X0202 4 2005-10-14 0 0001030339 NANOGEN INC NGEN 0001341186 Fort Mason Capital, LLC 456 MONTGOMERY STREET 22ND FLOOR SAN FRANCISCO CA 94104 0 0 1 0 Common Stock, par value $0.001 per share 2005-10-14 4 S 0 37424 2.7702 D 4863012 I By Limited Partnerships Common Stock, par value $0.001 per share 2005-10-17 4 S 0 21263 2.7961 D 4841749 I By Limited Partnerships Fort Mason Master, LP, a Cayman Islands limited partnership ("Master"), and Fort Mason Partners, LP, a Delaware limited partnership ("Partners" and, together with Master, the "Funds"), are the holders of, in the aggregate, 4,841,749 shares of the common stock, par value $0.001 per share (the "Shares"), of Nanogen, Inc., a Delaware corporation (the "Company"). In addition, the Funds are the holders of warrants that entitle the Funds to purchase up to an aggregate of 765,306 additional Shares. The Funds acquired such Shares and warrants in a registered direct offering of up to 6,802,721 units at $2.94 per unit, with each unit consisting of (i) one (1) Share and (ii) one (1) warrant to purchase 0.15 Shares. Fort Mason Capital, LLC, a Delaware limited liability company ("Capital"), serves as the investment manager of the Funds and possesses sole power to vote and direct the disposition of all securities of the Company held by the Funds. Thus, as of October 17, 2005, for the purposes of Reg. Section 240.13d-3, Capital is deemed to beneficially own 5,607,055 Shares. Capital's interest in the securities reported herein is limited to the extent of its pecuniary interest in the Funds, if any. /s/ Dan German, Managing Member 2005-10-18