Exhibit 4.2
THIRD SUPPLEMENTAL
INDENTURE , dated as of
August 14, 2008, (“ Third 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 Mellon Trust Company, N.A., a national banking
association, as Trustee (in such capacity, the “
Trustee ”). Capitalized terms not otherwise defined
herein shall have the meanings ascribed to them in the First
Supplemental Indenture (as defined below).
RECITALS OF THE COMPANY
The Company and the Trustee executed
and delivered that certain Indenture, dated as of August 27,
2007 (the “ Initial Indenture ”) to provide for
the issuance from time to time of securities as provided in the
Initial Indenture.
The Company and Trustee executed and
delivered that certain First Supplemental Indenture dated
August 27, 2007 (the “ First Supplemental
Indenture ”) in connection with the issuance of the
Company’s 6.25% Senior Convertible Notes Due 2010 (each a
“ Security ” and collectively, the “
Securities ”). The Securities are the first series of
securities authorized under the Initial Indenture.
The Company and Trustee executed and
delivered that certain Second Supplemental Indenture dated
March 27, 2008 (together with the Initial Indenture as
modified by the First Supplemental Indenture, the “
Indenture ”) in connection with the execution of that
certain Amendment and Exchange Agreement dated March 13, 2008
between the Company and each holder of the Securities (each a
“ Holder ”).
In accordance with Section 9.02
of the Indenture, the Company, the Trustee and each Holder wish to
enter into this Third Supplemental Indenture to further modify the
Indenture.
NOW, THEREFORE, THIS THIRD
SUPPLEMENTAL INDENTURE WITNESSETH, that, for and in consideration
of the premises, the Company agrees with the Trustee as
follows:
ARTICLE I
AMENDMENTS OF
INDENTURE
Section 1.01 Amendment to
Section 1.01 . Subject to Section 2.04 hereof, the
following definitions in Section 1.01 of the Indenture are
hereby amended and restated in their entirety as
follows:
1. “ Eligible Market
” means the Principal Market, The New York Stock Exchange,
Inc., the American Stock Exchange, The NASDAQ Global Select Market
or The NASDAQ Global Market.
3. “ Permitted
Indebtedness ” means (i) Existing Indebtedness;
(ii) other Indebtedness approved in writing by the Required
Holders; (iii) Permitted Subordinated Indebtedness;
(iv) this Note and the Other Notes; (v) Indebtedness to
finance the purchase price of personal property (“ Capital
Lease Product Indebtedness ”), provided that such
Indebtedness does not exceed the lesser of the cost or fair market
value of such property financed with such Indebtedness and does not
exceed $1,250,000 in the aggregate outstanding at any time;
(vi) (w) Indebtedness incurred by any Subsidiary which is
owed to any other Subsidiary, (x) Indebtedness permitted under
Section 14(m) hereof, or (y) Indebtedness incurred by the
Company which is owed to any Subsidiary not to exceed $100,000 in
the aggregate outstanding at any time of Indebtedness unless such
Indebtedness shall be unsecured and expressly subordinated in right
of payment to the Notes; (vii) Indebtedness in respect of
taxes and other governmental charges incurred in the ordinary
course of business and which are not due or are being contested in
good faith by appropriate proceedings and for which adequate
reserves have been provided for in accordance with GAAP;
(viii) Indebtedness resulting from the endorsement of
negotiable instruments in the ordinary course of business;
(ix) Indebtedness in respect of hedging arrangements entered
in the ordinary course of business designed to manage interest
rates or interest rate risk or to protect against fluctuations in
currency exchange rates, and not for purposes of speculations;
(x) the Letters of Credit and other letters of credit, and
reimbursement obligations in respect thereof, in support of trade
debt or statutory obligations and lease or similar obligations
incurred in the ordinary course of business; (xi) Indebtedness
incurred in the ordinary course of business of the Company and its
Subsidiaries, in respect of performance bonds, bid bonds, appeal
bonds, completion bonds, surety bonds, completion guarantees,
security deposits and similar obligations; (xii) Indebtedness
in respect of tenant improvements, tenant inducements or other
payments by landlords in respect of improvements or alterations to
property leased by the Company or its Subsidiaries outstanding as
of March 27, 2008; (xiii) Indebtedness of a Person that
becomes a Subsidiary, which Indebtedness existed at the time such
Person became a Subsidiary and was not incurred in contemplation of
such Person becoming a Subsidiary; (xiv) extensions,
refinancing and renewals of Indebtedness described in clause (i),
(iii) and (iv) of the definition of Existing
Indebtedness, provided that (A) any such refinancing is in an
aggregate principal amount not greater than the aggregate principal
amount of the Existing Indebtedness being renewed or refinanced,
plus the amount of any premiums required to be paid thereon
and reasonable fees and expenses associated therewith,
(B) such refinancing has a later or equal final maturity and
longer or equal weighted average life than the Existing
Indebtedness being renewed or refinanced, and (C) the
covenants, events of default, subordination and other provisions
thereof (including any guarantees thereof) shall be, in the
aggregate, no less favorable to the Holders than those contained in
the Existing Indebtedness being renewed or refinanced,
(xv) the Additional Senior Secured Convertible Notes,
(xvi) the Amended and Restated Notes, and (xvii) the
Bridge Notes.
4. “ Permitted Liens
” means (i) any Lien for taxes not yet due or delinquent
or being contested in good faith by appropriate proceedings for
which adequate reserves have been established in accordance with
GAAP, (ii) any statutory Lien arising in the ordinary course
of business by operation of law with respect to a liability that is
not yet due or delinquent, (iii) any Lien created by operation
of law, such as materialmen’s liens, mechanics’ liens
and other similar liens, arising in the ordinary course of business
with
2
respect to a liability that is not
yet due or delinquent or that are being contested in good faith by
appropriate proceedings, (iv) Liens in respect of security
deposits provided in the ordinary course of business and consistent
with past practices; (v) Liens (A) upon or in any
equipment acquired or held by the Company
