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Rapid, reliable, and inexpensive characterisation of biomolecules, particularly nucleic acids and proteins, has become increasingly important. Among the current sensors, engineered transmembrane protein pores have been advantageous candidates for sensing elements. This sensor has two electrolyte-filled pools, which are separated by a lipid bilayer having a protein pore (e.g. /spl alpha/-hemolysin). The specimen molecules place in one of the pools can stochastically pass via the pore. They produce a fluctuating binary response in the transmembrane ionic current (Bezrukov et al, 1994; Li-Qun Gu et al, 1999). Instead of the protein pore, we have proposed use of nanometer-sized holes in a SiN/sub x/ membrane as a sensor head. We have fabricated the biomolecular sensor with nanoholes using a Si bulk micromachining technique (Fertig et al, 2000) and observed the ionic current via nanoholes. Through-nanoholes are formed by FIB (focused ion beam) (Yamaguchi et al, 1985; Gierak et al, 1997).