Ex Parte Leproust et al

Board of Patent Appeals and Interferences

Apr 30, 2007

10278274 (B.P.A.I. Apr. 30, 2007)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte ERIC M. LEPROUST and ROBERT E. WOODWORTH
__________

Appeal 2006-0592
Application 10/278,274
Technology Center 1600
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DECIDED: April 30, 2007
__________

Before TONI R. SCHEINER, DEMETRA J. MILLS, and LORA M. GREEN,
Administrative Patent Judges.

SCHEINER, Administrative Patent Judge.

DECISION ON APPEAL
Appellants appeal under 35 U.S.C. § 134 from a final rejection of
claims 1-12, 14-18, and 20, all the claims remaining in the application. The
Examiner has rejected the claims as unpatentable under 35 U.S.C. § 103(a).
We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

Appeal 2006-0592
Application 10/278,274

DISCUSSION
Claims 1 and 15, the only independent claims on appeal, are
representative of the claimed subject matter:
1. A method of producing an array of at least two different nucleic
acid ligands covalently bonded to a surface of a substrate, said method
comprising:
(a) providing a substrate having a surface displaying functional
groups;
(b) contacting blocked nucleoside monomers to at least a first
location and a second location of said surface under conditions sufficient for
said blocked nucleoside monomers to covalently bond to said surface in said
first and second locations to produce a substrate surface displaying
covalently bound blocked monomers, wherein said blocked nucleoside
monomers are blocked with a labile blocking group;
(c) contacting said surface displaying blocked nucleoside
monomers with an oxidation solution to produce an oxidized surface;
(d) washing said oxidized surface with an organic solvent having a
vapor pressure at standard temperature and pressure (STP) of less than about
13 KPa;
(e) contacting said oxidized surface with a deblocking solution that
comprises a deblocking agent in said organic solvent to produce a deblocked
surface;
(f) removing excess deblocking solution from said deblocked
surface; and
(g) reiterating steps (b) to (f) least once to produce said array of at
least two different nucleic acid ligands.

15. A method of producing an array of at least two different nucleic
acid ligands covalently bonded to a surface of a substrate, said method
comprising:
(a) providing a substrate having a surface displaying hydroxyl
functional groups;
(b) contacting DMT blocked nucleoside monomers via pulse-jet
deposition to at least a first location and a second location of said surface
under conditions sufficient for said DMT blocked nucleoside monomers to
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Application 10/278,274

covalently bond to said surface in said first and second locations to produce
a substrate surface displaying covalently bound blocked monomers;
(c) immersing said substrate in a volume of an oxidation solution
to produce a substrate having an oxidized surface;
(d) washing said oxidized surface with toluene;
(e) immersing said substrate having an oxidized surface in a
volume of a deblocking solution that comprises an acid in toluene to produce
a substrate having a deblocked surface;
(f) removing excess deblocking solution from said substrate having
a deblocked surface by dripping; and
(g) reiterating steps (b) to (f) least once to produce said array of at
least two different nucleic acid ligands.

Claims 1 and 15 recite the same method steps, in the same order, but
differ in breadth. For example, both claims require a substrate displaying
functional groups in step (a), but claim 15 requires that the functional groups
are hydroxyl groups. Both claims require blocked nucleoside monomers in
step (b), but claim 15 requires DMT-blocked nucleoside monomers. Both
claims require that the organic solvent used to wash the oxidized substrate in
step (d) is the same organic solvent used in the deblocking solution of step
(e). However, claim 1 merely requires any organic solvent that has a vapor
pressure at STP of less than about 13 KPa, while claim 15 specifies that the
organic solvent is toluene. Claim 15 specifies that the blocking agent in the
blocking solution of step (e) is an acid. Finally, both claims require that
excess deblocking solution is removed before adding additional nucleoside
monomers to the substrate, but step (f) of claim 15 specifies that the
deblocking solution is removed by dripping.

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Application 10/278,274

REFERENCES
The Examiner relies on the following references:
Earhart US 6,300,137 B1 Oct. 9, 2001
Lowe US 2002/0081597 A1 Jun. 27, 2002
Perbost US 6,171,797 B1 Jan. 9, 2001

OBVIOUSNESS
The examiner rejected claims 1-12, 14-18, and 20 under 35 U.S.C.
§ 103(a) as unpatentable over Earhart, Lowe, and Perbost.
The Examiner’s Answer refers to the Office Action mailed September
27, 2004 (Office Action) for the factual findings supporting the rejection of
record. According to the Examiner, Earhart describes a method of
producing an array of at least two different nucleic acid ligands, covalently
bonded to the surface of a substrate, wherein Earhart’s method comprises, in
pertinent part:
• Providing a substrate having a surface displaying hydroxyl
groups (Earhart Col. 4, ll. 25-32; Figs. 2 and 4A). According to
the Examiner, this meets step (a) of the claimed method (Office
Action 8).

• Contacting the substrate with DMT-blocked reactive nucleoside
monomers (i.e., monomers blocked at the 5’ end with a labile
blocking group) to allow them to covalently bond to a plurality
of areas on the substrate (Earhart Col. 4, ll. 25-32; Col. 6, ll. 31-
35; Figs. 4A and 4B). According to the Examiner, this meets
step (b) of the claimed method (Office Action 8).

• Contacting the blocked nucleoside monomers on the substrate
with an oxidation solution (Earhart Col. 7, ll. 1-4; Claim 10).
According to the Examiner, this meets step (c) of the claimed
method (Office Action 8).

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• Rinsing the oxidizing solution from the surface of the substrate
(Earhart Col. 7, ll. 7-9; Claim 10). According to the Examiner,
this particular rinsing step is performed before activating
(deblocking) the blocked monomers, and so meets the washing
aspect of step (d) of the claimed method. However, the
Examiner acknowledges that Earhart does not specify any
particular washing or rinsing agent (Office Action 9).

• Contacting the substrate displaying blocked nucleoside
monomers with an activating (deblocking) solution comprising
3% trichloroacetic acid in toluene (Earhart Col. 7, ll. 7-11;
Claim 9). According to the Examiner, this meets step (e) of the
claimed method (Office Action 8). Further, there is no dispute
that toluene is an organic solvent with a vapor pressure at STP
of less than about 13 KPa.

• Removing excess deblocking solution. That is, the Examiner
concedes that Earhart “is not explicit in disclosing that excess
deblocking solution is removed,” but argues that Earhart
“applies the deblocking solution prior to adding [ ] additional 5’
blocked nucleotide monomers, which would necessarily require
the removal of the excess deblocking solution” (Office Action
8). According to the Examiner, Earhart therefore meets the
“removal of excess deblocking solution” aspect of step (f) of
the claimed method (id.). The Examiner acknowledges that
Earhart does not disclose removing the excess deblocking
solution by allowing it to drip away (id. at 9).

• Finally, Earhart teaches reiterating steps (b) through (f) to
elongate the chains of monomers to form a polymer array
(Earhart passim; Fig. 15A). According to the Examiner, this
meets step (g) of the claimed invention.

In addition, the Examiner notes that Earhart, in discussing a “capping”
step (performed prior to each round of deblocking, and recited in certain of
the present dependent claims, e.g, present claims 4 and 16), teaches that
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“[t]he remaining steps (oxidizing, deblocking, and washing) are performed
according to conventional oligonucleotide synthesis” (Earhart Col. 16, ll.
8-10; Answer 6).
Finally, the Examiner relies on Perbost’s “method of synthesizing an
array of polynucleotide[s],” wherein “after treating the array with silanizing
agent [dissolved] in toluene, the array is washed and dried with toluene”
(Office Action 10), and Lowe’s “microarray fabrication method[ ],” wherein
“toluene [is used] for washing steps” (id.), as evidence that toluene is a
conventional washing reagent in methods of making polynucleotide arrays.
According to the Examiner, it would have been obvious to one of
ordinary skill in the art “that the reagent toluene which was already
employed as a dissolving reagent in making the activating [(deblocking)]
reagent (of Earhart [ ]) would have been useful in the ‘rinsing’ or washing
step of Earhart” (Answer 8) - corresponding to instant steps (e) and (d),
repectively.
Appellants argue that “[t]he present invention is based on the
realization that by using an organic solvent, such as toluene, to limit
evaporation, one can reduce depurination reactions on the substrate surface
and therefore obtain better arrays” (Brief 14). “In particular, the
specification discloses . . . [that] [a] feature of the subject methods is that the
deblocking solution includes an acid present in an organic solvent that has a
sufficiently low vapor pressure such that . . . depurination reactions resulting
from the increase in effective acid deblocking agent during evaporation of
the solvent from the surface do not occur to any significant extent” (id.).
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This argument is irrelevant and therefore unpersuasive. According to
the specification, depurination is due to the action of the acid deblocking
agent (Specification 16, ¶ 57), and Earhart already discloses dissolving the
acid in toluene to form the deblocking solution.
Appellants also argue that Earhart “does not disclose washing the
oxidized surface of the substrate with an organic solvent” (Brief 9), while
Lowe and Perbost “disclose that toluene may be used to wash . . . a silanized
surface . . . generated when the glass slide is being prepared and prior to
any nucleic acid deposition, while the oxidized surface of the present claims
is generated during synthesis of the nucleic acids and after the glass slide
has been initially prepared” (id. at 10). Thus, Appellants contend that “the
combined teachings of [Earhart, Lowe and Perbost] fail to teach or suggest
contacting an oxidized surface with an organic solvent, such as toluene, and
then contacting the surface with a deblocking agent in the same organic
solvent” (id. at 8).
We have carefully considered this argument, and we agree that
Perbost and Lowe only disclose using toluene in the process of silanizing a
substrate prior to building nucleotide polymers on the silanized substrate.
However, that fact does not persuade us that the Examiner’s conclusion is in
error. We note that Earhart uses toluene after each round of nucleoside
application and oxidation - thus, we find that Earhart teaches that toluene is
a suitable solvent for contact with an oxidized surface displaying bound
nucleotides. Therefore, we agree with the Examiner that it would have been
obvious, and “one of ordinary skill in the art . . . would have been motivated
to use [ ] toluene (an organic [solvent] which Earhart [ ] already employed
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[to dissolve the deblocking reagent]) . . . as a washing reagent” (Office
Action 10-11).
Finally, Appellants argue that “neither Earhart, Lowe . . . and Perbost
teach or suggest removing the deblocking solution from the deblocked
surface by dripping” (Brief 15). Again, we agree with the Examiner that
“one of ordinary skill in the art would know well enough that excess solution
could be removed by dripping the solution off the substrate” (Answer 12),
regardless of whether there are subsequent washing steps.
We conclude that the Examiner has set forth a prima facie case that
claims 1-12, 14-18, and 20 would have been obvious over the cited prior art,
which Appellants have not adequately rebutted by argument or evidence.
We therefore affirm the Examiner’s rejection of the claims under 35 U.S.C.
§ 103(a).
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 CFR § 1.136(a)(1)(iv) (2006).

AFFIRMED

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