Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology

Hausmann, Michael; Hildenbrand, Georg; Pilarczyk, Götz

doi:10.1007/978-3-031-06573-6_1

Cited by 5 publications

(12 citation statements)

References 132 publications

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“…In combination with super-resolution localization microscopy and novel tools of data evaluation and interpretation by geometric and topological algorithms [61][62][63][64] COMBO-FISH probes offer new perspectives in understanding the reaction of chromatin as a system as a whole during gene expression, proliferation, or stress response [47].…”

Section: Discussionmentioning

confidence: 99%

“…COMBO-FISH probes carrying one fluorochrome molecule at one end of each oligonucleotide are ideal nano-probes for Single Molecule Localization Microscopy [23,24,43] (SMLM) in order to analyze chromatin structure and architecture on the nano-scale in subchromosomal regions of cell nuclei [32,[43][44][45][46][47].…”

Section: Combo-fish With Repetitively Binding Unique Single Probes An...mentioning

confidence: 99%

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Combinatorial Oligonucleotide FISH (COMBO-FISH): Computer Designed Probe Sets for Microscopy Research of Chromatin in Cell Nuclei

Hausmann¹,

Schmitt²

2023

Oligonucleotides - Overview and Applications

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Genome sequence databases of many species have been completed so that it is possible to apply an established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligonucleotide FISH). It makes use of bioinformatic sequence database search for probe design. Oligonucleotides of typical lengths of 15–30 nucleotides are selected in such a way that they only co-localize at the given genome target. Typical probe sets of 20–40 stretches label about 50–250 kb specifically. The probes are either solely composed of purines or pyrimidines, respectively, for Hoogsteen-type binding, or of purines and pyrimidines together for Watson-Crick type binding. We present probe sets for tumor cell analysis. With an improved sequence database analysis and sequence search according to uniqueness, a novel family of probes repetitively binding to characteristic genome features like SINEs (Short Interspersed Nuclear Elements, e.g., ALU elements), LINEs (Long Interspersed Nuclear Elements, e.g., L1), or centromeres has been developed. All types of probes can be synthesized commercially as DNA or PNA probes, labelled by dye molecules, and specifically attached to the targets for microscopy research. With appropriate dyes labelled, cell nuclei can be subjected to super-resolution localization microscopy.

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Section: Discussionmentioning

confidence: 99%

Section: Combo-fish With Repetitively Binding Unique Single Probes An...mentioning

confidence: 99%

Combinatorial Oligonucleotide FISH (COMBO-FISH): Computer Designed Probe Sets for Microscopy Research of Chromatin in Cell Nuclei

Hausmann¹,

Schmitt²

2023

Oligonucleotides - Overview and Applications

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“…657 The molecular dynamics and macromolecular organization must follow the chemical and physical laws of atomic and molecular binding, thermodynamics, electrodynamics, and physical chemistry within a limited volume. 663 Exposure to UV or ionizing radiation, such as X-rays, γ-rays, high-energy electrons or protons, high-energy particles or ions, etc,. causes chromatin damage of different types, for instance, base modifications, single-strand breaks (SSBs), and especially double-strand breaks (DSBs) of different complexity.…”

Section: Radiation-induced Dna Damage Repair and Response Mechanisms ...mentioning

confidence: 99%

“…Such networks characteristically rearranged themselves depending on cell fate 661 and under environmental stress such as exposure to ionizing irradiation, thereby interacting with epigenetic pathways and response loops. 663 In order to obtain quantitative parameters for networks and network dynamics, super-resolution SMLM 664 is used as a method for accurate (to within ten nanometers) registration of the coordinates of fluorescence labels of specific DNA sequences/chromatin domains and proteins. The major advantage of SMLM depends on this registration process, which results in a map of molecule coordinates without primarily processing an image.…”

Section: Chemicalmentioning

confidence: 99%

“…Although sometimes ATP-supported, it seems that this trafficking works somehow self-propelled and drives and governs the system perfectly . The molecular dynamics and macromolecular organization must follow the chemical and physical laws of atomic and molecular binding, thermodynamics, electrodynamics, and physical chemistry within a limited volume …”

Section: Case Studies Of Multiscale Phenomenamentioning

confidence: 99%

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Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

Solov’yov,

Verkhovtsev,

Mason

et al. 2024

Chem. Rev.

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This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

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Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)

Weidner¹,

Neitzel²,

Gote³

et al. 2023

Computational and Structural Biotechnology Journal

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Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology

Cited by 5 publications

References 132 publications

Combinatorial Oligonucleotide FISH (COMBO-FISH): Computer Designed Probe Sets for Microscopy Research of Chromatin in Cell Nuclei

Combinatorial Oligonucleotide FISH (COMBO-FISH): Computer Designed Probe Sets for Microscopy Research of Chromatin in Cell Nuclei

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)

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