Exhibit 4.1

 



ZQ|CERT#|COY|CLS|RGSTRY|ACCT#|TRANSTYPE|RUN#|TRANS#   . COMMON STOCK PAR VALUE $0.001 COMMON STOCK THIS CERTIFICATE IS TRANSFERABLE   IN CANTON, MA, JERSEY CITY, NJ AND COLLEGE STATION, TX Shares * * 000000 * *   * * * * * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * * *   * * * * * 000000 * * * * * * * * * * * * * * * * * * * * * 000000 * * * * * *   * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * Certificate   Number ZQ00000000 COMBIMATRIX CORPORATION INCORPORATED UNDER THE LAWS OF THE   STATE OF DELAWARE ** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David THIS CERTIFIES THAT Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander MR. SAMPLE & MRS. SAMPLE   & David Sample **** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample Sample **** Mr. AlexandeMr DaviRd Sam.ple S**** MAr. AleMxandePr   DavLid SEample *&*** Mr. AMlexanRder DaSvid S.ampSle ***A* Mr.MAlexanPder   DLavidESample **** Mr. Alexander **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David SEE REVERSE FOR CERTAIN DEFINITIONS   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Sample ****   Mr. Sample is the record holder of   **000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares***   *000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****   000000**Shar*es****0*000Z00**SEhareRs****00O0000**ShHares**U**0000N00**SDhares*R***000E000**DShares**T**000H000**SOhares*U***000S000**AShareNs****00D0000**Shares****0   00000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****00   0000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000   000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****0000   00**Shares****0Z0000E0**ShRares***O*000000*H*ShareUs****0N00000D**SharRes****0E0000D0**ShareAs****0N00000D**SharesZ****00E0000R**SharOes****0*000*00**Shares****00000   0**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000   **Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000*   *Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**   Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**S   FULLY-PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK $0.001 PAR VALUE, OF   CombiMatrix Corporation, transferable on the books of the Corporation in   person or by duly authorized attorney, upon surrender of this Certificate   properly endorsed. This Certificate is not valid unless countersigned and   registered by the Transfer Agent and Registrar. Witness the facsimile seal of   the Company and the facsimile signatures of its duly authorized officers.   DATED DD-MMM-YYYY COUNTERSIGNED AND REGISTERED: COMPUTERSHARE INC. TRANSFER   AGENT AND REGISTRAR, Chief Executive Officer 2002 DELAWARE By Chief Financial   Officer AUTHORIZED SIGNATURE N CUSIP Holder ID Insurance Value Number of   Shares DTC Certificate Numbers 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 Total Transaction XXXXXX XX X XXXXXXXXXX 1,000,000.00   123456 12345678 123456789012345 PO BOX 43004, Providence, RI 02940-3004   Num/No. Denom. Total 1 2 3 4 5 6 7 1 2 3 4 5 6 1 2 3 4 5 6 MR A SAMPLE   DESIGNATION (IF ANY) ADD 1 ADD 2 ADD 3 ADD 4 C CUSIP 20009T 50 1 


    




 






 



. COMBIMATRIX   CORPORATION A STATEMENT OF THE RIGHTS, PREFERENCES, PRIVILEGES AND   RESTRICTIONS GRANTED TO OR IMPOSED UPON THE RESPECTIVE CLASSES OR SERIES OF   SHARES OF STOCK OF THE CORPORATION AND UPON HOLDERS THEREOF AS ESTABLISHED BY   THE CERTIFICATE OF INCORPORATION OR BY ANY CERTIFICATE OF DESIGNATION OF   PREFERRED STOCK, AND THE NUMBER OF SHARES CONSTITUTING EACH SERIES AND THE   DESIGNATIONS THEREOF, MAY BE OBTAINED BY ANY SHAREHOLDER UPON REQUEST AND   WITHOUT CHARGE AT THE PRINCIPAL OFFICE OF THE CORPORATION. (Cust) (Minor)   (State) (Cust) and not as tenants in common (Minor) (State) PLEASE INSERT   SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE For value received,   hereby sell, assign and transfer unto (PLEASE PRINT OR TYPEWRITE NAME AND   ADDRESS, INCLUDING POSTAL ZIP CODE, OF ASSIGNEE) Shares of the capital stock   represented by the within Certificate, and do hereby irrevocably constitute   and appoint Attorney to transfer the said stock on the books of the   within-named Corporation with full power of substitution in the premises.   Dated: 20 Signature: Signature: Notice: The signature to this assignment must   correspond with the name as written upon the face of the certificate, in   every particular, without alteration or enlargement, or any change whatever. The   IRS requires that the named transfer agent (“we”) report the cost basis of   certain shares or units acquired after January 1, 2011. If your shares or   units are covered by the legislation, and you requested to sell or transfer   the shares or units using a specific cost basis calculation method, then we   have processed as you requested. If you did not specify a cost basis   calculation method, then we have defaulted to the first in, first out (FIFO)   method. Please consult your tax advisor if you need additional information   about cost basis. If you do not keep in contact with the issuer or do not   have any activity in your account for the time period specified by state law,   your property may become subject to state unclaimed property laws and   transferred to the appropriate state. Signature(s) Guaranteed: Medallion   Guarantee Stamp THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE   GUARANTOR INSTITUTION (Banks, Stockbrokers, Savings and Loan Associations and   Credit Unions) WITH MEMBERSHIP IN AN APPROVED SIGNATURE GUARANTEE MEDALLION   PROGRAM, PURSUANT TO S.E.C. RULE 17Ad-15. The following abbreviations, when   used in the inscription on the face of this certificate, shall be construed   as though they were written out in full according to applicable laws or   regulations: TEN COM - as tenants in common UNIF GIFT MIN ACT -   ............................................Custodian   ................................................ TEN ENT - as tenants by the   entireties under Uniform Gifts to Minors Act.........................................................   JT TEN - as joint tenants with right of survivorship UNIFTRF MIN ACT -   ............................................Custodian (until age   ................................) .............................under Uniform   Transfers to Minors Act ................... Additional abbreviations may also   be used though not in the above list.