Parkinson’s disease (PD) is considered one of the most frequent neurological brain diseases in the world. There is a need to study the early and efficient biomarkers of PD, such as changes in structural disorders like DNA/chromatin, especially at the subcellular level in the human brain. We used mesoscopic-physics-based techniques, partial wave spectroscopy (PWS), and inverse participation ratio (IPR) to probe structural alteration in the human brain tissue samples and DNA/chromatin in brain cell nuclei. Results show an increase in the structural disorder in tissues and DNA/chromatin. The rise in mass density fluctuations in the nuclei components, such as DNA/chromatin, can be linked to the aggregation of alpha-synuclein in the substantia nigra of the brain. This protein deposition is considered a significant cause of neuronal death in the brains of PD patients. We also did a histological analysis of brain tissues, which supports our results from dual photonics techniques.