In this work, the freezing process and cryoprotective function of three principally different cryoprotectants (antifreeze protein, trehalose and DMSO) were investigated in living cells as well as the phase transition processes of the cryoprotectants solutions. In order to gain deeper insight to the behaviour of the complex cell nucleus, the changes in the genome and nuclear envelope integrity were investigated simultaneously with the higher-order chromatin structure. Cells were cultured in standard medium and compared to cells that were treated with cryoprotectants at the initial unfrozen state, after freezing, and after melting. Analysis was performed after results were obtained from ab-initio modelling, molecular dynamics, Raman spectroscopy, differential scanning calorimetry and X-ray diffraction for each of the cryoprotectants solutions. Our results provide valuable experimental and computational data and help to design novel cryoprotective substances and develop more efficient cryoprotection protocols.