Paradigm Patent Documents

Patent applications for Arabidopsis bulk sequences  made by Paradigm Genetics Inc. (Icoria Inc. – Monsanto Co.)

The following is an example of one of the 9 patent applications by Paradigm Genetics Inc (now Icoria Inc.). The ‘940 A1 application has the earliest filing date of the 9 applications. All 9 applications are listed as “abandoned” on the USPTO website database.  However, one must remember that “abandoned” does not necessarily mean that Icoria or now Monsanto Co. have actually given up their attempts at patenting all or part of the claims. It may still be possible that future continuations, continuations-in-part, or divisional applications might appear as patent document publications.

Patent or Publication No. Title, Independent Claims and Summary Applicant
US 2001/44940 A1

  • Earliest priority – 27 Jan 2000
  • Filed – 26 Jan 2001
  • Granted -Abandoned
  • Expected expiry -N/A

PAIR link

Title – Expressed sequences of Arabidopsis thaliana

Claim 1
A nucleic acid comprising
a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911,
or a fragment thereof.
Claim 5
A nucleic acid comprising:
an ATG start codon;
an optional intervening sequence;
a coding sequence capable of hybridizing under stringent conditions as set forth in SEQ ID NO:1 to 911;
and an optional terminal sequence, wherein
at least one of said optional sequences is present, and wherein:
ATG is a start codon;
said intervening sequence comprises one or more codons in-frame with said coding sequence, and is free of in-frame stop codons;
and said terminal sequence comprises one or more codons in-frame with said coding sequence, and a terminal stop codon.
Claim 14
A transgenic plant comprising
an exogenous nucleic acid, wherein
said nucleic acid comprises
transcription regulatory sequences operably linked to a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911 or a fragment thereof, wherein
said sequence is expressed in cells of said plant.
Claim 24
A genetically modified cell, comprising
an exogenous nucleic acid, wherein
said nucleic acid comprises
transcription regulatory sequences operably linked to a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911, wherein
said sequence is expressed in cells of said plant.
Claim 26
A nucleic acid array comprising
at least one nucleic acid as set forth in SEQ ID NO:1-911 stably bound to a solid support.
Claim 27
An array comprising
at least one polypeptide encoded by a nucleic acid as set forth in SEQ ID NO:1-911, stably bound to a solid support.

The claims are generally drawn to:

  • A nucleic acid comprising
    • a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911,
    • or a fragment thereof.

Essentially, this claims the ESTs themselves, any homologues, allellic variants,..etc. and may cover the equivalent gene in other organisms. The “comprising” language in this claim makes the claim’s scope so broad that there almost certainly will be existing prior art.  Stringent hybridisation conditions are defined as “50°C or higher and 0.1×SSC”.  “A fragment thereof” is not clear in itself and could imply a 2bp sequence! The application arguably provides the following guidance “Preferably, hybridization is performed using at least 15 contiguous nucleotides…”.

  • A nucleic acid comprising:
    • an ATG start codon;
    • an optional intervening sequence;
    • a coding sequence capable of hybridizing under stringent conditions as set forth in SEQ ID NO:1 to 911;  and
    • an optional terminal sequence, wherein
      • at least one of the optional sequences is present, and
      • wherein: ATG is a start codon;
      •  the intervening sequence comprises
        • one or more codons in-frame with the coding sequence, and is free of in-frame stop codons; and
      • the terminal sequence comprises one or more codons in-frame with the coding sequence, and
      • a terminal stop codon.

This essentially claims DNA constructs or vectors containing the ESTs, or part of the ESTs, or their homologues, and any sequences from other organisms that satisfies the stringency conditions above (since no organism limits are made here!).  It is hard to imagine that none of these sequences would hybridize to DNA from other organisms (even human sequences!). How can an examiner be certain that any of these sequence claims are not invalidated by prior art (particularly other bulk sequence claims for rice and maize ESTs??!)

  • A transgenic plant comprising
    • an exogenous nucleic acid, wherein said nucleic acid comprises
      • transcription regulatory sequences operably linked to a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911 or a fragment thereof, wherein said sequence is expressed in cells of said plant.

This time the claim is towards a transgenic plant transformed with the claimed DNA. Arguably, the “operably linked” phrase mayallow a work around of at least part of this claim: by the use of transactivation technology (see PCT publication WO 01/21781).

  • A genetically modified cell, comprising
    • an exogenous nucleic acid, wherein said nucleic acid comprises
      • transcription regulatory sequences operably linked to a sequence capable of hybridizing under stringent conditions to a sequence set forth in SEQ ID NO:1 to 911, wherein said sequence is expressed in cells of said plant.

Similar to the previous claim, for cells transformed with the claimed DNA. Again, consider transactivation technology and PCT publication WO 01/21781. Interestingly, the qualifier “plant” is not used to describe the cell. Does this imply that this claim covers animal, fungal, and protist cells, whereas the previous did not cover transgenic animals?

  • A nucleic acid array comprising
    • at least one nucleic acid as set forth in SEQ ID NO:1-911 stably bound to a solid support.

Attempts to cover use in microarray technologies. What does stably bound mean? What if the bond is reversible?

  • An array comprising
    • at least one polypeptide encoded by a nucleic acid as set forth in SEQ ID NO:1-911, stably bound to a solid support.

As above for DNA arrays, in this case for peptide arrays.  However, no mention is made of peptide length – this could mean anything from full length peptides to 2-amino acids! (There is no specification for this in the application)

Original Applicant:

PARADIGM GENETICS, INC.,
104 ALEXANDER DRIVE,
BUILDING 2,
PO BOX 14528, RTP,
NC, 277094528.

Which recently became:

Icoria
108 Alexander Drive
P. O. Box 14528
Research Triangle Park
North Carolina 27709-4528
Phone: 919-425-3000
Fax: 919-544-8094)

Monsanto has since acquired selected agricultural genomics assets from Icoria:

Monsanto Company
800 North Lindbergh Boulevard
St. Louis, MO-63167
(314) 694-1000

We would suggest that interested parties should try to contact:

Charles W Burson  Executive Vice President, General Counsel, and Secretary
Monsanto Company
800 North Lindbergh Boulevard
St. Louis, Missouri 63167-7843

Telephone: 314-694-1000

Remarks Given the broad scope of the claims above, it is not expected that Paradigm’s 9 bulk sequence applications would produce a granted patent over all the sequences listed.  Instead Paradigm’s goal is probably to establish a priority date for all the sequences, and the opportunity to select from this group sequences that may become valuable and can be patented in divisional, CIPs, and continuation applications in the future.

This unfortunately introduces uncertainty for those working on these or related genes.  Since it is virtually impossible to tell which genes will be the focus of future active applications.  It is also possible that future efforts by others to study the function of these genes may produce results that influence’s Paradigm’s/Icoria’s/Monsanto’s decision on which gene(s) to continue patenting efforts.  Future research that shows gene ‘X’ to be useful (valuable) might be sufficient to initiate further applications for that gene in divisional applications.

The remaining 8 applications are:

Application No.

Document Title

Sequences Claimed

US 2002/23280 Expressed sequences of arabidopsis thaliana 999
US 2002/23281 Expressed sequences of arabidopsis thaliana 999
US 2002/40489 Expressed sequences of arabidopsis thaliana 999
US 2002/40490 Expressed sequences of arabidopsis thaliana 999
US 2002/59663 Expressed sequences of arabidopsis thaliana 999
US 2002/62014 Expressed sequences of arabidopsis thaliana 999
US 2002/142319 Expressed sequences of arabidopsis thaliana 900
US 2003/115639 Expressed sequences of arabidopsis thaliana 999


The 8 remaining applications are:

Publication No. Application No. Filing Date Publication Date

Document Title

Sequences Claimed

US 2002/23280 60/178,502 26 Jan 2001 21 Feb 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/23281 60/178,472 26 Jan 2001 21 Feb 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/40489 60/178,503 26 Jan 2001 04 Apr 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/40490 60/178,512 26 Jan 2001 04 Apr 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/59663 60/178,506 26 Jan 2001 16 May 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/62014 60/178,480 26 Jan 2001 23 May 2002 Expressed sequences of arabidopsis thaliana 999
US 2002/142319 60/148,784 07 Aug 2001 03 Oct 2002 Expressed sequences of arabidopsis thaliana 900
US 2003/115639 60/178,466 26 Jan 2001 19 Jun 2003 Expressed sequences of arabidopsis thaliana 999