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Atomic force microscope (AFM), as its high resolution and precision, was employed to directly probe intermolecular hydrogen bonds between self-assembled purines and pyrimidines. In the experiment, we directly stretch the DNA double strands that are attached to the planar modified glass surfaces and AFM tip respectively. However, distinguishing from previous literatures we focus on the NaCl density and holding time influencing the rupture force of DNA double helix and monitor the probing process under three different densities of sodium chloride (NaCl): 0mM, 50mM, and 100mM. The result shows complementary DNA strands are easier to bond as the density of NaCl increases. At the same time we test the probing process considering three holding durations: 0S, 10S, and 40S. We find the complementary DNA strands bond forming well under the situation of 40S. Then we separately do experiments with three lengths of strands: 10bp, 14bp, 20bp. Using cluster analysis method we find that the clustering center intervals are about 0.21nN, 0.29nN, and 0.39nN, and we can calculate the hydrogen bond of the single G-C is about 20pN.