Ex Parte Amontov et al

Board of Patent Appeals and Interferences

Jan 20, 2012

10539726 (B.P.A.I. Jan. 20, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
10/539,726 07/19/2006 Sergey Amontov CH920020037US1 8613
48062 7590 01/20/2012
RYAN, MASON & LEWIS, LLP
1300 POST ROAD
SUITE 205
FAIRFIELD, CT 06824
EXAMINER
BERTAGNA, ANGELA MARIE
ART UNIT PAPER NUMBER
1637
MAIL DATE DELIVERY MODE
01/20/2012 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte SERGEY AMONTOV,
EMMANUEL DELAMARCHE, and BRUNO MICHEL
__________

Appeal 2011-004970
Application 10/539,726
Technology Center 1600
__________

Before DEMETRA J. MILLS, ERIC GRIMES, and LORA M. GREEN,
Administrative Patent Judges.

GREEN, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134 from the
Examiner‟s rejection of claims 1, 4-14, 17, and 20-22.
1
We have jurisdiction
under 35 U.S.C. § 6(b).

1
Claim 23 is also pending, but stands withdrawn from consideration (App.
Br. 2; see also Ans. 2).
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STATEMENT OF THE CASE
Claim 1 is the only independent claim on appeal, and reads as follows:
1. A method for producing a monolayer of molecules on a surface, the
method comprising:
loading a stamp with seed molecules;
transferring seed molecules from the stamp to a flat surface, wherein
the transferring comprises transferring a fraction of the seed molecules
loaded on the stamp to the flat surface and wherein the transferring
comprises adsorbing the seed molecules to the stamp and adsorbing the seed
molecules to the flat surface, the adsorption of the seed molecules to the
stamp being stronger than the adsorption of the seed molecules to the flat
surface; and
self-completing amplification of the seed molecules via an amplifying
reaction to produce the monolayer on the flat surface, wherein self-
completing amplification of the seed molecules via an amplifying reaction to
produce the monolayer comprises producing a homogeneous area, wherein
the homogeneous area comprises a monolayer of molecules on the flat
surface, and wherein the monolayer of molecules on the flat surface has no
diffusive seed molecules that can relocate and destroy amplification
accuracy.

The following grounds of rejection are before us for review:
I. Claims 1, 4-7, 9, 10, 14, 17, and 20-22 stand rejected under 35
U.S.C. § 102(b) as being anticipated by Church.
2

II. Claim 8 stands rejected under 35 U.S.C. § 103(a) as being rendered
obvious by the combination of Church and Richter.
3

III. Claims 11 and 13 stand rejected under 35 U.S.C. § 103(a) as being
rendered obvious by the combination of Church and Korlach.
4

2
Church, US 6,432,360 B1, issued Aug. 13, 2002.
3
Richter et al., Nanoscale Palladium Metallization of DNA, 12 ADVANCED
MATERIALS 507-510 (2000).
4
Korlach et al., US 2003/0044781 A1, issued Mar. 6, 2003.
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IV. Claim 12 stands rejected under 35 U.S.C. § 103(a) as being
rendered obvious by the combination of Church and Mian.
5

We reverse.
ISSUE
Does the preponderance of evidence of record support the Examiner‟s
conclusion that Church teaches a method of producing a monolayer of
molecules on a surface, wherein producing the monolayer comprises
producing a homogeneous area, wherein the homogeneous area comprises a
monolayer of molecules on the flat surface, as required by independent
claim 1?

FINDINGS OF FACT
FF1. The Specification teaches that the “invention generally relates to
surface treatment and particularly relates to methods for coating surface
areas with molecular monolayers” (Spec.
6
1).
FF2. The Specification discloses:
In accordance with the present invention, there is now provided
a method for producing a monolayer of molecules on a surface,
the method comprising: loading a stamp with seed molecules;
transferring seed molecules from the stamp to the surface; and,
amplifying the seed molecules via an amplifying reaction to
produce the monolayer.

(Id. at 6.)

5
Mian et al., US 5,686,271, issued Nov. 11, 1997.
6
All references to the Specification are to the Specification dated July 19,
2006.
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FF3. Figure 1 of the instant disclosure is reproduced below:

“Figure 1 is a block diagram of a surface treatment process embodying the
present invention” (id. at 9).
FF4. The Specification teaches:
Referring . . . to Figure 1, in a preferred embodiment of the
present invention, there is provided a method for forming a
molecular monolayer on surface 1. The method comprises
transferring a seed layer of molecules 3,4 to the surface via a
stamp 2. The seed layer comprises a molecular monolayer
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sparsely populated with molecules 3,4. The seed layer
deposited on the surface 1 is then grown by an amplifying
reaction to complete the monolayer on the surface 1. Different
types of molecules 3,4 may be disposed on different active
zones 5,6 of the stamp 2. This technique solves the problem of
incomplete molecular transfer from the stamp 2 by transferring
at least a catalytic amount of molecules and thereafter
amplifying the molecules printed on the surface 1 to saturation
density.

(Id. at 10.)
FF5. As to the limitation that producing “the monolayer comprises
producing a homogeneous area, wherein the homogeneous area comprises a
monolayer of molecules on the flat surface,” the Examiner finds:
Church also teaches an embodiment of the method that
produces a monolayer wherein all of the nucleic acids
comprising the monolayer are the same length (see column 21,
lines 34-57). Also, it is noted that the monolayers resulting
from the amplification reactions of Church consist of one type
of molecule (nucleic acid or protein). Thus, Church teaches
homogeneous monolayers as required by claim 1.

(Ans. 5.)
FF6. The Examiner further explains:
[T]he replica transfer and amplification steps taught by Church
at columns 8-15 result in a self-completing amplification
reaction that produces a homogeneous area comprising a
monolayer of nucleic acid molecules having the same length
attached to a flat surface. As noted by Appellant at pages 5-6
[of the Appeal Brief], the arrays produced by the method of
Church are randomly patterned, but Church teaches that the
arrays are “randomly patterned” with respect to the identity of
the molecules at each discrete location and further teaches that
the array surface is patterned such that different molecules are
present in different features (see, for example, column 1, line 64
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- column 2, line 19). Thus, the production of a randomly
patterned array does not preclude the formation of a
homogeneous area comprising a monolayer on the flat surface
. . . .

(Id. at 11.)
FF7. Church teaches:
The invention provides a method of producing a plurality
of a nucleic acid array, comprising, in order, the steps of
amplifying in situ nucleic acid molecules of a first randomly-
patterned, immobilized nucleic acid array comprising a
heterogeneous pool of nucleic acid molecules affixed to a
support, transferring at least a subset of the nucleic acid
molecules produced by such amplifying to a second support,
and affixing the subset so transferred to the second support to
form a second randomly-patterned, immobilized nucleic acid
array, wherein the nucleic acid molecules of the second array
occupy positions that correspond to those of the nucleic acid
molecules from which they were amplified on the first array, so
that the first array serves as a template to produce a plurality.

(Church, col. 1, ll. 43-55.)
FF8. Church defines
the terms “randomly-patterned” or “random” . . . [as] a non-
ordered, non-Cartesian distribution (in other words, not
arranged at pre-determined points along the x- and y axes of a
grid or at defined „clock positions‟, degrees or radii from the
center of a radial pattern) of nucleic acid molecules over a
support, that is not achieved through an intentional design (or
program by which such a design may be achieved) or by
placement of individual nucleic acid features. Such a
“randomly-patterned” or “random” array of nucleic acids may
be achieved by dropping, spraying, plating or spreading a
solution, emulsion, aerosol, vapor or dry preparation
comprising a pool of nucleic acid molecules onto a support and
allowing the nucleic acid molecules to settle onto the support
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without intervention in any manner to direct them to specific
sites thereon.

(Id. at col. 1, l. 64-col. 2, l. 11.)
FF9. Church defines
the term “array” . . . [as] a heterogeneous pool of nucleic acid
molecules that is distributed over a support matrix; preferably,
these molecules differing in sequence are spaced at a distance
from one another sufficient to permit the identification of
discrete features of the array.

(Id. at col. 2, ll. 15-19.)
FF10. Church defines
the term “heterogeneous” . . . [as] a population or collection of
nucleic acid molecules that comprises a plurality of different
sequences; it is contemplated that a heterogeneous pool of
nucleic acid molecules results from a preparation of RNA or
DNA from a cell which may be unfractionated or partially-
fractionated.

(Id. at col. 2, ll. 20-35.)
FF11. Church provides the following embodiments:
In a preferred embodiment, the method further comprises
the steps after contacting the amplified sequences of the
chromosome with a support of amplifying the molecules of the
first array by PCR and contacting the first array with a second
support, such that at least a subset of the amplified nucleic acid
molecules are transferred to the support, and covalently affixing
the nucleic acid molecules to the second support to form a
second immobilized nucleic acid array, wherein the positions of
the members of the second array correspond to their positions
on the first array.
Another aspect of the present invention is a method for
localizing RNA molecules within a cell or a tissue section,
comprising providing an immobilized nucleic acid array,
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comprising the steps of providing an immobilized cell or a
tissue section, reverse transcribing RNA molecules of the cell
or tissue section to produce an array of features comprising
reverse transcripts, contacting the array with a support, such
that at least a subset of reverse transcripts are retained by the
support, covalently affixing the reverse transcripts to the
support to form an immobilized nucleic acid array, and
localizing the RNA molecules, comprising identifying the
features of the array, wherein the positions of features on the
array correspond to the positions of the RNA molecules in the
cell or tissue section.

(Id. at col. 5, ll. 31-55.)
FF12. Church teaches that the method is drawn to basically five steps: “1)
providing a pool of nucleic acid molecules; 2) plating or other transfer of the
pool onto a solid support; 3) in situ amplification; 4) replica printing of the
amplified nucleic acids; and 5) identification of features” (id. at col. 8, ll. 25-
29).
FF13. Example 1 of Church is drawn to production of a nucleic acid array
(see id. at col. 8, ll. 39-40). In step 2:
The nucleic acid pool is diluted (“plated”) out onto a
semi-solid medium (such as a polyacrylamide gel) on a solid
surface such as a glass slide such that amplifiable molecules are
0.1 to 100 micrometers apart. Sufficient spacing is maintained
that features of the array do not contaminate one another during
repeated rounds of amplification and replication. It is estimated
that a molecule that is immobilized at one end can, at most,
diffuse the distance of a single molecule length during each
round of replication. Obviously, arrays of shorter molecules are
plated at higher density than those comprising long molecules.

(Id. at col. 9, ll. 26-36.)
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FF14. Column 21, lines 34-57 of Church, relied upon by the Examiner,
teaches:
A method provided by the invention for the easy
orientation of the nucleic acid molecules of a set of arrays
relative to one another is “array templating”. A homogeneous
solution of an initial library of single-stranded DNA molecules
is spread over a photolithographic all-10-mer ss-DNA oligomer
array under conditions which allow sequences comprised by
library members to become hybridized to member molecules of
the array, forming an arrayed library where the coordinates are
in order of sequence as defined by the array. For example, a 3'-
immobilized 10-mer (upper strand), binds a 25-mer library
member (lower strand) . . . .
Covalent linkage of the 25-mer sequence to the support,
amplification and replica printing are performed by any of the
methods described above. Further characterization, if required,
is carried out by SBH, fluorescent dNTP extension or any other
sequencing method applicable to nucleic acid arrays, such as
are known in the art. This greatly enhances the ability to
identify the sequence of a sufficient number of oligomer
features in the replicated array to make the array useful in
subsequent applications.

ANALYSIS
The issue in this case turns on the interpretation of the phrase
“wherein self-completing amplification of the seed molecules via an
amplifying reaction to produce the monolayer comprises producing a
homogeneous area, wherein the homogeneous area comprises a monolayer
of molecules on the flat surface,” as required by claim 1.
We recognize that during prosecution before the Office, claims are to
be given their broadest reasonable interpretation consistent with the
Specification as it would be interpreted by one of ordinary skill in the art. In
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re American Academy Of Science Tech Center, 367 F.3d 1359, 1364 (Fed.
Cir. 2004). Claim language, however, “should not [be] treated as
meaningless.” Bicon, Inc. v. Straumann Co., 441 F.3d 945, 951 (Fed. Cir.
2006). Moreover, “the claims themselves provide substantial guidance as to
the meaning of particular claim terms.” Phillips v. AWH Corp., 415 F.3d
1303, 1314 (Fed. Cir. 2005) (en banc).
We interpret the phrase “wherein self-completing amplification of the
seed molecules via an amplifying reaction to produce the monolayer
comprises producing a homogeneous area, wherein the homogeneous area
comprises a monolayer of molecules on the flat surface,” in light of the
teachings of the Specification, as requiring the amplification to completely
fill in with a monolayer of molecules a specified area on the flat surface
seeded by the stamp. That is, the amplification reaction at a specified area
of the flat surface runs to completion, such that the flat surface is saturated
by the molecules to produce a monolayer that completely covers the
specified area of the flat surface (see, e.g. App. Br. 6 “Applicants also
submit that self-completing amplification cannot exist in a setting such as
taught by Church because the surface in a gel is larger than on a flat surface
such that it would not be possible to saturate the gel matrix and run into a
self-completion.”). Thus, in the claimed process, the placement of the seed
molecule is not maintained from the stamp to the surface, as the seed
molecule becomes only one of the molecules that make up the monolayer,
and is indistinguishable from the other molecules that make up the
monolayer.
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Appellants assert that the “randomly-patterned” array of Church,
wherein the molecules are “allowed to settle on the support wherever they
may fall does [sic] is wholly distinct from the . . . claimed step of producing
a homogeneous area comprising a monolayer of molecules” (App. Br. 6).
We agree. As taught by Church, the positions of the nucleic acid molecules
of the second array occupy positions that correspond to those of the nucleic
acid molecules from which they were amplified on the first array (FF7; see
also FF11 (teaching that the members of the second array correspond to their
positions on the first array)). Thus, in the array of Church, when the array is
replicated onto a second surface, the amplification reaction is not run to
completion so as to saturate a specified area of a flat surface, such that one
loses the position of the original seed molecules. Thus, Church does not
teach each and every limitation of the claimed method, see Karsten Mfg.
Corp. v. Cleveland Golf Co., 242 F.3d 1376, 1383 (Fed. Cir. 2001) (“To
anticipate, every element and limitation of the claimed invention must be
found in a single prior art reference, arranged as in the claim”), and we are
compelled to reverse the rejection.

CONCLUSION OF LAW
We conclude that the preponderance of evidence of record does not
support the Examiner‟s conclusion that Church teaches a method of
producing a monolayer of molecules on a surface, wherein producing the
monolayer comprises producing a homogeneous area, wherein the
homogeneous area comprises a monolayer of molecules on the flat surface,
as required by independent claim 1.
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We thus reverse the rejection of Claims 1, 4-7, 9, 10, 14, 17, and 20-
22 stand rejected under 35 U.S.C. § 102(b) as being anticipated by Church.
As Richter, Korlach, and Mian were not relied upon by the Examiner
to remedy the deficiencies of Church (see Ans. 7-10), we also reverse the
rejection of:
claim 8 under 35 U.S.C. § 103(a) as being rendered obvious by the
combination of Church and Richter;
claims 11 and 13 under 35 U.S.C. § 103(a) as being rendered obvious
by the combination of Church and Korlach; and
claim 12 under 35 U.S.C. § 103(a) as being rendered obvious by the
combination of Church and Mian.

REVERSED

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