Super-resolution binding activated localization microscopy through reversible change of DNA conformation

Abstract

Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

Intermingling of chromosome territories

“…DNA was demonstrated to have a very heterogeneous distribution across the cell nucleus with some regions essentially depleted of it. In this experiment, clusters rich in DNA were shown to be surrounded by DNA‐poor sites with approximately two orders of magnitude less dense DNA . In this experiment, positions of individual chromosomes have not been visualized.…”

“…It can also be understood as the existence of chromatin domains being a merge of DNA from more than one chromosomes. Chromosome intermingling regions do not seem to differ morphologically from the rest of the genome . DNA‐rich and DNA‐poor regions interlace throughout all the nuclear space.…”

“…Chromosome intermingling regions do not seem to differ morphologically from the rest of the genome. 57 DNA-rich and DNA-poor regions interlace throughout all the nuclear space. Intermingling regions do not have different DNA condensation from not intermingling chromosome territory region.…”

“…Chromatin‐designated DNA structure fluctuation‐assisted binding activated localization microscopy (fBALM) was developed recently to show chromatin structure at the level of domains (10‐200 nm) . DNA was demonstrated to have a very heterogeneous distribution across the cell nucleus with some regions essentially depleted of it.…”

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

“…A further improvement of resolution beyond the reach of 3D SIM (lateral ~100 nm; axial ~300 nm) is essential both with respect to the precision of target localization and with respect to absolute quantitative measurements of 3D CD compaction within CDCs. A higher 3D resolution can be achieved by single‐molecule localization microscopy (SMLM) with a localization precision of fluorescent macromolecules in the order of about 10 nm . Such a resolution may allow quantitative measurements of the true compaction of active and inactive chromatin located within the ANC and INC, respectively.…”