title: Relationship between chromatin compactness and dye uptake for in situ chromatin stained with DAPI.
abstract: BACKGROUND
  This study investigated the relationship between chromatin compactness, which is directly related to chromatin condensation, and DAPI uptake. Materials and Methods For the structural characterization of in situ chromatin, we used fluorescence microscopy and differential scanning calorimetry on calf thymocytes. The compactness of nuclear chromatin was altered by permeabilizing native cells with NP40 detergent. A time-dependent analysis of detergent effects was performed by acquiring nuclear images at different time intervals after permeabilization. In order to compare nuclei of different sizes, we implemented a geometrical correction in the calculation of the integrated fluorescence intensity. For a quantitative evaluation of chromatin condensation we introduced two new parameters, "average chromatin packing ratio" and "average dye spatial density."
  
  
  RESULTS
  This approach allowed us to estimate the effects of NP40 detergent at the level of in situ chromatin. Detergent effects could be modulated by changing the ionic composition of buffer. Moreover, changes of chromatin condensation induced by detergent were inversely related to modifications of nuclear volume.
  
  
  CONCLUSIONS
  The combination of complementary information obtained by fluorescence microscopy, supported by a proper geometrical correction, and differential calorimetry allowed us to interpret the patterns of fluorescence intensities inside the nucleus in terms of chromatin structure.
authors.affiliation: X-Istituto di Calcolo Scientifico, Institute for Scientific Computing, Genoa, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Mascetti
authors.forename: S
authors.initials: S
authors.lastname: Carrara
authors.forename: L
authors.initials: L
authors.lastname: Vergani
mesh_terms: D000818:Animals; D002417:Cattle; D002843:Chromatin / Q000502:physiology*; D005456:Fluorescent Dyes / Q000493:pharmacokinetics*; D007211:Indoles / Q000493:pharmacokinetics*; D013194:Staining and Labeling / Q000379:methods
chemical_list: D002843:Chromatin; D005456:Fluorescent Dyes; D007211:Indoles; C007293:DAPI