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DNA molecules adopt many different structures including kinks, bends, bulges and distortions. The different structures and inappropriate physical contacts may result in the controversy of DNA conductivity reported over the last decade. In order to prove this hypothesis, an AFM based experimental method has been developed in this paper. The AFM based nanomanipulation system can be used either as a nanolithography tool to make small-gap electrodes or a nanomanipulation tool to elongate, deform and cut DNA molecules. By measuring the conductivity of DNA molecules in different shapes, it is promising to find conclusive evidences to verify the electrical conductivity of DNA molecules.