Affymax Technologies N.V. v Diversa Corporation
[2001] APO 52
•5 October 2001
OFFICIAL NOTICE
DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS
Application : No. 703264 in the name of Affymax Technologies N.V.
Title: DNA mutagenesis by random fragmentation and reassembly
Action: Opposition under section 59 by Diversa Corporation and objections to an extension of time under regulation 5.10(2) to serve evidence in answer and a direction under regulation 5.10(1) to defer service of evidence in answer until amendments under section 104 to the specification were finalised
Decision: Issued .
Abstract
The nature of the amendments to the broad claims is such that they are likely to have a significant effect on the type of evidence that needs to be adduced and also are necessary to more “completely and fairly defined” the invention. The amendments have been diligently processed to date and the public and applicant’s interest resides in deferring the evidence in answer because of the pending amendments.
A direction was therefore provided under regulation 5.10(1)(a) to defer evidence in answer pending determination of the amendments. An extension of time was also granted under regulation 5.10(2) up until leave was granted to amend. Both the direction and extension of time under regulation 5.10 have been granted on the understanding that the preparation of evidence will be diligently progressed as much as possible while evidence has been stayed so that there are no undue delays in completing evidence in answer once amendments have been finalised.
PATENTS ACT 1990
DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS
Re:Patent Application No. 703264 by Affymax Technologies N.V and opposition under Section 59 of the Patents Act 1990 by Diversa Corporation. Objections to an extension of time to service evidence in answer under regulation 5.10(2) and to a direction under regulation 5.10(1) to defer service of evidence in answer until amendments filed under section 104 to the specification were finalised
BACKGROUND
Patent Application 703264 was filed on 17 February 1995 under the provisions of the PCT by Affymax Technologies N.V., claiming priority from a US basic application (US 198,431) filed on 17 February 1994. The Australian application was advertised accepted on 25 March 1999 and a notice of opposition was filed by Diversa Corporation (Diversa) on 23 June 1999.
The Statement of Grounds and Particulars was filed on 23 September 1999 and evidence in support was completed on 25 January 2001, after 7 extensions of time under regulation 5.10(2). As a consequence, evidence in answer was initially due on 10 April 2001. The applicant applied for, and was granted, a first extension of time up until 10 July 2001 without objection from the opponent. Within this extended period (on 18 May 2001), the applicant filed amendments under section 104. At the same time, they also sought a direction under reg 5.10(1) to defer evidence in answer until 1 month the amendments were finalised.
The delegate proposed a direction on 1 June 2001 in the following terms:
"The time for serving evidence in answer will expire 1 month after the date the Commissioner notifies the parties of the allowance or refusal of the request for leave to amend filed on 18 May 2001 or if that request is withdrawn, 1 month after the date of withdrawal.
However, as the time taken for processing the amendments is largely in the hands of the applicant, the applicant will need to obtain extensions of time (if needed) under Regulation 5.10(2) up until the applicant is advised that leave to amend has been granted."
The opponent was given 14 days in which to provide written comments or to object to this direction. On 14 June 2001, the opponent provided comments concerning the direction. The delegate reconsidered the proposed direction in light of these comments but on 10 July 2001, advised that he considered the direction still appropriate. The opponent then requested to be heard on the proposed direction.
On 10 July 2001, the applicant also requested an extension of time under regulation 5.10(2) until 10 October 2001 citing the pending amendments as the main reason for the need for further time. The opponent also objected to this extension of time request and the 2 matters were set for hearing on 29 August 2001 in Canberra. The applicant was represented by Katrina Howard of counsel, assisted by Dr Andrew Blattman, patent attorney of Spruson & Ferguson, Sydney and the opponent was represented by David Catterns QC, assisted by James Cherry, patent attorney from Freehills, Carter Smith and Beadle, Melbourne. Dr Greg Shen also attended the hearing on behalf of the opponent.
RELEVANT PROVISIONS
The Commissioner is empowered under regulation 5.10 to issue directions relating to the conduct of opposition proceedings, and to extend the time within which a party may take a step prescribed by Chapter 5, including the service of evidence in answer. Regulation 5.10 relevantly reads as follows:
The Commissioner may, on his or her own motion or on the application of a party:
(a) give a direction that is not inconsistent with the Act or these regulations for the conduct of proceedings to which this Chapter applies; or
(b) determine that a period prescribed in this Chapter (except in regulation 5.3 or 5.3AA, paragraph 5.4 (a) or subparagraph 5.8 (1) (a) (i)) is to be extended by such further period as the Commissioner reasonably allows.
The Commissioner may extend the time within which the party may take a step prescribed in this Chapter (not being a step that is taken under regulation 5.3 or 5.3AA, paragraph 5.4 (a) or subparagraph 5.8 (1) (a) (i)):
(a) on the application of a party in the approved form; and
(b) on such reasonable terms (if any) as the Commissioner specifies; and
(c) after the party has served the application on the other party.
Both these powers are subject to the requirements of subregulation 5.10(5):
(5) The Commissioner must not give a direction under subregulation (1) or grant an application under subregulation (2) or (4) unless the Commissioner:
(a) if he or she proposes to grant an application by a party — is reasonably satisfied that the other party has been notified of the application; and
(b) if he or she proposes to act on his or her own motion — ensures that the parties are notified of the proposed action; and
(c) in either case:
(i) gives the parties a reasonable opportunity to make representations concerning the application or proposed action; and
(ii) is reasonably satisfied that a direction, an extension of time or the serving of further evidence is appropriate in all the circumstances.
DECISION
Regulations 5.10(1)(b) and (2) both explicitly empower the Commissioner to extend the time for a party to serve evidence in opposition proceedings. Regulation 5.10(1)(a) also allows the Commissioner to issue a direction with regard to the conduct of proceedings. Before granting an extension under either regulations 5.10(1)(b) or (2), or making a direction under regulation 5.10(1)(a), the Commissioner has to be satisfied under regulation 5.10(5) that the extension, or direction, is “appropriate in all the circumstances”. This law has been thoroughly considered by Burchett J in Ferocem Pty Ltd v Commissioner of Patents (1994) 28 IPR 243 and more recently by Sackville J in A Goninan & Co Ltd v Commissioner of Patents (1997) 38 IPR 213. These decisions make it clear that reg. 5.10 confers a broad discretion that cannot be reduced to imperative compliance with particular requirements. It requires proper, genuine and realistic consideration of all the relevant aspects that pertain to the application.
Regulation 5.10(2) is the more commonly used provision. It allows the Commissioner to extend the time to serve evidence by a set period following an application by a party who has been unable to finalise their evidence within the original time provided. In contrast, regulation 5.10(1) is used, among other reasons, to defer evidence because of a pending action which is directly relevant to the opposition but which is outside of the immediate opposition proceedings.
The “outside” action is likely to have a significant bearing on the evidence to be adduced and is generally outside the control of the parties concerned. In these cases, a direction would be given under regulation 5.10(1)(a) to suspend the time to serve evidence until a certain length of time (generally 1 or 3 months) after the “outside” action has been finalised.
Examples of circumstances where a direction under regulation 5.10(1)(a) has been provided by the Commissioner in the past in relation to service of evidence include where there are:
a)pending court actions which are directly relevant to the opposition;
b)more than 1 opposition on a case file and the applicant needs to consolidate their evidence in answer to address all the opponents’ evidence;
c)significant amendments proposed to the specification under section 104; and
d)pending oppositions on related applications which are directly relevant to the opposition.
Of the four examples above, circumstance (c) is the most common reason for a direction under regulation 5.10(1)(a). The direction is most frequently requested by applicants in relation to evidence in answer. This is presumably because amendments are more likely to be proposed at that stage (once the applicant has completed their review of evidence in support), although similar directions are occasionally requested by opponents, for example when amendments are filed by the applicant after consideration of the statement under regulation 5.4.
The Commissioner’s long-standing practice with regard to a direction under regulation 5.10(1)(a) based on pending amendments at evidence in answer stage is that the direction would only become effective once leave has been granted to amend. Prior to this, the applicant has to apply for an extension under the provisions of regulation 5.10(2). The reason for this is that there is no time limit for the applicant to respond to an adverse report under section 104 and, should there be an adverse report, there is potential for an applicant to stall the opposition proceedings indefinitely.
In the current case, the applicant is seeking a direction under regulation 5.10(1)(a) to defer evidence in answer until amendments proposed to the specification on 18 May 2001 have been finalised. The history of the amendments is as follows:
Amendments proposed to the specification on 18 May 2001.
Amendments forwarded to the opponent on 30 May 2001 for their comments within 2 months under the provisions of regulation 10.2(7).
An adverse report issued on 17 July 2001.
Opponent provided a number of comments on 30 July 2001.
Examiner considered the opponents comments but did not issue a further adverse report.
Applicant advised in their extension of time request of 10 July 2001 that they were reviewing the specification in light of the objection to the proposed direction to determine whether it was appropriate to file further amendments
Applicant filed further amendments on 1 August 2001 in response to the adverse report issued on 17 July 2001.
Opponent was provided with a copy of these further amendments on 8 August 2001 and allowed 21 days to provide comments.
Examiner advised on 13 August 2001 that the amendments were now in order for acceptance but as the time for comments had not expired, leave would not be granted to amend.
No further comments were received within the time frame provided in the Commissioner’s letter of 8 August 2001.
Applicant advised at the hearing of 29 August 2001 that they would not be seeking further amendment.
Leave has not been granted to date and, consistent with the Commissioner’s practice, the applicant has also made a request under regulation 5.10(2) to cover the intervening period.
In their application for an extension of time under regulation 5.10(2), the applicant provided a number of reasons, of which the following is a summary :
As a result of a review of the claims, extensive amendments were proposed to the specification on 18 May 2001.
Three Australian experts were sent the voluntary amendments and asked to continue their review of the Evidence in Support on the basis of claims as proposed to be amended.
Subsequently, one of the experts had advised that they were unable to continue acting as an expert for the applicant because of ill health.
In light of the reasons given in the objection to the proposed direction, the applicants have decided to conduct a further review of the specification and claims to determine whether it is appropriate to file a further amendment.
An American expert has been identified and sent material for review.
However, the applicant conceded at the hearing that the main reason for their extension request under regulation 5.10(2) was that there were pending amendments under section 104. Most of the argument at the hearing was therefore focussed on the broad question whether it is appropriate to delay evidence in answer because of the current amendments.
The opponent referred to the following office decisions in which the same issue had been considered:
Stena Rederi Aktiebolag v Danyard A/S (1996) 34 IPR 111 in which the delegate found inter alia that an extension of time should only be granted if the amendments are non-trivial. He pointed out the impropriety of allowing the applicant to unnecessarily protract opposition proceedings by filing trivial amendments.
Exxon Chemical Patents Inc v Lubrizol Corporation (1998) 41 IPR 126 in which the delegate did not provide a direction under regulation 5.10(1) even though the amendments were non-trivial in nature [as per Stena (supra)]. In his view, there was an excessive delay in filing an amendment request. There was only one non-trivial amendment among the request to amend and there was some doubt as to whether this would have any effect on the evidence.
Airsense Technology Ltd v Vision Systems Ltd (1999) 48 IPR 483 in which the delegate found that a direction under regulation 5.10(1) was not appropriate to defer evidence in answer. His view was that the amendments neither resolved the opposition nor overcame significant grounds of the opposition. He further noted that the amendments did not dramatically affect the case the applicant had to answer. In fact, the applicant had conceded they would be able to file their evidence in answer shortly, irrespective of the proposed amendments. As a result, the delegate found that there was no justification to delay the evidence further
In contrast. the applicant referred to a recent court decision, University of Georgia Research Foundation Inc v BioChem Pharma [2001] FCA 688. In that decision, Tamberlin J found it was preferable to stay the appeal pending the determination of amendments. He considered that the patent applicant would be put to unnecessary time and expense in preparing what may well prove to be irrelevant evidence if they were required to file evidence in answer without being certain of the final form of the amendments.
The applicant referred to Tamberlin J comments in paragraph 9 in which he noted that his decision to stay accorded with:
“the general principle of avoiding a multiplicity of proceedings and the wastage of time and expense that may arise from the presentation and consideration of what may well prove to be irrelevant evidence or material,”
According to the applicant, these comments reflected the court’s view that proceedings should always be stayed if there are pending amendments. However, such a hard and fast rule does not sit well with the broad discretionary test of whether the extension is “appropriate in all the circumstances” that I must apply under regulation 5.10(5). In any case, I am not convinced that the court advocated such a hard and fast rule. Tamberlin’s comments regarding the “general principle to avoid a multiplicity of proceedings” were made after he had already decided that an order to stay was appropriate and were only a secondary factor in his decision.
Tamberlin’s primary decision was based on a consideration of the nature of the amendments. These amendments arguably involved a selection and because of this, Tamberlin J felt that it was essential that the amendments be determined to ensure that the patent under appeal is “completely and fairly defined”. I also note that even after Tamberlin J had decided that a stay was appropriate, he was not prepared to make such an order until he was satisfied that there would be no undue delay in prosecuting the opposition. This suggests that his decision to stay also had to properly balance the interests of the parties.
Of course, his assessment of a number of factors is then similar to the approaches made in the office decisions referred to above by the opponent. All these cases suggest that there are a number of factors to consider in determining whether a direction under regulation 5.10(1)(a) is appropriate where there are pending amendments, including:
the nature of the amendments;
whether there would be any undue delays in proposing (or processing) the amendments; and
the interests of the parties and the public.
I will consider each of these factors in turn.
The nature of the amendments
In the cases referred to by the parties, a decision to defer evidence was only provided where the proposed amendments were non-trivial and likely to have a significant effect on the evidence required in the main opposition. In the current case, the applicant provided a statutory declaration by Joseph Liebeschuetz, a partner in the firm of Townsend and Townsend and Crew, Palo Alto California, who has been assisting in the prosecution of the opposition. Joseph Liebeschuetz stated in his declaration that he believed that the amendments will have a significant effect on the nature and scope of the evidence in answer and will narrow and simplify the issues in dispute between the parties. Unfortunately, Mr Liebeschuetz’s declaration did not explain the basis for his opinion and therefore his declaration is, in my view, of limited value.
The applicant’s submissions at the hearing were more helpful. The applicant argued that the most significant proposed amendment to claim 1 is the addition of a screening step [step (e)] after the population of mutagenised polynucleotides were generated [see annex 1]. According to the applicant, much of the evidence in support was directed to PCR methods and the additional step was important to more clearly distinguished the claims from this prior art. The opponent, in contrast, suggested that a large number of the amended claims remain virtually identical to claims and have simply been rewritten or reformatted so as to differ only in “trivial” aspects (as per Stena Rederi v Danyard [supra]). According to the opponent, such claims have already dealt with in the opponent’s evidence and the applicant should be required to file evidence in answer at this stage.
I note that both parties agree that claim 1 as proposed to be amended is significantly narrower than the claims as accepted. Therefore, while the original evidence in support might have broadly covered the amended claims, there could be a significant portion of evidence which may not be relevant in relation to the broader claims. More importantly, the key issues of dispute are not likely to be the same between the accepted and proposed claims. As the applicant argued, many of the documents raised in evidence in support appear to be directed at PCR techniques rather than at the “shuffling method” per se. The limitations introduced by the amendments may be important to distinguish the claims from these documents and hence may fundamentally change the nature of the arguments of novelty and inventive step. This suggests that the nature of the amendments to the broad claims is likely to have an significant effect on the type of evidence that needs to be adduced and that there would be more than “a couple of paragraphs” difference between the evidence required for the different sets of claims (as submitted by the opponent).
The opponent argued that the addition of step (e) simply makes explicit what was the implicit purpose of the “shuffling method” rather than introducing a new limitation to that method. While this might be true, that implicit purpose is not a feature in the accepted claims, either explicitly or implicitly and, as noted above, the feature may be important to distinguish the claims from the prior art. Further, step (e) appears to be critical to how the “shuffling method” operates and its proposed inclusion in the broadest claims is important to more “completely and fairly defined” the invention (as per University of Georgia v BioChem Pharma [supra]).
The applicant also argued that the narrowing of claim 1 is likely to significantly narrow and simplify the issues in dispute between the parties. I accept this is likely to be true in relation to the broad independent claims because the amendments, if allowed, will result in significant narrowing of the broad independent claims. However, I note that part of the same amendment request is the addition of 60+ completely new claims (which the opponent referred to as the “species” claims). These claims include a new independent claim (claim 32) directed to a method of recombining template polynucleotides to provide a chimeric polynucleotide having a desired functional property, and a series of dependent claims which are more specific examples of applications of the broader claimed methods. None of these amendments appear to address any of the evidence in support. In fact, it is not clear to me why the applicant has chosen to add them at this stage and I do not see how the addition of so many new claims could simplify the issues. Their addition has simply resulted in an extra and unnecessary complication to the current opposition proceedings.
The opponent argued that new “species” of claims brought forward new issues in the opposition proceedings. The opponent therefore suggested that the most expeditious path forward for the opposition would be to decide on fundamental issues to the broader accepted claims and then have amendments made by the applicant once these are decided. I note that the opponent did not provide an explanation of what the new issues could be introduced by the 60+ new claims nor is it self-evident what these issues are. I therefore do not find the addition of the new claims to be the scale of problem that the opponent has suggested. In any case, I do not accept the opponent’s argument for the following reasons:
The fundamental issues have, in fact, been changed by the proposed amendments to the broader claims, in particular the addition of step (e) to claim 1. These amendments need to be finalised before the evidence is completed. There is no basis to separate the broader claims from the narrower "species" claims which are part of the same amendment request.
The opponent’s suggested approach to dealing with the opposition proceedings is piece meal. It has the potential of complicating any appeal proceedings and, in my view, would delay reaching a final outcome to these proceedings.
Having said that, I have some sympathy with an opponent having to review their evidence because of barrage of new claims after evidence in support has been finalised. However, in these circumstances, the remedy seems to me to be in asking for a variation in the award of costs at the substantive hearing rather than proceeding with evidence in answer at this stage.
The opponent was also concerned that consideration of the new “species” claims may not embrace the true or finalised intentions of the applicant with respect to what is patentable in this opposition. Instead, according to the opponent, the amendments could represent a continually moving target which creates undue burden and cost to the opponent. I note that the applicant has advised that they will not be proposing further amendments at this stage and therefore the opponent’s fears appear to be unfounded.
In any case, the applicant is entitled to exercise their right to amend the specification as they see fit. The amendments have to comply with section 102 (2)(b) that any amendment to the claims has to result in a claim falling in substance within the scope of the claims before amendments. Given this, it appears to me that any target can only get smaller rather than “move”. Of course, if there is still a residual issue of costs, this can argued at the main hearing in relation to an award of costs.
In my view, while the presence of the extra claims is an unnecessary complication, it does not alter the nature of the amendments to the broad claims that are part of the same amendment request. Because the amendments to the broad claims are likely to have a significant effect on the type of evidence that needs to be adduced and are necessary to more “completely and fairly defined” the invention, there are reasonable grounds to defer evidence pending the determination of the amendment request filed on 18 May 2001.
Is there an undue delay in proposing or processing the amendments?
While there were four months between when evidence in support was finalised and when amendments were proposed, this does not seem unreasonable given the need to review the evidence in support thoroughly before committing to particular amendments. Therefore, in my view, and in contrast to the circumstances in Exxon v Lubrizol [supra], there was not an undue delay in proposing amendments.
With regard to processing the amendments, the applicant referred to the University of Georgia Research decision [supra] and noted that Tamberlin J was only prepared to make an order to that effect if the opponent in that case gave an undertaking to the effect that its opposition to the amendment will be prosecuted in a timely and expeditious manner. In light of this decision, the patent applicant in the current opposition advised at the hearing that they were prepared, if required, to provide a similar undertaking before the Patent Office to support their application for a stay of the current opposition proceedings.
In my view, a similar undertaking is unnecessary in this case because the outstanding actions to process the amendments to the stage of granting of leave to amend are currently in the Commissioner’s control rather than the applicant’s. The applicant has advised that there will be no further amendments at this stage and so, leave to amend is ready to be granted. I note that the opponent has not ruled out opposing the amendments. However, should this occur, the Commissioner would expect all parties in that opposition (as in all oppositions) to prosecute their opposition in a timely and expeditious manner. In this case, an undertaking of the type requested by Tamberlin J seems superfluous.
The interests of the parties and the public
The interest of the applicant is obviously in deferring the evidence to allow some certainty to the final form of the amendments before presenting their evidence. The opponent argued that their interest and the public interest was against any such deferral. In this regard, they particularly relied on comments made in Genetics Institute Inc v Johnson & Johnson (1993) 27 IPR 277 in which the delegate found that the over-riding principle in an opposition proceedings is that proceedings not be unduly delayed.
In my view, having an “over-riding” principle as expounded in the Genetics Institute decision is inconsistent with both the Ferocem and Goninan decisions (supra) who suggest that the test is a “broad discretion that cannot be reduced to imperative compliance with particular requirements”. I also note that the Genetics Institute decision pre-dates both the Ferocem and Goninan decisions.
The opponent also referred to the Airsense v Vision Systems Ltd (supra) in which the delegate did not defer evidence in answer because of pending amendments. However, in contrast to the current case, the nature of the amendments proposed in Airsense v Vision Systems decision was not significant. The nature of the current amendments to the broad claims is such that they are likely to have a fundamental effect on the type of evidence that needs to be adduced and also are necessary to more “completely and fairly defined” the invention. Because of this, I believe it is in the parties’ interest as well as the public interest, to finalise the amendments before continuing with the evidence. This enables the parties to focus key issues of dispute for the substantive hearing thereby ensuring a more efficient evidentiary process and hearing. I note that this also includes evidence in reply as if the proceedings are not stayed, the opponent is likely to be in a position of preparing and serving evidence in reply that may well be irrelevant.
Given the nature of the current amendments, my view is that the advantage of being able to focus the evidence outweighs any disadvantage that might occur if evidence is delayed. In any case, I agree with the comments noted by the delegate in a letter of 10 July 2001 that staying evidence in answer will not protract the opposition as substantially as the opponent has suggested because the opposition cannot be fully determined until the amendments are finalised, whether or not the substantive proceedings are stayed. Having said that, delays can be minimised if the applicant works diligently on their evidence as much as possible during the stay so that they are in the best possible position to complete their evidence once the amendments have been finalised. I note from the reasons provided by the applicant in their application for an extension of time under regulation 5.10(2), that this appears to have been the case to date.
At the hearing, the opponent also did not rule out opposing the amendments and has made a substantial number of comments in relation to the proposed amendments under regulation 10.2(7). The possibility of a direction under regulation 5.10(1)(a) also including a section 104 opposition period was therefore canvassed at the hearing. I note that a section 104 opposition could potentially further delay the substantive opposition. However, my view is that this delay will occur with, or without, the stay of evidence. Therefore, I do not believe that the possibility of a hearing is a reason to proceed with the evidence before the amendments are finalised.
For similar reasons, I also observe that, although the presence of 60+ new claims potentially could delay proceedings if the opponent chooses to serve further evidence to address these new claims, this delay would also occur with, or without, a stay in proceedings. Therefore, I do not believe that the possibility of having to serve further evidence because of the 60+ extra claims changes the balance in favour of proceeding with evidence in answer before finalising the amendments.
In my view, the applicant and public interest reside in deferring evidence in answer until the amendments filed on 18 May 2001 have been finalised. These interests outweigh the interest of the opponent in proceeding with the evidence at this time.
Conclusion
The nature of the amendments to the broad claims is such that they are likely to have a significant effect on the type of evidence that needs to be adduced and also are necessary to more “completely and fairly defined” the invention. The amendments have been diligently processed to date and the public and applicant’s interest resides in deferring the evidence in answer because of the pending amendments.
I therefore direct under regulation 5.10(1)(a) that the time for serving evidence in answer will expire 1 month from the date the Commissioner notifies the parties of the allowance or refusal of the request for leave to amend filed on 18 May 2001 or if that request is withdrawn, 1 month after the date of withdrawal. I will be forwarding the case to the appropriate examination section for them to grant leave on the amendments as soon as possible. I also grant an extension under regulation 5.10(2) until 10 October 2001 to cover the intervening period from when evidence was due from the last extension to the date of this decision
Both the direction under regulation 5.10(1) and the extension of time under regulation 5.10(2) have been granted on the understanding that the preparation of evidence will be progressed as much as possible while evidence has been stayed so that there are no undue delays in completing evidence in answer once amendments have been finalised.
Costs
Costs would normally follow the event. In this case, while the applicant has been successful in demonstrating that evidence in answer should be deferred because of pending amendments to the broad claims, they have failed to show why it was also necessary to add 60+ new claims in the same amendment request. Such claims do not appear to address any of the evidence in support and have added an extra and unnecessary complication to proceedings. For these reasons, I do not
believe an award of costs is appropriate.
Karen Ayers
Delegate of the Commissioner of Patents
Patent attorneys for the applicant : Spruson & Ferguson, Sydney
Patent attorneys for the opponent : Freehills, Carter Smith and Beadle, Melbourne
Annex 1
Accepted claim 1:
A method for forming a mutagenised double-stranded polynucleotide from a template double-stranded polynucleotide comprising:
a) providing overlapping double-stranded fragments of the template double-stranded polynucleotide,
one or more single or double-stranded oligonucleotides, wherein said oligonucleotides comprise an area of homology and an area of heterology to the template double-stranded polynucleotide;
b) denaturing the resultant mixture of double-stranded overlapping fragments and oligonucleotides into single-stranded fragments;
c) incubating the resultant population of single-stranded fragments with a polymerase under conditions which result in the annealing of said single-stranded fragments at said areas of homology to form pairs of annealed fragments, said areas of homology being sufficient for one member of a pair to primer replication of the other thereby forming a mutagenised double-stranded polynucleotide; and
d) repeating steps (b) and (c) for at least two further cycles, wherein the resultant mixture in step (b) of a further cycle includes the mutagenised double-stranded polynucleotides from step (c) of the previous cycle and the further cycle forms further mutagenised double-stranded polynucleotides whereby the average length of the mutagenised polynucleotides increases in each cycle.
Claim 1 as proposed to be amended
A method for forming a mutagenised double-stranded polynucleotide from a template double-stranded polynucleotide comprising:
a) treating a sample comprising a template double-stranded polynucleotide under conditions which provide for the cleavage of the template polynucleotide into random overlapping double-stranded fragments of the template double-stranded polynucleotide, and providing overlapping double-stranded fragments of the template double-stranded polynucleotide,
one or more single or double-stranded oligonucleotides, wherein said oligonucleotides comprise an area of homology and an area of heterology to the template double-stranded polynucleotide;
b) denaturing the resultant mixture of double-stranded overlapping fragments and oligonucleotides into single-stranded fragments;
c) incubating the resultant population of single-stranded fragments with a polymerase under conditions which result in the annealing of said single-stranded fragments at said areas of homology to form pairs of annealed fragments, said areas of homology being sufficient for one member of a pair to primer replication of the other thereby forming a mutagenised double-stranded polynucleotide; and
d) repeating steps (b) and (c) for at least two further cycles, wherein the resultant mixture in step (b) of a further cycle includes the mutagenised double-stranded polynucleotides from step (c) of the previous cycle and the further cycle forms further mutagenised double-stranded polynucleotides whereby the average length of the mutagenised polynucleotides increases in each cycle.
e) Screening or selecting the further mutagenised double-stranded polynucleotides and thereby identifying a further mutagenised double-stranded polynucleotide having a desired functional property.
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