It is very important both in medicine and biology to clarify the chromosomal structure to understand its functions. In a standard cytogenetic procedure, chromosomes are often fixed in a mixture of acetic acid and methanol. This process most likely changes the mechanical property of chromosomes. We adopted a method to prepare native and unfixed chromosomes from mouse 3T3 cells and used tapping and contact mode atomic force microscopy (AFM) to image and manipulate them. Modified AFM tips were used to image chromosomes in contact mode in air, and then the chromosome samples were immobilized on a substrate and placed in a buffer solution to pull out DNA-histone complexes from them after they were optimally treated with trypsin. From the AFM images, we could see several bands and granular structures on chromosomes. We obtained force curves indicating long fiber extensions from native chromosomes both with low (in high concentration of NaCI) and high forces (physiological conditions). The result suggested that the degree of chromosome condensation decreased in high concentration of salt. It agrees with the known fact of histone H I dissociation in a high concentration of salt. We intend to pull out DNA-histone complexes from chromosomes for later molecular operations on them using an AFM. (C) 2002 Elsevier Science B.V. All rights reserved.