes RNA and DNA structures, and demonstrates improved imaging of thin organic films with molecular resolution.

Findings

AFM artefacts like broadening and height reduction can be modeled and corrected.

RNA release from virus particles was visualized, confirming asymmetry.

Partially compacted DNA structures were resolved and analyzed.

Abstract

We developed the models and algorithms to describe two main artefacts of AFM: (i) broadening effect and (ii) decreased heights of profiles for individual objects adsorbed on a hard substrate. It was shown how to measure elastic properties of a single adsorbed microobject. From the viewpoint of contact deformation theory we analysed mechanism of AFM visualisation of an atomic (molecular) structure of a flat surface. We tested technique of immobilisation on a substrate for free single-stranded RNA molecules in an extended state. Using AFM we visualised stages of processes of RNA release from protein coat of tobacco mosaic virus particles. The asymmetry of this process regarding two ends of a macromolecule was confirmed. The dynamics of compaction for DNA T4 molecules was traced using AFM in real time regime. The partially compacted macromolecules were clearly resolved. We detected that the partially compacted structures consisted of toroidal parts formed by different macromolecular strands. The real geometry of the compacted structures was reconstructed on the basis of systematic AFM measurements. That allowed us to calculate the amount of molecules combining each condensed DNA particle. We demonstrated clear benefits of horizontal deposition method for formation of LB films. Using AFM we achieved molecular resolution for some thin film coating and detected lattice parameters with the precision determined by the errors within a few percent. We demonstrated that the structure of the film is determined by the concurrence of several factors: by the closest packing principle for hydrocarbon tails, by the values of surface areas of polar heads at water subphase as well as by the substrate influence.