Deoxyribonucleic acid (DNA) serves as the repository of hereditary data in nature, possessing the capacity to encode genetic instructions that govern biological growth and operation, notably in the regeneration of proteins and cells. The double helical structure of DNA is fundamental in preserving the resemblance between successive generations of organisms, facilitating the transmission and perpetuation of genetic material. Understanding the three-dimensional (3D) atomic structure of individual double-stranded DNA molecules can enhance comprehension of their biological functions. In this paper, we demonstrate a novel approach utilizing simulated annealing and energy minimization techniques, to infer the 3D atomic structure of a single double-stranded λ-DNA molecule from a low-dose high-resolution transmission electron microscopy (TEM) image.

In the process of DNA TEM imaging, the impact of the spherical aberration coefficient, defocus value, and dose rate are examined through theoretical calculations and experimental validation. It is noted that moderate spherical aberration and under focus settings can improve image contrast, although this improvement will come at the expense of resolution. High-resolution imaging of individual DNA molecules and DNA bundles using TEM, with and without a spherical corrector is documented in Chapter 4. The resulting high-contrast TEM images offer detailed insights into the characteristics of B-form DNA at nearly atomic resolution. Furthermore, the work analyzes electron-beam radiation damage on DNA by assessing changes in the shape and diameter of DNA filaments.

In order to reconstruct the 3D atomic structure of a single double-strand DNA molecule, a combination of simulated annealing and energy minimization techniques is utilized based on a TEM image containing a portion of the individual double-strand DNA molecule. The simulated annealing process involves generating a simulated TEM image after each atomic adjustment in the initial model, which is then compared to the experimental image to evaluate the effectiveness of the adjustment. Energy minimization is employed to decrease the potential energy of the system and achieve a state of local equilibrium, thereby rationalizing the atomic movements. By incorporating energy minimization constraints, the 3D atomic conformation can be refined after simulated annealing from the initial model. The resulting model, which accounts for distortion and puckering of structural components, provides localized insights into the behavior of the DNA molecule under electron irradiation. Notably, the TEM analysis reveals a more expanded state of the single DNA molecule compared to X-ray measurements. This refined 3D structure facilitates a detailed understanding of the structure-function relationship. Furthermore, the integration of TEM imaging with simulated annealing and energy minimization techniques can be extended to the analysis of other beam-sensitive materials, offering a novel approach for characterizing structures at room temperature.