Ex Parte Dong et al

Patent Trial and Appeal BoardSep 25, 2012

11298234 (P.T.A.B. Sep. 25, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte FENGGAO DONG, BRIAN M. HAUGE, and CHRISTOPHER M. OGGERO __________ Appeal 2011-006323 Application 11/298,234 Technology Center 1600 __________ Before TONI R. SCHEINER, DEMETRA J. MILLS, and LORA M. GREEN, Administrative Patent Judges. MILLS, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134. The Examiner has rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). Appeal 2011-006323 Application 11/298,234 2 STATEMENT OF THE CASE Claim 7 is the only claim on appeal and reads as follows: 7. A method for assembling a DNA construct of DNA molecules with a substantially identical DNA segment in an inverted repeat of said substantially identical DNA segment, said method comprising: a) providing at least two double-stranded DNA molecules, wherein each molecule has terminal, single-stranded, DNA segments in a length of from 10 to 30 nucleotides extending from the termini; wherein terminal, single-stranded DNA segments on each double- stranded DNA molecule do not hybridize to each other; wherein a terminal, single-stranded DNA segments on a first double-stranded DNA molecule and a terminal, single-stranded DNA segments extending from a second double-stranded DNA molecule hybridize to each other to allow for specific annealing and linkage of the first and second DNA molecules in a predetermined order; and wherein said first and second double-stranded DNA molecules comprise a substantially identical DNA segment; in reverse complement order and wherein one of said double-stranded DNA molecules comprises a spacer region of DNA that is not substantially identical with DNA in the other molecule; b) incubating said DNA molecules under conditions suitable to promote the specific annealing and assembling of the DNA molecules to provide a construct of said molecules wherein said substantially identical DNA elements are arranged as inverted repeat segments; and c) wherein the spacer region is between the first and second double- stranded DNA molecules and comprises restriction endonuclease sites permitting the digestion of inverted repeat segments to facilitate DNA sequencing of said inverted repeat segments. Cited References The Examiner relies on the following prior art references: Harney US 6,495,318 B2 Dec. 17, 2002 Appeal 2011-006323 Application 11/298,234 3 Mesa et al. US 2003/0150017 A1 Aug. 7, 2003 Grounds of Rejection  Claim 7 on appeal stands rejected under 35 U.S.C. §103(a) as being unpatentable over Harney in view of Mesa. FINDINGS OF FACT The Examiner’s findings of fact are set forth in the Answer at pages 3- 6. Discussion ISSUE The Examiner concludes that Harney teaches claimed steps a) and b) and Mesa teaches the spacer of step c) (Ans. 4-5). The Examiner concludes that it would have been obvious to include Mesa’s spacer in Harney’s assembly of nucleic acid components in order to “produc[e] a construct for use in a particular application that can be generated quickly” (id. at 5). Appellants argue “Mesa…do not demonstrate or suggest restriction endonuclease sites within the spacer or intron sequence. Instead, the restriction endonuclease sites shown by Mesa… in figures 6D and 6E (see figures 6D and 6E in the evidence appendix) provide restriction endonuclease sites that are outside of the spacer (6D) or processable intron (6E).” (Reply Br. 3.) The issue is: Does the cited prior art teach or suggest a spacer region which comprises restriction endonuclease sites permitting the digestion of Appeal 2011-006323 Application 11/298,234 4 inverted repeat segments to facilitate DNA sequencing of said inverted repeat segments, as claimed? PRINCIPLES OF LAW “In rejecting claims under 35 U.S.C. § 103, the examiner bears the initial burden of presenting a prima facie case of obviousness. Only if that burden is met, does the burden of coming forward with evidence or argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed. Cir. 1993) (citations omitted). In order to determine whether a prima facie case of obviousness has been established, we consider the factors set forth in Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content of the prior art; (2) the differences between the prior art and the claims at issue; (3) the level of ordinary skill in the relevant art; and (4) objective evidence of nonobviousness, if present. Moreover, “obviousness requires a suggestion of all limitations in a claim.” CFMT, Inc. v. Yieldup Intern. Corp., 349 F.3d 1333, 1342 (Fed. Cir. 2003) (citing In re Royka, 490 F.2d 981, 985 (CCPA 1974)). ANALYSIS The claim before us requires a “spacer region” which “comprises restriction endonuclease sites permitting the digestion of inverted repeat segments to facilitate DNA sequencing of said inverted repeat segments.” (Claim 7.) Appellants urge a claim interpretation such that the restriction endonuclease sites are within the spacer. (See App. Br. 3.) Such a claim interpretation would appear to be consistent with Fig. 9 of the Specification reproduced below. Appeal 2011-006323 Application 11/298,234 5 Figure 9 of the Specification shows restriction endonuclease sites within the spacer region. This interpretation would also appear to be consistent with the Specification page 4, lines 10-15 which states that “[t]he terminal, single-stranded DNA segments for the inverted repeat construct can be designed in such a manner as to allow the production of restriction endonuclease sites within the region joining the repeats. This enhancement allows one skilled in the art to digest and cleave the DNA construct in between the repeats facilitating the sequencing of the repeat region.” We agree with Appellants’ claim interpretation. The Examiner argues that: Mesa et al. further teach the spacer between the first and second double-stranded DNA molecules that form an inverted repeat could be a functional (i.e. sliceable) intron (Figure 6E). Mesa et al. also teach that the spacer contains restriction enzymes such as Kpnl, Clal (Figure 6D and 6E). (Ans. 5.) Figure 6 D and E of Mesa are reproduced below: Appeal 2011-006323 Application 11/298,234 6 Figures 6 D and E show a spacer or intron bordered by restriction endonuclease sites. Appellants further argue that: Non-terminated single-stranded amplified fragments of DNA produced during the amplification reaction have the potential to act as primers for further amplification using either segment of the inverted repeat as template for amplification. An inverted repeat DNA structure is comprised of two DNA segments with at least a portion of each segment sharing sequence identity with the other. The non-terminated single-stranded amplified fragments of DNA produced during the amplification process will hybridize to one or the other DNA segment of the inverted repeat and will continue polymerizing during the amplification phase of the sequencing reaction until encountering a ddNTP that terminates polymerization. The resulting sequence mixture when examined will demonstrate multiple nucleotides in each position after the region of shared identity between the inverted repeat segments, making it difficult to determine the actual sequence of each DNA segment of the inverted repeat. Thus, Mesa et al. are only able to perform DNA sequencing on the DNA fragments prior to cloning and are left to infer their constructs are correct at the end of the cloning process by determining the size of fragments derived from restriction digestion. Appeal 2011-006323 Application 11/298,234 7 (Reply Br. 4.) We agree with Appellants that Mesa does not disclose a spacer region which comprises restriction endonuclease sites, i.e., with restriction endonuclease sites within the spacer region, and therefore does not suggest assembling a DNA construct with substantially identical DNA elements arranged as inverted repeats, and including a spacer region with restriction endonuclease sites permitting the digestion of inverted repeat segments to facilitate DNA sequencing of said inverted repeat segments, as claimed. Thus, the cited prior art does not teach or suggest each element claimed, and the obviousness rejection is reversed. CONCLUSION OF LAW The cited references do not support the Examiner’s obviousness rejection. REVERSED alw