0001193125-07-189336 Sample Contracts

SECURITIES PURCHASE AGREEMENT
Securities Purchase Agreement • August 27th, 2007 • Nanogen Inc • Laboratory analytical instruments • New York

SECURITIES PURCHASE AGREEMENT (the “Agreement”), dated as of August 26, 2007, by and among Nanogen Inc., a Delaware corporation, with headquarters located at 10398 Pacific Center Court, San Diego, California 92121 (the “Company”), and the investors listed on the Schedule of Buyers attached hereto (individually, a “Buyer” and collectively, the “Buyers”).

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NANOGEN, INC. $20 Million in 6.25% Senior Convertible Notes due 2010 and Warrants to Purchase 17,322,833 Shares of Common Stock PLACEMENT AGENCY AGREEMENT
Placement Agency Agreement • August 27th, 2007 • Nanogen Inc • Laboratory analytical instruments • New York

The sale and issuance of the Notes and the Warrants shall be made pursuant to a Securities Purchase Agreement by and among the Company and the Investors dated on or about the date hereof (the “Securities Purchase Agreement”). The Notes will be issued under the indenture by and between the Company and The Bank of New York Trust Company, N.A., as trustee (“Trustee”), dated on or about the date hereof as supplemented by the first supplemental indenture dated on or about the date hereof between the Company and Trustee (the “Indenture”). The Company has engaged Seven Hills Partners LLC as its sole and exclusive placement agent (the “Placement Agent”) to introduce the Company to the Investors. The Notes, together with the Conversion Shares, the Interest Shares, the Warrants, and the Warrant Shares are referred to herein as the “Securities.” The Securities are described more fully in the Securities Purchase Agreement and the Registration Statement (as hereinafter defined).

FIRST SUPPLEMENTAL INDENTURE Dated as of August 27, 2007
First Supplemental Indenture • August 27th, 2007 • Nanogen Inc • Laboratory analytical instruments • New York

FIRST SUPPLEMENTAL INDENTURE, dated as of August 27, 2007, ("First Supplemental Indenture") between Nanogen, Inc., a corporation duly organized and existing under the laws of the State of Delaware, as Issuer (the "Company"), having its principal office at 10398 Pacific Center Court, San Diego, California 92121, and The Bank of New York Trust Company, N.A., a national banking association, as Trustee (in such capacity, the "Trustee").

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