Ex Parte Shannon

Board of Patent Appeals and Interferences

Jun 2, 2010

11179813 (B.P.A.I. Jun. 2, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte KAREN W. SHANNON
____________

Appeal 2009-011484
Application 11/179,813
Technology Center 1600
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Decided: June 2, 2010
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Before DONALD E. ADAMS, RICHARD M. LEBOVITZ, and
FRANCISCO C.PRATS, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the appeal under 35 U.S.C. § 134 by the Patent
Applicant from the Patent Examiner’s rejections of claims 32-50 in U.S.
Application 11/179,813. The Board’s jurisdiction for this appeal is under 35
U.S.C. § 6(b). We affirm-in part.

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STATEMENT OF THE CASE
All the claims in this application involve methods for producing RNA.
The steps comprise synthesizing a double-stranded cDNA, and then
transcribing the cDNA into RNA. In independent claims 32, 41, and 46, the
transcribing step occurs in the presence of reverse transcriptase (RT), an
enzyme which is used to copy RNA into DNA (Spec. 8:16-30).
Claims 32-59 are pending and stand rejected by the Examiner under
35 U.S.C. § 103(a) as obvious in view of Wang (US 5,932,451, issued Aug.
3, 1999), Gold (US 5,693,502, issued Dec. 2, 1997), and Klaveness (WO
91/06554 published May 16, 1991).
Claims 32 and 51 are representative and read as follows:
32. A method for producing RNA, comprising:
(a) converting an RNA molecule to double-stranded cDNA, wherein
one terminus of the double-stranded cDNA comprises an RNA polymerase
promoter region; and
(b) transcribing the double-stranded cDNA with an RNA polymerase
and ribonucleotides in the presence of a reverse transcriptase that is
incapable of RNA-dependent DNA polymerase activity during the
transcribing step.
51. A method for producing RNA comprising:
(a) contacting an RNA molecule with a promoter-primer in the
presence of a first polymerase having RNA-dependent DNA polymerase
activity and lacking RNaseH activity under conditions sufficient for first
strand cDNA synthesis to occur to produce a hybrid of the RNA molecule
and a first strand cDNA, wherein the promoter-primer comprises an binding
site for the RNA molecule linked to a RNA polymerase promoter sequence;
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(b) contacting the hybrid with an enzyme having RNaseH activity
under conditions sufficient to convert the complex to a double-stranded
cDNA molecule;
and
(c) transcribing the double-stranded cDNA with an RNA polymerase
and ribonucleotides in the presence of ddNTPs, wherein said reverse
transcriptase is incapable of RNA-dependent DNA polymerase activity.

STATEMENT OF THE ISSUE
Did Wang, Gold and Klaveness suggest a method in which cDNA is
transcribed into RNA in the presence of reverse transcriptase?

PRINCIPLES OF LAW
A patent may not be obtained though the invention is not
identically disclosed or described as set forth in section 102 of
this title, if the differences between the subject matter sought to
be patented and the prior art are such that the subject matter as a
whole would have been obvious at the time the invention was
made to a person having ordinary skill in the art to which said
subject matter pertains.
35 U.S.C. § 103(a).
FACTS (“F”)
Wang patent
1. Wang describes a method of preparing amplified RNA (aRNA) from
mRNA (col. 11, ll. 20-25).
2. In the first step, cDNA is synthesized from hippocampal RNA using
AMV RT (col. 11, ll. 38-42).
3. Several phenol/chloroform extractions are performed during the cDNA
synthesis (col. 11, ll. 43-44, 55-57, & 60-61).
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4. The cDNA is amplified using biotinylated primers to produce first strand
cDNA which is biotinylated at its ends (col. 11, l. 63-col. 12, l. 5).
5. In step C, the biotinylated first strand cDNA is captured on streptavidin
magnetic beads and washed four times (col. 12, ll. 14-17).
6. Double-stranded cDNA is produced from the first strand, denatured, and
the “sense strand cDNA is then separated from the solid phase bound ss
cDNA and recovered” (col. 12, ll. 25-33).
7. Wang does not describe how the cDNA is recovered.
8. Another round of amplification is performed with biotinylated primers,
and the product is captured on streptavidin magnetic beads “as described in
Step C” (col. 12, ll. 34-50).
9. After conversion to cDNA using a T7 RNA polymerase primer, the ds
DNA is purified and transcribed into aRNA with T7 RNA polymerase (col.
12, ll. 45-60).
ANALYSIS
Claims 32-50
Independent claims 32, 41, and 46 are directed to methods of
producing RNA comprising the steps of converting an RNA molecule to
double-stranded cDNA and then transcribing the cDNA “in the presence of a
reverse transcriptase.” The Examiner found that Wang described a method
of preparing cDNA with RT and transcribing it to produce RNA as in claims
32, 41, and 46, but that Wang did not teach performing transcription in the
presence of RT (Ans. 4-5). The Examiner found that Wang removed the RT
from the reaction mixture with phenol/chloroform extraction (id.). The
Examiner determined that it would have been obvious to a person of
ordinary skill in the art to modify Wang’s method by replacing the
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extraction steps with RT inhibitors as taught by Gold and Klaveness to
increase “the efficiency of the amplification process”, to avoid exposure to
hazardous phenol/chloroform, and “reduce the level background [during]
DNA amplification” (id.).
The Examiner did not establish a prima facie case of obviousness.
After the phenol/chloroform extraction steps (F3), the cDNA was amplified,
captured on magnetic beads, and washed four times (F4 & F5). Additional
processing steps were performed, including another round of magnetic bead
capture (F8). Transcription of the cDNA was accomplished in the last step
(F9). Because of the extent and number of DNA processing steps carried
out in Wang’s method after the addition of RT (F2-F8), which include at
least explicit four washes (F5 & F8), persons of ordinary skill in the art
would have reasonably concluded that the RT would have been depleted
from the reaction mixture used in the final RNA production step (App. Br.
8). Thus, even if inhibitors were added to Wang’s reaction mixture, RT
would not be present during the transcribing step, and the claim limitation of
transcribing cDNA “in the presence of a reverse transcriptase” would not be
met.
As the Examiner did not provide sound scientific reasoning or
evidence that RT would be present when cDNA was transcribed into aRNA
during Wang’s method, and such deficiency was not found to have been
addressed by Klaveness or Gold, it has not been shown that the differences
between the claimed subject matter and the prior art would have been
obvious to a person of ordinary skill in the art.

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Claims 51-59
Independent claim 51 is directed to a method for producing RNA, but
does not recite transcribing the cDNA in the presence of reverse
transcriptase. In contrast to claims 32-50, claim 51 does not require the
transcribing step to occur with the RT. As RNA transcription without RT is
taught by Wang (F9), we affirm the rejection of claim 51, and dependent
claims 52-59 which incorporate all its limitations. 37 C.F.R.
§ 41.37(c)(1)(vii).

CONCLUSION OF LAW & SUMMARY
Wang, Gold, and Klaveness did not suggest a method in which
transcribing cDNA into RNA is accomplished in the presence of reverse
transcriptase as required by claims 32, 41, and 46. We reverse the
obviousness rejection of claim 32, 41, and 46, and dependent claims 33-40,
42-45, and 47-50.
The obviousness rejection of claims 51-59 is affirmed.

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED-IN-PART

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