Appeal No. 2006-2194 Page 6
Application No. 09/866,925
Francois1 teaches that “oligonucleotides consisting of two oligimer
sequences linked by a chemical tether can also bind two single-stranded
noncontiguous sites in RNA with secondary structures.” Id. at page 65, column
2. Thus, it would have been obvious to thus use a computer design the
oligonucleotide consisting of two oligomer sequences (reads on a pair of non-
adjacent DNA sequences” and then predict its binding to the noncontiguous sites
of the RNA (reads on two regions of an RNA molecule), which appears to be all
that is required by claim 20.
Claim 22 recites “detecting [by computer] changes in expression of
different gene collections in a genome that result in the level of control
sequences caused by exogenous stimuli.” At first blush, this claim appears to
have many issues.
One issue appears to be that the claim is indefinite under 35 U.S.C. § 112,
second paragraph. It is unclear if the exogenous stimuli is physical or
computational. If it is physical, it is unclear how that step is being performed in
the context of the computational method.
If the exogenous stimuli is computational, the claim would not appear to
meet the written description and/or enablement requirements of 35 U.S.C. § 112,
first paragraph.2 As discussed in the background, the specification teaches a
1 Francois et al. (Francois), Recognition and Cleavage of Singgle-Stranded DNA Containing
Hairpin Structures by Oligonucleotides Forming Both Watson-Crick and Hoogsteen Hydrogen
Bonds,” Biochemistry, Vol. 34, pp. 65-72 (1995), first page only.
2 We recognize that the written description and enablement requirements of 35 U.S.C. § 112, first
paragraph, are distinct, and should be analyzed separately. See Vas-Cath Inc. v. Mahurkar, 935
F.2d 1555, 1563-64, 19 USPQ2d 1111, 1116-17 (Fed. Cir. 1991) (noting that the requirement for
written description under the first paragraph of section 112 is separate and distinct from the
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