USPTO Update: BCP Art Groups Discuss Restriction Practice for Nucleic Acid Molecules

    By Christopher P. Singer --

As previously reported on Patent Docs, the biotechnology and chemical pharmaceuticals technology groups at the U.S. Patent Office held their most recent quarterly customer partnership meeting on September 12, 2007.  While we were unable to attend the webcast on the day of the meeting, we will summarize a couple of the presentations (available at www.cabic.com/bcp) based on the archived slideshows.

One presentation focused on restriction requirement practice as applied to inventions claiming nucleic acid molecules.  Julie E. Burke, QAS/PM, from Technology Center 1600 presented the slideshow (available here), which provided some background on how restriction practice relating to nucleic acids has evolved, basic restriction guidelines and tests for distinctness of invention/species and examples of proper restriction practice in seven common types of claims relating to nucleic acid technology, and in which of those types of claims Applicants will be restricted to a single sequence in an application.  These seven examples include inventions where: (1) different sequence identifiers (SEQ ID NOs) describe a single invention; (2) when sequences fully overlap; (3) practice for a combination claim; (4) distinct nucleic acid molecules; (5) a single sequence identifier may encompass two or more species; (6) a claim that depends upon, but does not link plural distinct inventions; and (7) a dependent claim that cannot be restricted from its independent and intervening claim(s).

1st Example:

1.  An isolated nucleic acid comprising SEQ ID NO: 1.
2.  An isolated nucleic acid encoding a protein having SEQ ID NO: 2.

-- The specification discloses a nucleic acid comprising SEQ ID NO: 1 which contains the open reading frame for a protein having SEQ ID NO: 2.
-- Claims 1 and 2 are not distinct from each other because the claims merely define the nucleic acid using different limitations.

Restriction between Claims 1 and 2 is NOT APPROPRIATE.

2nd Example:

1.  An isolated nucleic acid molecule comprising SEQ ID NO: 1.
2.  An isolated nucleic acid molecule comprising SEQ ID NO: 2.
3.  An isolated nucleic acid molecule comprising SEQ ID NO: 3.

-- The term "comprising" permits additional nucleic acids at either end of the sequence.
-- The sequence listing shows that SEQ ID NOs: 1, 2, and 3 fully overlap with each other.
-- Assume that the sequences are:

SEQ ID NO: 1 = ATGTGCGATA
SEQ ID NO: 2 = ATGTGCGATA ATCTG
SEQ ID NO: 3 = ATGTGCGATA ATCTGTTATA

-- The nucleic acid molecules comprising SEQ ID NO: 1, 2, and 3 are not distinct from each other, as claimed.
-- As a practice tip, the PTO suggests using this claim format to refer to a single sequence in order to highlight the common region and avoid improper restriction:

1.  An isolated nucleic acid molecule comprising residues 1-10 of SEQ ID NO: 3.
2.  An isolated nucleic acid molecule comprising residues 1-15 of SEQ ID NO: 3.
3.  An isolated nucleic acid molecule comprising SEQ ID NO: 3.

Restriction to a single sequence of SEQ ID NOs: 1, 2, and 3 is NOT APPROPRIATE.

3rd Example:

1.  A kit comprising primers having SEQ ID NO: 1-100.

-- The presence of one novel and nonobvious sequence within the combination will render the entire combination allowable.
-- The combination will be searched until one nucleotide sequence is found to be allowable.
-- The order of searching will be chosen by the examiner to maximize the identification of an allowable sequence.
-- If no individual nucleotide sequence is found to be allowable, the examiner will consider whether the combination of sequences taken as a whole renders the claim allowable.

In general restriction of a combination of nucleotide molecules is NOT APPROPRIATE.

4th Example:

1.  An isolated nucleic acid comprising SEQ ID NO: 1.
2.  An isolated nucleic acid comprising SEQ ID NO: 2.

-- The specification teaches that SEQ ID NO: 1 encodes a ribosomal protein and SEQ ID NO: 2 encodes an enzyme.
-- Thus, claims 1 and 2 are distinct from each other because the mutually exclusive characteristic of SEQ ID NO: 1 is not encompassed by claim 2, and the mutually exclusive characteristic of SEQ ID NO: 2 is not encompassed by claim 1.
-- Examination of Claim 1 and 2 would be burdensome because (a) each sequence requires a different search query, and (b) prior art for one sequence is not likely to teach the other sequence.

Restriction between the nucleic acid molecules comprising SEQ ID NO: 1 and SEQ ID NO: 2 is APPROPRIATE.

5th Example:

1.  An isolated nucleic acid consisting of SEQ ID NO: 1.

-- Claim 1 refers to a single sequence identifier and uses closed transitional language "consisting of."
-- The phrase "consisting of" followed by a single sequence identifier generally limits a claim to a single fully defined nucleic acid molecule.
-- The sequence listing shows that SEQ ID NO: 1 is ATGSTAMATR, where S is G or C, M is A or C, and R is G or A.
-- Therefore SEQ ID NO: 1 actually encompasses eight patentably distinct sequences:

ATGGTAAATG
ATGGTAAATA
ATGCTAAATG
ATGCTAAATA
ATGGTACATG
ATGGTACATA
ATGCTACATG
ATGCTACATA

Restriction in this situation can include an election of species because generic claim 1 reads upon all eight disclosed species.

6th Example:

1.  An isolated nucleic acid having SEQ ID NO: 1.
2.  An isolated nucleic acid having SEQ ID NO: 2.
3.  A vector comprising the nucleic acid of claim 1 or claim 2.
4.  A host cell comprising the vector of claim 3.

-- SEQ ID NO: 1 and SEQ ID NO: 2 are distinct from each other as in the 4th Example (ribosomal protein and enzyme, respectively).
-- A linking claim must be broader in scope than the linked claims.  Thus, claims 3 and 4 are NOT linking claims because claims 3 and 4 are narrower in scope that claims 1 and 2.
-- The claims may be grouped as follows:

• Group I:  claim 1 and claims 3 and 4, in part, drawn to nucleic acid, vector, and host cell having SEQ ID NO: 1.
• Group II:  claim 2 and claims 3 and 4, in part, drawn to nucleic acid, vector and host cell having SEQ ID NO: 2.

Restriction between the two Groups is APPROPRIATE.

7th Example:

1.  An isolated nucleic acid comprising SEQ ID NO: 1.
2.  An isolated nucleic acid of claim 1, further comprising SEQ ID NO: 2 added to the 3' end.
3.  An isolated nucleic acid of claim 2, further comprising SEQ ID NO: 3 added to the 3' end.

-- Alignment of the sequences shows that SEQ ID NOs: 1, 2, and 3 are distinct from each other:

SEQ ID NO: 1 = ATGTGCGATA
SEQ ID NO: 2 = TGGTACATGC
SEQ ID NO: 3 = ATTTAGCTATT

-- Claims 1, 2, and 3 are not distinct from each other, because the claims could be alternatively presented as:

1.  A nucleic acid comprising ATGTGCGATA.
2.  A nucleic acid comprising ATGTGCGATA TGGTACATGC.
3.  A nucleic acid comprising ATGTGCGATA TGGTACATGC ATTTAGCTATT.

-- A dependent claim must incorporate all the limitations of the independent and any intervening claims.

Restriction between the nucleic acids of claims 1, 2, and 3 is NOT APPROPRIATE.

Conclusion:

While many of the issues and questions surrounding restriction practice under the New Rules regarding Claims and Continuing Application Practice will not be answered or come to light until after November 1, 2007, this presentation at least provides some guidance to Applicants with inventions that relate to nucleic acid molecules.  This guidance allows for some degree of prospective planning in application and claim drafting strategies.

Comments

[Richard]

From example 3

"The presence of one novel and nonobvious sequence within the combination will render the entire combination allowable"

I don't understand. Why are the obvious + non-novel sequences permitted to be used in the kit? Isn't that infringement? Wouldnt it matter how the sequences are used together to 'allow the claim to the combination". What if they're used one at a time?

Baffled

[Chris Singer]

Richard-
As a disclaimer to what I'm about to say, I did not listen to the PTO's webcast of this presentation, so my reasoning may not be totally on point.

I think the basis for this Example is that the claim is to the combination of sequences/primers, and for purposes of restriction, each sequence in such a combination is not considered "patentably distinct" (the invention is the combination of sequences as a kit, not each individual sequence). Thus, one novel sequence will impart novelty to the combination, sort of like a claim to a composition derives novelty (in many cases) from a new active agent, which is combined with known formulation agents.

The issues of novelty and obviousness will likely be hashed out later during prosecution, depending on the types of prior art references that exist. For example, art disclosing a kit with many of the same primers, or sequences used to target the same gene transcripts (orthologs/variants) as the recited primers, but still failing to disclose the novel primer(s) will likely become a topic of discussion between the applicant and Examiner (obviousness). Also, your point about "one at a time" is interesting but may go beyond the scope of this Example...the claim they use is to the kit itself, and not a method for using the kit.

I hope that helped at least a little. Thanks for the comment and thanks for reading.