Abstract
Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.
Highlights
Function of the genome depends on the chromosome architecture [1]
Classical banding protocols for studying chromosomes provide only the basic morphological information regarding the structures of chromosomes, while spectral karyotyping using nanoscale imaging techniques is chromosome specific and provides additional chemical information and improved characterization of aberrant chromosomes that contain DNA sequences not identifiable using conventional banding methods
Our optimized protocol helped to successfully isolate chromosomes from the quinoa root tip and was able to image without staining using scanning electron microscopy (SEM), atomic force microscopy (AFM), scanning transmission X-ray microscope (STXM), and confocal laser scanning microscopy (CLSM)
Summary
Function of the genome depends on the chromosome architecture [1]. For predictive gene diagnosis and for personalized medicine, simultaneous understanding of the structural and chemical makeup of chromosomes is essential [2]. To integrate biomolecular and clinical data for cancer research, spectral-based biomarker libraries of chromosomes of species are required. Conventional cytogenetic analysis such as karyotyping involves the observation of defects on the surface of chromosomes using optical microscopy and thereby relates to the physiological attributes and disease state of the species. Classical banding methods provide only basic information regarding the structure and identities of chromosomes, while spectral karyotyping has the potential to provide improved characterization of aberrant. Accurate topology of the chromatin (DNA and protein composition) network inside a single chromosome has not yet been characterized precisely. A chromosome is made up of DNA and associated proteins and other compounds in the nanoscale domain containing the genomic information. To understand the structure– property relationship of any organic material, quantitative compositional analysis at length scales below 100 nm is required [9]
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