Abstract
The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.
Highlights
Heterochromatin and euchromatin are two distinct types of chromatin structure
We study the methylation state at the sub-chromosome scale with a resolution approaching the order of 10 nm, enabling the chemical characterization of very small amounts of material
The results provided by The Human Genome Sequencing Consortium are consistent with the amounts of the particular type of chromatin, which was detected by infrared nanospectroscopy
Summary
Heterochromatin and euchromatin are two distinct types of chromatin structure. Heterochromatin is a tightly packed form of DNA and has a condensed structure, containing ∼20% of the mapped human genome, which can be defined as transcriptionally inactive, but necessary for the maintenance of structural integrity [1,2,3,4]. Euchromatin is the lightly packed form of DNA, which is the early replicating variety of chromatin containing most of the housekeeping genes [3,4]. DNA methylation affects activity of genes and mechanical properties of DNA [5,6,7,8]. These structural modifications may influence interactions between DNA and proteins [9] or other molecules such as drugs, dyes and the resistance to strand separation [10]
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