International Journal of Medical Sciences

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18 October 2017

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Int J Med Sci 2013; 10(9):1136-1148. doi:10.7150/ijms.6121

Research Paper

Spatial Localization of Genes Determined by Intranuclear DNA Fragmentation with the Fusion Proteins Lamin KRED and Histone KRED und Visible Light

Waldemar Waldeck1, Gabriele Mueller1, Karl-Heinz Glatting3, Agnes Hotz-Wagenblatt3, Nicolle Diessl4, Sasithorn Chotewutmonti4, Jörg Langowski1, Wolfhard Semmler2, Manfred Wiessler2, Klaus Braun2 ✉

1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany;
2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany;
3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Germany;
4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany.

Abstract

The highly organized DNA architecture inside of the nuclei of cells is accepted in the scientific world. In the human genome about 3 billion nucleotides are organized as chromatin in the cell nucleus. In general, they are involved in gene regulation and transcription by histone modification. Small chromosomes are localized in a central nuclear position whereas the large chromosomes are peripherally positioned. In our experiments we inserted fusion proteins consisting of a component of the nuclear lamina (lamin B1) and also histone H2A, both combined with the light inducible fluorescence protein KillerRed (KRED). After activation, KRED generates reactive oxygen species (ROS) producing toxic effects and may cause cell death. We analyzed the spatial damage distribution in the chromatin after illumination of the cells with visible light. The extent of DNA damage was strongly dependent on its localization inside of nuclei.

The ROS activity allowed to gain information about the location of genes and their functions via sequencing and data base analysis of the double strand breaks of the isolated DNA. A connection between the damaged gene sequences and some diseases was found.

Keywords: Chromatin architecture, DNA-topology, fluorescent proteins, genome architecture, KillerRed, Photo-Dynamic-Therapy, subcellular localization.

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See http://ivyspring.com/terms for full terms and conditions.
How to cite this article:
Waldeck W, Mueller G, Glatting KH, Hotz-Wagenblatt A, Diessl N, Chotewutmonti S, Langowski J, Semmler W, Wiessler M, Braun K. Spatial Localization of Genes Determined by Intranuclear DNA Fragmentation with the Fusion Proteins Lamin KRED and Histone KRED und Visible Light. Int J Med Sci 2013; 10(9):1136-1148. doi:10.7150/ijms.6121. Available from http://www.medsci.org/v10p1136.htm