Atomic force microscopy study of chromosome surface structure changed by protein extraction

Relating centromeric topography in fixed human chromosomes to α-satellite DNA and CENP-B distribution

Despite extensive analyses on the centromere and its associated proteins, detailed studies of centromeric DNA structure have provided limited information about its topography in condensed chromatin. We have developed a method with correlative fluorescence light microscopy and atomic force microscopy that investigates the physical and structural organization of α-satellite DNA sequences in the context of its associated protein, CENP-B, on human metaphase chromosome topography. Comparison of centromeric DNA and protein distribution patterns in fixed homologous chromosomes indicates that CENP-B and α-satellite DNA are distributed distinctly from one another and relative to observed centromeric ridge topography. Our approach facilitates correlated studies of multiple chromatin components comprising higher-order structures of human metaphase chromosomes.

Saponaria officinalis karyology and karyotype by means of image analyzer and atomic force microscopy

The aim of this work was to offer a contribution to the characterization of taxonomic entity of Saponaria officinalis (2n = 28; an herbaceous perennial species; saporin, a type 1 Ribosome Inactivating Protein, is present in leaves and seeds) by a cytogenetic and karyomorphological approach. We investigated the karyotype's morphometry correlated with Stebbin's symmetric index; the same information has been used for computing the indices resemblance between chromosomes (REC), symmetric indices (SYI), and total form (TF%) which allow the comparison between species and evaluation of karyological evolution. Fluorescence intensities of the stained nuclei were measured by a flow cytometer and, for the first time, values for nuclear DNA content were estimated by comparing nuclei fluorescence intensities of the test population with those of appropriate internal DNA standards. Our study is also aimed to introduce chromosomal volumes, which were determined by atomic force microscopy (AFM), as novel karyomorphological parameter which could allow for chromosome discrimination especially when tiny ones are present.

Atomic Force Microscopic Examination of Chromosomes Treated with Trypsin or Ethidium Bromide

Trypsin treatment is frequently used during chromosome preparation for removal of cellular contaminants, and ethidium bromide (EB) staining of bands is often used to facilitate high-resolution observations by optical microscopy. However, conventional optical microscopy is unable to visualize potential aberrations of chromosome structures caused by these physicochemical treatments. In this article, we use atomic force microscopy (AFM) in the tapping mode to obtain and analyze high-resolution images of chromosome surface structure damage associated with trypsinization and EB treatment. According to our results, the trypsin-based digestion effects became more severe as incubations increased across a range from 10 to 40 s; a digestion time of 10 to 20 s appeared to be most suitable for observation by AFM. In terms of chromosomal damage induced by EB treatment, addition of EB into the media of cultured human blood cells induced chromosomal breakage in a dose-dependent fashion, and the results indicate centromeric region damnifyed severer than arms. Together, these results indicate that EB staining and the standard chromosomal preparative techniques of trypsinization can induce chromosomal damage that may affect the observed results.

Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy

Acetic acid treatment has been frequently used to remove cellular contaminants from plant chromosome samples for structural analyses by scanning electron microscopy and atomic force microscopy (AFM). We evaluated the effects of various concentrations of acetic acid treatments on barley chromosome structures by using AFM. The long-term 45% acetic acid treatment significantly damaged the chromosome structures, although the treatment effectively removed the cellular contaminants. On the other hand, the treatment with 15% acetic acid could not obtain sufficiently clean chromosome samples and the chromosome surface structures could not be observed. In contrast, we obtained clean chromosome preparation without severe damage by using an intermediate concentration (30%) of acetic acid treatment. In the centromeric region, we could observe fiber structures with a width of 100 nm, which were composed of ca. 50-nm granules and aligned to the axes of chromosomes. Thus, AFM analysis of chromosomes appropriately treated with acetic acid will provide important insights into the organization of higher-order structures of plant chromosomes.

Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit

Fluorescence in situ hybridization (FISH) is widely used in molecular biological study. However, high-resolution analysis of fluorescent signals is theoretically limited by the 300-nm resolution optical limit of light microscopy. As an alternative to detection by light microscopy, we used Scanning Near-field Optical/Atomic Force Microscopy (SNOM/AFM), which can simultaneously obtain topographic and fluorescent images with nanometer-scale resolution. In this study, we demonstrated high-resolution SNOM/AFM imaging of barley chromosome (Hordeum vulgare, cv. Minorimugi) FISH signals using telomeric DNA probes. Besides detecting the granular structures on chromosomes in a topographic image, we clearly detected fluorescent signals in telomeric regions with low-magnification imaging. The high-resolution analysis suggested that one of the telomeric signals could be observed by expanded imaging as two fluorescent regions separated by approximately 250 nm. This result indicated that the fluorescent signals beyond the optical limit were detected with higher resolution scanning by SNOM/AFM.

Atomic force microscopic imaging of 30 nm chromatin fiber from partially relaxed plant chromosomes

We have developed a procedure for partially relaxing the barley metaphase chromosomes and exposing fibrous structures from the chromosomes. The observation by atomic force microscopy (AFM) showed that the fibrous structures are typically 0.5 to 1 microm long and 40 to 50 nm in diameter. In higher magnification imaging, we found the fibrous structures were composed of aligned granules and looked like "knobby fiber." These observations are consistent with previously reported features of chromatin fiber observed by AFM and scanning electron microscopy, suggesting that the structures correspond to 30 nm chromatin fibers. We observed the chromatin fiber extending straight from the periphery of the chromosomes in most cases, but fibers with different shapes, such as loop and spiral, were also observed. The procedure reported here will provide a new approach for observing the organization of chromatin fiber to higher-order structures by AFM and other high-resolution microscopy.