AU1006201A - Recombinational cloning using engineered recombination sites - Google Patents

Description

P/00/011 Regulation 3.2

AUSTRALIA

Patents Act 1990 COMPLETE SPECIFICATION FOR A DIVISIONAL PATENT

ORIGINAL

i "TO BE COMPLETED BY APPLICANT Name of Applicant: INVITROGEN CORPORATION Actual Inventors: James L. Hartley and Michael A. Brasch Address for Service: CALLINAN LAWRIE, 711 High Street, Kew, Victoria 3101, Australia Invention Title: RECOMBINATIONAL CLONING USING ENGINEERED RECOMBINATION SITES The following statement is a full description of this invention, including the best method of performing it known to me:- 02/01/01,mgdiv cov1,1 WO 96/40724 PCT/US96/10082 Recombinational Cloning Using Engineered Recombination Sites Background of the Invention Field of the Invention 10 The present invention relates to recombinant DNA technology. DNA and vectors having engineered recombination sites are provided for use in a recombinational cloning method that enables efficient and specific recombination of DNA segments using recombination proteins. The DNAs, vectors and 1* :methods are useful for a variety of DNA exchanges, such as subcloning of DNA, 15 in vitro or in vivo.

S; *4 RelatedArt Site specfic recombinases. Site specific recombinases are enzymes that are present in some viruses and bacteria and have been characterized to have both endonuclease and ligase properties. These recombinases (along with associated 20 proteins in some cases) recognize specific sequences of bases in IMA and exchange the DNA segments flanking those segments. The recombinases and associated proteins are collectively referred to as "recombination proteins" (see, V.e Landy, Current Opinion in Biotechnology 3:699-707 (1993)).

Numerous recombination systems from various organisms have been r described. See, Hoess et al., Nucleic Acids Research 14(6):2287 (1986); bremski et al., J. Biol. Chem.261(l):391 (1986); Campbell,

J.

WO 96/40724 P TU9/08 -2- Bacteriol 174(23):7495 (1992); Qian et al.,J S Bo. Chem. 267(1l 0:7794 (1992); Arak JMo0. Biol. 225(l):25 (1992); Maeser and Kahunann (199 1) Mo!0.

Gen. Genet. 230:170-176).

Many of these belong to the integrase family Of recombinases (Argos eta!. EMBOJ 5:433-440 (1986)). Perhaps the best studied of these are the Integrase/att system from bacteriophage I. (Landy, A. Current opinions in Genetics and Devel. 3:699-707 (1993)), the Cre/loxp system from bacteriophage P1I (Hoess and Abremsi (1990) In Nucleic.Acids and Molecular Biology, vol. 4.

Eds.: Eckstein and Lilley, Berlin-Heideberg: Springer-Verlag; pp. 90-109), and the FLP/PRT system from the-Saecharomyces cerevisiae 2 ;L circle plasmid (Broach et a. Cell 29:227-234 (1982)).

While these recombination system have been characterized for particular organisms, the related art has Only taught using recombinant DNA flanked by recombination sites, for in vivo recombination.

Patent No. 4,673,640) discloses the in vivo use of.

recoinbinase to recombine a protein producing DNA segment by enzymatic sitespecific recombinaion using wild-type recombination sites attB and attp.

flasan and Szybalski (Gene 56:145.151 (1987)) discloses the use of X Int recombinase In vivo for intramolecular recombination between wild type attP 14and aftB sites which flank a promoter. Because the orientations ofthssiear inverted relative to each Other, this Causes an irreversible fipnofthe proter region relative to the gene of interest.

Palazzolo et Gene 88:25-36 (1990), discloses phage lambda vectors having bacteriopae X. arms that contain restriction sites positioned outside a i~'4 Cloned DNA sequence and between wild-type loxP sites. Infection ofE ccli Us

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that express the Crc recombinase with these phage vectors results in recombination between the loxP sites and the in vivo excision of the plasmid replicon, including the cloned cDNA.

P6sfai et al. (Nuc!. Acids Res. 22:23 92-2398 (1994)) discloses a method for inserting into genomic DNA partial expression vectors having a selectable RA44// makerflanked by two wild-type FRT recognition sequences. FLP site-specific ((~~ombinse as Present in the cells is used to integrate the vectors into the WO 96/40724 PCT/US96/10082 -4-

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1 20 Devine and Boeke Nucl. Acids Res. 22:3765-3772 (1994), discloses the construction of artificial transposons for the insertion of DNA segments, in vitro, into recipient DNA molecules. The system makes use of the integrase of yeast TYI virus-like particles. The DNA segment of iaterest is cloned, using standard methods, between the ends of the transposon-like element TYI. In the presence of the TY1 integrase, the resulting element integrates randomly into a second target DNA molecule.

DNA cloning. The cloning of DNA segments currently occurs as a daily routine in many research labs and as a prerequisite step in many genetic analyses.

The purpose of these clonings is various, however, two general purposes can be considered: the initial cloning of DNA from large DNA or RNA segments (chromosomes, YACs, PCR fragments, mRNA, etc.), done in a relative handful of known vectors such as pUC, pGem, pBlueScript, and the subcloning of these DNA segments into specialized vectors for functional analysis. A great deal of time and effort is expended both in the initial cloning of DNA segments and in the transfer of DNA segments from the initial cloning vectors to the more specialized vectors. This transfer is called subcloning.

The basic methods for cloning have been known for many years and have changed little during that time. A typical cloning protocol is as follows: digest the DNA of interest with one or two restriction enzymes; gel purify the DNA segment of interest when known; prepare the vector by cutting with appropriate restriction enzymes, treating with alkaline phosphatase, gel purify etc., as appropriate; ligate the DNA segment to vector, with appropriate controls to estimate background of uncut and self-ligated vector, introduce the resulting vector into an E. coli host cell; pick selected colonies and grow small cultures overnight; make DNA minipreps; and analyze the isolated plasmid on agarose gels (often after diagnostic restriction enzyme digestions) or by PCR.

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WO 96/40724 PCT/US96/10082 The specialized vectors used for subcloning DNA segments are functionally diverse. These include but are not limited to: vectors for expressing genes in various organisms; for regulating gene expression; for providing tags to aid in protein purification or to allow tracking of proteins in cells; for modifying the cloned DNA segment generating deletions); for the synthesis of probes riboprobes); for the preparation of templates for DNA sequencing; for the identification of protein coding regions; for the fusion of various protein-coding regions; to provide large amounts of the DNA of interest, etc. It is common that a particular investigation will involve subcloning the DNA segment of interest into several different specialized vectors.

As known in the art, simple subclonings can be done in one day the DNA segment is not large and the restriction sites are compatible with those of the subcloning vector). However, many other subclonings can take several weeks, especially those involving unknown sequences, long fragments, toxic genes, unsuitable placement of restriction sites, high backgrounds, impure enzymes, etc. Subcloning DNA fragments is thus often viewed as a chore to be done as few times as possible.

Several methods for facilitating the cloning of DNA segments have been S. described, as in the following references.

20 Ferguson, et al. Gene 16:191 (1981), discloses a family of vectors for subcloning fragments of yeast DNA. The vectors encode kanamycin resistance.

Clones of longer yeast DNA segments can be partially digested and ligated into the subcloning vectors. If the original cloning vector conveys resistance to ampicillin, no purification is necessary prior to transformation, since the selection 25 will be for kanamycin.

Hashimoto-Gotoh, et al. Gene 41:125(1986), discloses a subcloning vector with unique cloning sites within a streptomycin sensitivity gene; in a streptomycin-resistant host, only plasmids with inserts or deletions in the dominant sensitivity gene will survive streptomycin selection.

Accordingly, traditional subcloning methods, using restriction enzymes Sand ligase, are time consuming and relatively unreliable. Considerable labor is xpended, and if two or more days later the desired subclone can not be found WO 96/40724 WO 9640724PCT/1JS96/10082 -6among the candidate plasnids, the entire process must then be repeated with alternative conditions attempted. Althoughi site specific recombinases have been used to recombine DNA in vivo, the successful use of such enzymes in vitro was expected to suffer from several problems. For example, the site specificities and efficiencies were expected to differ in vitro; topologically-linked products were expected; and the topology of the DNA substrates and recombination proteins was expected to differ significantly in vitro (see, Adams et a, J MoU BioL 226:661-73 (1992)). Reactions that could go on for many hours in vivo were expected to occur in significantly less time in vitro before the enzymes -became inactive. Multiple DNA recombination products were expected in the *biological host used, resulting in unsatisfactory reliability, -specificity or efficiency of subcloning. In vitro recombination reactions were not expected to be sufficiently efficient to yield the desired levels of product.

Accordingly, there is a long felt need to provide an alternative subcloning system that provides advantages over the known use of restriction enzymes and ligases.

Summary of the Invention The present invention provides nucleic acid, vectors and methods for obtaining chimeric nucleic acid using recombination proteins and engineered recombination sites, in vitro or in vivo. These methods are highly specific, rapid, and less labor intensive than what is disclosed or suggested in the related background art. The improved specificity, speed and yields of the present invention facilitates DNA or RNA subcloning, regulation or exchange useful for any related purpose. Such purposes include in vitro recombination of DNA segments and in vitro or in vivo insertion or modificatian of transcribed, replicated, isolated or genomic DNA or RNA.

T'he present invention relates to nucleic acids, vectors and methods for moving or exchanging segments of DNA using at least -one engineered recombination site and at least one recombination protein to provide chimeric DNA molecules which have the desired characteristic(s) and/or DNA segment(s).

25 WO 96/40724 PCT/US96/10082 -7- Generally, one or more parent DNA molecules are recombined to give one or more daughter molecules, at least one of which is the desired Product DNA segment or vector. The invention thus relates to DNA, RNA, vectors and methods to effect the exchange and/or to select for one or more desired products.

One embodiment of the present invention relates to a method of making chimeric DNA, which comprises combining in vitro or in vivo an Insert Donor DNA molecule, comprising a desired DNA segment flanked by a first recombination site and a second recombination site, wherein the first and second recombination sites do not recombine with each other, (ii) a Vector Donor DNA molecule containing a third recombination site and a fourth recombination site, wherein the third and fourth recombination sites do not recombine with each other, and (iii) one or more site specific recombination proteins capable of recombining the first and third recombinational sites and/or the second and fourth recombinational. sites; thereby allowing recombination to occu, so as to produce at least one Cointegrate DNA molecule, at least one desired Product DNA molecule which 20 comprises said desired DNA segment, and optionally Byproduct DNA molecule; and then, optionally,.

selecting for the Product or Byproduct DNA molecule.

Another embodiment of the present invention relates to a kit comprising a carrier or receptacle being compartmentalized to receive and hold therein at 25 least one container, wherein a first container contains a DNA molecule comprising a vector having at least two recombination sites flankingr cloning :site or a Selectable marker, as described herein. The it optionally further .ooo comprises: a second container containing a Vector Donor plasmid comprising a subcloning vector and/or a Selectable marker of which one or both are flanked byone or more enierdrecombination sites; and/or WO 96/40724 PCT/US96/10082 (ii) a third container containing at least one recombination protein which recognizes and is capable of recombining at least one of said recombination sites.

Other embodiments include DNA and vectors useful in the methods of tile present invention. In particular, Vector Donor molecules are provided in one embodiment wherein DNA segments within the Vector Donor are separated either by, in a circular Vector Donor, at least two recombination sites, or (ii) in a linear Vector Donor, at least one recombination site, where the recombination sites are preferably engineered to enhance specificity or efficiency of recombination.

One Vector Donor embodiment comprises a first DNA segment and a second DNA segment, the first or second segment comprising a Selectable marker. A second Vector Donor embodiment comprises a first DNA segment and a second DNA segment, the first or second DNA segment comprising a toxic gene. A third Vector Donor embodiment comprises a first DNA segment and a second DNA segment th e first or second DNA segment comprising an inactive fr'agment of at least one Selectable marker, wherein the inactive fragment of the Selectable marker is capable of reconstituting a functional Selectable marker when recombined across the first or second recombination site with another 20 inactive fragment of at least one Selectable marker.

T7he present recombinational cloning method possesses several advantages o.ver previous in vivo methods. Since single molecules of recombination products can be introduced into a biological host, propagation of the desired Product DNA in the absence of other DNA molecules starting molecules, intermediates, 25 and by-products) is more readily realized. Reaction conditions can be fr-eely adjusted in vitro to optimize enzyme activities. DNA molecules can be incompatib le with the desired biological host YACs, genomic DNA, etc.), can be used. Recombination proteins from diverse sources can be employed, together or sequentially.

Other embodiments will be evident to those of ordinary skill in the art from the teachings contained herein in combination with what is known to the art.

WO 96/40724 PCT/US96/10082 -9- Brief Description of the Figures Figure 1 depicts one general method of the present invention, wherein the starting (parent) DNA molecules can be circular or linear. The goal is to exchange the new subcloning vector D for the original cloning vector B. It is desirable in one embodiment to select for AD and against all the other molecules, including the Cointegrate. The square and circle are sites of recombination: e.g., loxP sites, all sites, etc. For example, segment D can contain expression signals, new drug markers, new origins of replication, or specialized functions for mapping or sequencing DNA.

Figure 2A depicts an in vitro method of recombining an Insert Donor plasmid (here, pEZC705) with a Vector Donor plasmid (here, pEZC726), and obtaining Product DNA and Byproduct daughter molecules. The two recombination sites are attP and loxP on the Vector Donor. On one segment defined by these sites is a kanamycin resistance gene whose promoter has been 15 replaced by the tetOP operator/promoter from transposon TnO.1 See Sizemore et al., Nucl. Acids Res. 18(10):2875 (1990). In the absence of tet repressor \protein, E. coli RNA polymerase transcribes the kanamycin resistance gene from the tetOP. If tet repressor is present, it binds to tetOP and blocks transcription of the kanamycin resistance gene. The other segment of pEZC726 has the let repressor gene expressed by a constitutive promoter. Thus cells transformed by pEZC726 are resistant to chloramphenicol, because of the chloramphenicol acetyl transferase gene on the same segment as tetR, but are sensitive to kanamycin.

The recombinase-mediated reactions result in separation of the tetR gene from the regulated kanamycin resistance gene. This separation results in kanamycin resistance in cells receiving only the desired recombination products. The first recombination reaction is driven by the addition of the recombinase called Integrase. The second recombination reaction is driven by adding the recombinase Cre to the Cointegrate (here, pEZC7 Cointegrate).

A Figure 2B depicts a restriction map of pEZC705.

Figure 2C depicts a restriction map of pEZC726.

Figure 2D depicts a restriction map of pEZC7 Cointegrate.

WO 96/40724 PCT/US96/10082 Figure 2E depicts a restriction map of Intprod.

Figure 2F depicts a restriction map ofIntbypro.

Figure 3A depicts an in vitro method of recombining an Insert Donor plasmid (here, pEZC602) with a Vector Donor plasmid (here, pEZC629), and obtaining Product (here, EZC6prod) and Byproduct (here, EZC6Bypr) daughter molecules. The two recombination sites are loxP and loxP 511. One segment of pEZC629 defined by these sites is a kanamycin resistance gene whose promoter has been replaced by the tetOP operator/promoter from transposon TnlO. In the absence of tet repressor protein, E. coli RNA polymerase transcribes the kanamycin resistance gene from the tetOP. If tet repressor is present, it binds to tetOP and blocks transcription of the kanamycin resistance gene. The other segment of pEZC629 has the tet repressor gene expressed by a constitutive promoter. Thus cells transformed by pEZC629 are resistant to chloramphenicol, because of the chloramphenicol acetyl transferase gene on the same segment as tetR, but are sensitive to kanamycin. The reactions result in separation of the tetR gene from the regulated kanamycin resistance gene. This separation results in kanamycin resistance in cells receiving the desired recombination product The first and the second recombination events are driven by the addition of the same recombinase, Cre.

20 Figure 3B depicts a restriction map of EZC6Bypr.

Figure 3C depicts a restriction map of EZC6prod.

.Figure 3D depicts a restriction map of pEZC602.

Figure 3E depicts a restriction map of pEZC629.

Figure 3F depicts a restriction map of EZC6coint.

25 Figure 4A depicts an application of the in vitro method of recombinational cloning to subclone the chloramphenicol acetyl tranerse gene into a vector for expression in eukaryotic cells. The Insert Donor plasmid, pEZC843, is comprised of the chloramphenicol acetyl transferase gene of E. coil, cloned between loxP and attB sites such that the loxP site is positioned at the A 5'-end of the gene. The Vector Donor plasmid, pEZC1003, contains the cytomegalovirus eukaryotic promoter apposed to a loxP site. The supercoiled plasmids were combined with lambda Integrase and Cre recombinase in vitro.

WO 96/40724 PCT/US96/10082 -11 After incubation, competent E. coli cells were transformed with the recombinational reaction solution. Aliquots of transformations were spread on agar plates containing kanamycin to select for the Product molecule (here CMVProd).

Figure 4B depicts a restriction map ofpEZC843.

Figure 4C depicts a restriction map ofpEZC1003.

Figure 4D depicts a restriction map of CMVBypro.

Figure 4E depicts a restriction map of CMVProd.

Figure 4F depicts a restriction map of CMVcoint.

Figure 5A depicts a vector diagram ofpEZC1301.

Figure 5B depicts a vector diagram ofpEZC1305.

Figure 5C depicts a vector diagram ofpEZC1309.

Figure 5D depicts a vector diagram ofpEZCl313.

Figure SE depicts a vector diagram of pEZCl317.

Figure 5F depicts a vector diagram ofpEZC1321.

Figure 5G depicts a vector diagram ofpEZC1405.

S. Figure 5H depicts a vector diagram of pEZC1502.

Figure 6A depicts a vector diagram of pEZC603.

Figure 6B depicts a vector diagram ofpEZC1706.

20 Figure A depicts a vector diagrm ofpEZC2901.

Figure 7B depicts a vector diagram of pEZC2913 20 Figure 7C depicts a vector diagram ofpEZC3101.

Figure 7D depicts a vector diagram ofpEZC1802.

Figure 8A depicts a vector diagram of pOEX-2TK.

25 Figure 8B depicts a vector diagram ofpEZC3501.

Figure SC depicts a vector diagram ofpEZC3601.

Figure 8D depicts a vector diagram ofpEZC3609.

Figure 8E depicts a vector diagram ofpEZC3617.

Figure 8F depicts a vector diagram ofpEZC3606.

Figure 8G depicts a vector diagram of pEZC3613.

Figure 8H depicts a vector diagram ofpEZC3621.

Figure 81 depicts a vector diagram of GST-CAT.

WO 96/40724 PCTIUS96/10082 12- Figure 8J depicts a vector diagram of GST-phoA.

Figure 8K depicts a vector diagram of pEZC32Ol.

Detailed Description of the Preferred Embodiments It is unexpectedly discovered in the present invention that subcloming reactions can be provided using recombinational cloning. Recombination cloning according to the present invention uses DNAs, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins. These methods provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s).

The present invention thus provides nucleic acid, vectors and methods for obtaining chimeric nucleic acid using recombination proteins and engineered recombination sites, in vitro or in vivo. These methods are highly specific, rapid, and less labor intensive than what is disclosed or suggested in the related background art. The improved specificity, speed and yields of the present 15 invention facilitates DNA or RNA subcloning, regulation or exchange useful for any related purpose. Such purposes include in vitro recombination of DNA segments and in vitro or in vivo insertion or modification of transcribed, replicated, isolated or genomic DNA or RNA.

Definitions 090.e: 20 In the description that follows, a number of terms used in recombinant *DNA technology are utilized extensively. In order to provide a~lear and consistent understanding of the specification and claims, including'.the scope to be given such terms, the following definitions are provided.

Byproduct: is a daughter molecule (a new clone produced after the second recombination event during the recombinational cloning process) lacking the DNA which is desired to be subeloned.

WO 96/40724 PCT/US96/10082 -13- Cointegrate: is at least one recombination intermediate DNA molecule of the present invention that contains both parental (starting) DNA molecules.

It will usually be circular. In some embodiments it can be linear.

Host: is any prokaryotic or eukaryotic organism that can be a recipient of the recombinational cloning Product. A "host," as the term is used herein, includes prokaryotic or eukaryotic organisms that can be genetically engineered.

For examples of such hosts, see Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York (1982).

Insert: is the desired DNA segment (segment A of Figure 1) which one wishes to manipulate by the method of the present invention. The insert can have one or more genes.

Insert Donor: is one of the two parental DNA molecules of the present invention which carries the Insert. The Insert Donor DNA molecule comprises the Insert flanked on both sides with recombination signals. The Insert Donor can be linear or circular. In one embodiment of the invention, the Insert Donor is a circular DNA molecule and further comprises a cloning vector sequence outside of the recombination signals (see Figure 1).

Product: is one or both the desired daughter molecules comprising the A and D or B and C sequences which dre produced after the second recombination 20 event during the recombinational cloning process (see Figure The Product contains the DNA which was to be cloned or subeloned.

Promoter: is a DNA sequence generally described as the 5'-region of a gene, located proximal to the start codon. The transcription of an adjacent DNA segment is initiated at the promoter region. A repressible promoter's rate of 25 transcription decreases in response to a repressing agent An inducible promoter's rate of transcription increases in response to an inducing agent. A cnstitutive .promoter's rate of transcription is not specifically regulated, though it can vary under the influence of general metabolic conditions.

WO 96/40724 PCT/US96/10082 14- Recognition sequence: Recognition sequences are particular DNA sequences which a protein, DNA,. or RNA molecule restriction endonuclease, a modification methylase, or a recombinase) recognizes and binds.

For example, th6 recognition sequence for Cre recombinase is loxP which is a 34 base pair sequence comprised of two 13 base pair inverted repeats (serving as the recombinase binding sites) flanking an 8 base pair core sequence. See Figure 1 of Sauer, -Current Opinion in Biotechnology 5:521-527 (1994). Other examples of recognition sequences are the attB, artP, attL, and attR sequences which are recognized by the recombinase enzyme I Integrase. attB is an approximately 25 base pair sequence containing two 9 base pair core-type Int binding sites and a 7 base pair overlap region. attP is an approxinmately 240 base pair sequence containing core-type Int binding sites and arm-type Int binding sites as well as sites for auxiliary proteins IHF, FIS, and Xis. See Landy, Current Opinion in Biotechnology 3:699-707 (1993). Such sites are also engineered according to the present invention to enhance methods and products.

Recombinase: is an enzyme which catalyzes the exchange of DNA segments at specific recombination sites.

•.Recombinational Cloning: is a method described herein, whereby segments of DNA molecules are exchanged, inserted, replaced, substituted or modified, in vitro or in vivo.

Recombination proteins: include excisive or integrative proteins, enzymes, co-factors or associated proteins that are involved in recombination 99*9 reactions involving one or more recombination sites. See, Landy (1994), infra.

Repression cassette: is a DNA segment that contains a repressor of a 25 Selectable marker present in the subcloning vector.

Selectable marker: is a DNA segment that allows one to select for or against a molecule or a cell that contains it, often under particular conditions.

These markers can encode an activity, such as, but not limited to, production of RNA, peptide, or protein, or can provide a binding site for RNA, peptides, proteins, inorganic and organic compounds or compositions and the like.

Examples of Selectable markers include but are not limited to: DNA segments that encode products which provide resistance against otherwise toxic WO 96/40724 PCT/US96/! 0082 compounds antibiotics); DNA segments that encode products which are otherwise lacking in the recipient cell tRNA genes, auxotrophic markers); DNA segments that encode products which suppress the activity of a gene product; DNA segments that encode products which can be readily identified phenotypic markers such as P-galactosidase, green fluorescent protein (GFP), and cell surface proteins); DNA segments that bind products which are otherwise detrimental to cell survival and/or function; DNA segments that otherwise inhibit the activity of any of the DNA segments described in Nos. above antisense oligonucleotides); DNA segments that bind products that modify a substrate restriction endonucleases); DNA segments that can be used to isolate a desired molecule specific protein binding sites); (9) DNA segments that encode a specific nucleotide sequence which can be otherwise non-functional for PCR amplification of subpopulations of molecules); and/or (10) DNA segments, which when absent, directly or indirectly confer sensitivity to particular compounds.

Selection scheme: is any method which allows selection, enrichment, or identification of a desired Product or Product(s) from a mixture containing the Insert Donor, Vector Donor, and/or any intermediates, (e.g a Cointegrate) S"Byproducts. The selection schemes of one preferred embodiment have at least 20 two components that are either linked or unlinked during recombinational cloning. One component is a Selectable marker. The other component controls the expression in vitro or in vivo of the Selectable marker or survival of the cell harboring the plasmid carrying the Selectable marker. Generally, this controlling element will be a repressor or inducer of the Selectable marker, but other means 25 for controlling expression of the Selectable marker can be used. Whether a repressor or activator is used will depend on whether the marker is for a positive *or negative selection, and the exact arrangement of the various DNA segments, as will be readily apparent to those skilled in the art. A preferred requirement is that the selection scheme results in selection of or enrichment for only one or more desired Products. As defined herein, to select for a DNA molecule includes selecting or enriching for the presence of the desired DNA molecule, and (b) WO 96/40724 PCT/US96110092 -16selecting or enriching against the presence of DNA molecules tha are not the desired DNA molecule.

In one embodiment, the selection schemes (which can be carried out reversed) will take one of three forms, which will be discussed in terms of Figure 1. ThIe first exemplified herein with a Selectable marker and a repressor therefor, selects for molecules having segment D and lacking segment C The second selects against molecules having segment C and for molecules having segment D. Possible embodiments of the second form would have a DNA segment carrying a gene toxic to cells into which the in vitro reaction products are to beintroduced. A toxic genecan be aDNA that is expressed as atoxicge product (a toxic protein or RNA), or can be toxic in and of itself. (In the latter case, the toxic gene is understood to carry its classical definition of "heritable trait".) Examples of such toxic gene products are well known in the art, and include, but are not limited to, restriction endonucleases Dpnl) and genes that kill hosts in the absence of a suppressing function, kicS. A toxic gene can alternatively be selectable in vitro, a restriction site.

In the second form, segment D carries a Selectable marker. The toxic gene would eliminate transformants harboring the Vector Donor,.Cointegrhte, and Byproduct molecules, while the Selectable marker can be used to select for cells containing the Product and against cells harboring only the Insert Donor.

.The third fomseects forcestthaveothsegmets A and Din cison the same molecule, but not for cells that have both segments in trams on different molecules. This could be embodied by a Selectable marker that is split into two 25 inactive fragments, one each on segments A and D.

The friagments are so arranged relative to the recombinatioArsites that when the segments are brought together by the recombination event, they reconstitute a functional Selectable marker. For example, the recombinational event can link a promoter with a structural gene, can link two fragments of a structural gene, or can link genes that encode a heterodimeric gene product ,~,needed for survival, or can link portions of a replicon.

WO 96/40724 PCTIUS96110082 -17- Site-specific recombinase: is a type of recombinase which typically has at least the following four activities: recognition of one or two specific DNA sequences; cleavage of said DNA sequence or sequences; DNA topoisomerase activity involved in strand exchange; and DNA ligase activity to reseal the cleaved strands of DNA. See Sauer, Current Opinions in Biotechnology 5:521-527 (1994). Conservative site-specific recombination is distinguished from homologous recombination and transposition by a high degree of specificity for both partners. The strand exchange mechanism involves the cleavage and rejoining of specific DNA sequences in the absence of DNA synthesis (Landy, A. (1989) Ann. Rev. Biochem 58:913-949).

Subcloning vector. is a cloning vector comprising a circular or linear DNA molecule which includes an appropriate replicon. In the present invention, the subloning vector (segment D in Figure 1) can also contain functional and/or regulatory elements that are desired to be incorporated into the final product to act upon or with the cloned DNA Insert (segment A in Figure The subeloning vector can also contain a Selectable marker (contained in segment C in Figure 1).

Vector: is a DNA that provides a useful biological or biochemical property to an Insert. Examples include plasmids, phages, and other DNA 0000 sequences which are able to replicate or be replicated in vitro or in a host cell, or 20 to convey a desired DNA segment to a desired location within a host cell A Vector can have one or more restriction endonuclease recognition sites at which the DNA sequences can be cut in a determinable fashion without loss of an essential biological function of the vector, and into which a DNA fragment can be spliced in order to bring about its replication and cloning. Vectors can further 25 provide primer sites, for PCR, transcriptional and/or translational initiation and/or regulation sites, recombinational signals, replicons, Sele ,tadblmarkers, etc. Clearly, methods of inserting a desired DNA fragment which do not require the use of homologous recombination or restriction enzymes (such as, but not limited to, UDG cloning of PCR fragments Patent No. 5,334,575, entirely incorporated herein by reference), T'A cloning, and the like) can also be applied RA clone a fragment of DNA into a cloning vector to be used according to the WO 96/40724 PCT/US96/10082 present invention. The cloning vector can further contain a Selectable marker suitable for use in the identification of cells transformed with the cloning vector.

Vector Donor- is one of the two parental DNA molecules of the present invention which carries the DNA segments encoding the DNA vector which is to become part of the desired Product. The Vector Donor comprises a subcloning vector D (or it can be called the cloning vector if the Insert Donor does not already contain a cloning vector) and a segment C flanked by recombination sites (see Figure Segments C and/or D can contain elements that contribute to selection for the desired Product daughter molecule, as described above for selection schemes. The recombination signals can be the same or different, and can be acted upon by the same or different recombinases. In addition, the Vector Donor can be linear or circular.

Description One general scheme for an in vitro or in vivo method of the invention is 15 shown in Figure 1, where the Insert Donor and the Vector Donor can be either circular or linear DNA, but is shown as circular. Vector D is exchanged for the original cloning vector A. It is desirable to select for the daughter vector containing-elements A and D and against other molecules, including one or more Cointegrate(s). The square and circle are different sets of recombination sites lox sites or att sites). Segment A or D can contain at least one Selection Marker, -expression signals, origins of replication, or specialized functions for detecting, selecting, expressing, mapping or sequencing DNA, where D is used in this example.

Examples of desired DNA segments that can be part of Element A or D include, but are not limited to, PCR products, large DNA segments, genomic clones or fr-agments, cDNA clones, functional elements, etc., and genes or partial genes, which encode useful nucleic acids or proteins. Moreover, the recombinational cloning of the present invention can be used to make ex vivo and RAQ in vivo gene transfer vehicles for protein expression and/or gene therapy.

WO 96/40724 PCT/US96/10082 -19- In Figure 1, the scheme provides the desired Product as containing vectors D and A, as follows. The Insert Donor (containing A and B) is first recombined at the square recombination sites by recombination proteins, with the Vector Donor (containing C and to form a Co-integrate having each of A-D- C-B. Next, recombination occurs at the circle recombination sites to form Product DNA (A and D) and Byproduct DNA (Cand However, if desired, two or more different Co-integrates can be formed to generate two or more Products.

In one embodiment of the present in vitro or in vivo recombinational cloning method, a method for selecting at least one desired Product DNA is provided. This can be understood by consideration of the map of plasmid pEZC726 depicted in Figure 2. The two exemplary recombination sites are attP and loxP. On one segment defined by these sites is a kanamycin resistance gene whose promoter has been replaced by the tetOP operator/promoter from transposon Tnl 0. In the absence of tet repressor protein, E. coli RNA polymerase transcribes the kanamycin resistance gene from the tetOP. If tet repressor is present, it binds to tetOP and blocks transcription of the kanamycin resistance gene. The other segment of pEZC726 has the tet repressor gene expressed by a constitutive promoter. Thus cells transformed by pEZC726 are resistant to 20 chloramphenicol, because of the chloramphenicol acetyl transferase gene on the same segment as tetR, but are sensitive to kanamycin. The recombination reactions result in separation of the tetR gene from the regulated kanamycin resistance gene. This separation results in kanamycin resistance in cells receiving the desired recombination Product.

25 Two different sets of plasmids were constructed to demonstrate the in vitro method. One set, for use with Cre recombinase only (cloning vor 602 and subcloning vector 629 (Figure contained loxP and loxP 511 sites. A second set, for use with Cre and integrase (cloning vector 705 and subcloning vector 726 (Figure contained loxP and att sites. The efficiency of production of the desired daughter plasmid was about 60 fold higher using both enzymes n using Cre alone. Nineteen of twenty four colonies from the Cre-only WO 96/40724 PCT/US96/10082 reaction contained the desired product, while thirty eight of thirty eight colonies from the integrase plus Cre reaction contained the desired product plasmid.

Other Selection Schemes A variety of selection schemes can be used that are known in the art as they can suit a particular purpose for which the recombinational cloning is carried out. Depending upon individual preferences and needs, a number of different types of selection schemes can be used in the recombinational cloning method of the present invention. The skilled artisan can take advantage of the availability of the many DNA segments or methods for making them and the different methods of selection that are routinely used in the art. Such DNA segments include but are not limited to those which encodes an activity such as, but not limited to, production of RNA, peptide, or protein, or providing a binding site for such RNA, peptide, or protein. Examples of DNA molecules used in devising a selection scheme are given above, under the definition of "selection scheme" Additional examples include but are not limited to: Generation of new primer sites for PCR juxtaposition of two DNA sequences that were not previouslyjuxtaposed); (ii) Inclusion of a DNA sequence acted upon by a restriction endonuclease tr other DNA modifying enzyme, chemical, 20 ribozyme, etc.; (iii) Inclusion of a DNA sequence recognized by a DNA binding protein, RNA, DNA, chemical, etc.) for use as an affinity •tag for selecting for or excluding from a population) (Davis, Nucl.

Acids Res. 24.702-706(1996); J. Virol. 69: 8027-8034 (1995)); 25 (iv) In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr virus-expressed RNA Cy using randomized and eDNA-derived RNA libraries; (vi) The positioning of functional elements whose activity requires a specific orientation or juxtaposition a recombination site which reacts poorly in trans, but when placed in cis, in the (0 presence of the appropriate proteins, results in recombination that destroys certain populations of molecules; reconstitution of WO 96140724 PCTfUS96/10082 -21a promoter sequence that allows in vitro RNA synt .hesis). The RNA can be used directly, or can be reverse transcribed to obtain the desired DNA construct; (vii) Selection of the desired product by size fractionation) or other physical property of the molecule(s); and (viii) Inclusion of a DNA sequence required for a specific modification methylation) that allows its identification.

After formation of the Product and Byproduct in the method of the present invention, the selection step can be carried out either in vitro or in vivo depending upon the particular selection scheme which has been optionally devised in the particular recombinational cloning procedure.

For example, an in vitro method of selection can be devised for the Insert Donor and Vector Donor DNA molecules. Such scheme can involve engineering a rare restriction site in the starting circular vectors in such a way that after the recombination events the rare cutting sites end up in the Byproduct Hence, when the restriction enzyme which binds and cuts at the rare restriction site is added to the reaction mixture in vitro, all of the DNA molecules carrying the rare cutting site, L the starting DNA molecules, the Cointegrate, and the Byproduct, will be cut and rendered nonreplicable in the intended host cell. For example, cutting sites in segments Band C(see Figure1) can be used toselect against all molecules except the Product Alternatively, only a cutting site in C is needed if o o...:one is able to select for segment D, by a drug resistance gene not found on B.

Similarly, an in vitro selection method can be devised when dealing with linear DNA molecules. DNA sequences complementary to a POR primer sequence can be so engineered that they are transferred, through the ooooo recombinational cloning method, only to the Product moldcule. AZfter the 0 reactions are completed, the appropriate primers are added to the reaction solution and the sample is subjected to PORL Hence, all or part of the Product molecule is amplified.

Other in vivo selection schemes can be used with a variety of E. col! cell RA lines. One is to put a repressor gene on one segrmn ftesbloigpamd V and a drug marker controlled by that repressor on the other segment of the same WO 96/40724 PCT/US96/10082 -22plasmid. Another is to put a killer gene on segment C of the subcloning plasmid (Figure Of course a way must exist for growing such a plasmid, there must exist circumstances under which the killer gene will not kill. There are a number of these genes known which require particular strains of E. coli. One such scheme is to use the restriction enzyme DpnI, which will not cleave unless its recognition sequence GATC is methylated. Many popular common E. coli strains methylate GATC sequences, but-there are mutants in which cloned DpnI can be expressed without harm.

Of course analogous selection schemes can be devised for other host organisms. For example, the tet repressor/operator of TnlO has been adapted to control gene expression in eukaryotes (Gossen, and Bujard, Proc. Natl.

Acad Sci. USA 89:5547-5551 (1992)). Thus the same control of drug resistance by the tet repressor exemplified herein can be applied to select for Product in eukaryotic cells.

Recombination Proteins.

In the present invention, the exchange of-DNA segments is achieved by the use of recombination proteins, including recombinases and associated co-factors and proteins. Various recombination proteins are described in the art.

o* Examples of such recombinases include: S 20 Cre: A protein from bacteriophage Pl (Abremski and Hoess, J. Biol.

Chem. 259(3):1509-1514 (1984)) catalyzes the exchange causes recombination) between 34 bp DNA sequences called loxP (locus of crossover) sites (See Hoess et al., Nucl. Acids Res. 14(5):2287 (1986)). Cre is available S. commercially (Novagen, Catalog No. 69247-1). Recombination mediaed by Cre is freely reversible. From thermodynamic considerations it is not surprising that Cre-mediated integration (recombination between two molecules to form one molecule) is much less efficient than Cre-mediated excision (recombination between two loxP sites in the same molecule to form two daughter molecules).

R Cre works in simple buffers with either magnesium or spermidine as a cofactor, as is well known in the art. The DNA substrates can be either linear or WO 96/40724 PCT/US96/10082 -23- 20 *o *oo *oo oo** *o supercoiled. A number of mutant loxP sites have been described (Hoess et al., supra). One of these, loxP 511, recombines with another loxP 511 site, but will not recombine with a loxP site.

Integrase: A protein from bacteriophage lambda that mediates the integration of the lambda genome into the E. coli chromosome. The bacteriophage I Int recombinational proteins promote irreversible recombination between its substrate att sites as part of the formation or induction of a lysogenic state. Reversibility of the recombination reactions results from two independent pathways for integrative and excisive recombination. Each pathway uses a unique, but overlapping, set of the 15 protein binding sites that comprise ant site DNAs. Cooperative and competitive interactions involving four proteins (Int, Xis, IHF and FIS) determine the direction of recombination.

Integrative recombination involves the hit and IHF proteins and sites attP (240 bp) and attB (25 bp). Recombination results in the formation of two new sites: attL and attR. Excisive recombination requires Int, IHF, and Xis, and sites attL and attR to generate attP and attB. Under certain conditions, FIS stimulates excisive recombination. In addition to these normal reactions, it should be appreciated that attP and attB, when placed on the same molecule, can promote excisive recombination to generate two excision products, one with attL and one with attR. Similarly, intermolecular .recombination between molecules containing attL and attR, in the presence of Int, IHF and Xis, can result in integrative recombination and the generation attP and attB. Hence, by flanking DNA segments with appropriate combinations of engineered aft sites, in the presence of the appropriate recombination proteins, one can direct excisive or integrative recombination, as reverse reactions of each other.

Each of the art sites contains a 15 bp core sequence; individualCsequence elements of functional significance lie within, outside, and across the boundaries of this common core (Landy, Ann. Rev. Biochen 58:913 (1989)). Efficient recombination between the various att sites requires that the sequence of the central common region be identical between the recombining partners, however, the exact sequence is now found to be modifiable. Consequently, derivatives of WO 96/40724 PCT/US96/10082 -24the att site with changes within the core are now discovered to recombine as least as efficiently as the native core sequences.

Integrase acts to recombine the attP site on bacteriophage lambda (about 240 bp) with the attB site on the E. coli genome (about 25 bp) (Weisberg, R.A.

and Landy, A. in Lambda II, p. 211 (1983), Cold Spring Harbor Laboratory)), to produce the integrated lambda genome flanked by attL (about 100 bp) and attR (about 160 bp) sites. In the absence of Xis (see below), this reaction is essentially irreversible. The integration reaction mediated by integrase and IHF works in vitro, with simple buffer containing spermidine. Integrase can be obtained as described by Nash, HA., Methods ofEnzymology 100:210-216 (1983). IHF can be obtained as described by Filutowicz, etal., Gene 147:149-150 (1994).

In the presence of the .protein Xis (excise) integrase catalyzes the reaction of attR and attL to form attP and attB, Le., it promotes the reverse of the reaction described above. This reaction can also be applied in the present invention.

Other Recombination Systems. Numerous recombination systems from various organisms can also be used, based on the teaching and guidance provided herein. See, Hoess et al., Nucleic Acids Research 14(6)-2287 (1986); Abremski et al., J. Biol. Chem.261(l):391 (1986); Campbell, J. Bacteriol.

174(23):7495 (1992); Qian et aL, J. Biol. Chem. 267(11):7794 (1992); Araki et al,, J Mol. Biol. 225(1):25 (1992)). Many of these belong to the integrase family of recombinases (Argos et al. EMBO J. 5:433-440 (1986)). Perhaps the best studied of these are the Integrase/att system from bacteriophage X (Landy, A. (1993) Current Opinions in Genetics and Devel. 3:699-707), the CrelloxP 25 system from bacteriophage P (Hoess and Abremski (1990) In Nucleic Acids and Molecular Biology, vol. 4. Eds.: Eckstein and Lilley, Berlin-Hidelberg: Springer-Verlag; pp. 90-109), and the FLP/FRT system from the Saccharomyces cerevisiae 2 I circle plasmid (Broach et al. Cell 29:227-234 (1982)).

Members of a second family of site-specific recombinases, the resolvase family y6, Tn3 resolvase, Hin, Gin, and Cin) are also known. Members of SRA,/ this highly related family of recombinases are typically constrained to _Z intramolecular reactions inversions and excisions) and can require host- WO 96/40724 PCT/US96/10082 encoded factors. Mutants have been isolated that relieve some of the requirements for host factors (Maeser and Kahnmann (1991) Mol. Gen. Genet.

230:170-176), as well as some of the constraints of intramolecular recombination.

Other site-specific recombinases similar to X Int and similar to P1 Cre can be substituted for Int and Cre. Such recombinases are known. In many cases the purification of such other recombinases has been described in the art. In cases when they are not known, cell extracts can be used or the enzymes can be partially purified using procedures described for Cre and Int.

While Cre and Int are described in detail for reasons of example, many related recombinase systems exist and their application to the described invention is also provided according to the present invention. The integrase family of sitespecific recombinases can be used to provide alternative recombination proteins and recombination sites for the present invention, as site-specific recombination proteins encoded by bacteriophage lambda, phi 80, P22, P2,186, P4 and P1. This group of proteins exhibits an unexpectedly large diversity of sequences. Despite this diversity, all of the recombinases can be aligned in their C-terminal halves.

A 40-residue region near the C terminus is particularly well conserved in all the proteins and is homologous to a region near the C terminus of the yeast 2 mu plasmid Flp protein. Three positions are perfectly conserved within this family: histidine, arginine and tyrosine are found at respective alignment positions 396, 399 and 433 within the well-conserved C-terminal region. These residues contribute to the active site of this family of recombinases, and suggest that tyrosine-433 forms a transient covalent linkage to DNA during strand cleavage and rejoining. See, Argos, P. et al., EMBOJ. 5:433-40 (1986).

25 Alternatively, IS231 and other Bacillus thuringiensis transposable elements could be used as recombination proteins and recombinton sites.

Bacillus thuringiensis is an entomopathogenic bacterium whose toxicity is due to the presence in the sporangia of delta-endotoxin crystals active against agricultural pests and vectors of human and animal diseases. Most of the genes coding for these toxin proteins are plasmid-bome and are generally structurally Sassociated with insertion sequences (IS231, IS232, IS240, ISBTI and ISBT2) and Stransposons (Tn4430 and Tn5401). Several of these mobile elements have been WO 96/40724 PCT/US96/10082 -26shown to be active and participate in the crystal gene mobility, thereby contributing to the variation of bacterial toxicity.

Structural analysis of the iso-IS231 elements indicates that they are related to IS1151 from Clostridiumperfringens and distantly related to IS4 and IS186 from Escherichia coli. Like the other IS4 family members, they contain a conserved transposase-integrase motif found in other IS families and retroviruses.

Moreover, functional data gathered from IS231A in Escherichia coli indicate a non-replicative mode of transposition, with a preference for specific targets. Similar results were also obtained in Bacillus subtilis and B.

-thuringiensis. See, Mahillon, J. et aL, Genetica 93:13-26 (1994); Campbell, J. Bacteriol. 7495-7499 (1992).

The amount of recombinase which is added to drive the recombination reaction can be determined by using known assays. Specifically, titration assay is used to determine the appropriate amount of a purified recombinase enzyme, or the appropriate amount of an extract.

Engineered Recombination Sites. The above recombinases and corresponding recombinase sites are suitable for use in recombination cloning according to the present invention. However, wild-type recombination sites 0 contain sequences that reduce the efficiency' or specificity of recombination reactions as applied in methods of the present invention. For example, multiple' stop codons in attB, attR, attP, attL and loxP recombination sites occur in multiple reading frames on both strands, so recombination efficiencies are reducted, where the coding sequence must cross the recombination sites, (only one reading frame is available on each strand of loxP and attB sites) or impossible (in attP, attR or attL).

Accordingly, the present invention also provides egineered recombination sites that overcome these problems. For example, att sites can be 'engineered to have one or multiple mutations to enhance specificity or efficiency of the recombination reaction and the properties of Product DNAs attl, att2, and att3 sites); to decrease reverse reaction removing P1 and HI from attB).

S e testing of these mutants determines which mutants yield sufficient WO 96/40724 PCT/UJS96/10082 -27recombinational activity to be suitable for recombination subcloning according to the present invention.

Mutations can therefore be introduced into recombination sites for enhancing site specific recombination. Such mutations include, but are not limited to: recombination sites without translation stop codons that allow fusion proteins to be encoded; recombination sites recognized by the same proteins but differing in base sequence such that they react largely or exclusively with their homologous partners allow multiple reactions to be contemplated. Which particular reactions take place can be specified by which particular partners are present in the reaction mixture. For example, a tripartite protein fusion could be accomplished with parental plasmids containing recombination sites attRi and attR2; attLI and attL3; and/or attR3 and attL2.

There are well known procedures for introducing specific mutations into nucleic acid sequences. A number of these are described in Ausubel, F.M. et al., Current Protocols in Molecular Biology, Wiley Interscience, New York (1989- 1996). Mutations can be designed into oligonucleotides, which can be used to modify existing cloned sequences, or in amplification reactions. Random mutagenesis can also be employed if appropriate selection methods are available to isolate the desired mutant DNA or RNA. The presence of the desired S 20 mutations can be confirmed by sequencing the nucleic acid by well known methods.

The following non-limiting methods can be used to engineer a core region of a given recombination site to provide mutated sites suitable for use in the present invention: 25 1. By recombination of two parental DNA sequences by site-spfic (e.g.

.attL and attR to give attB) or other homologous) recombination mechanisms. The DNA parental DNA segments containing one or more base alterations resulting in thefinal core sequence; 2. By mutation or mutagenesis (site-specific, PCR, random, spontaneous, Retc) directly of the desired core sequence; WO 96/40724 PCTAIS96/10082 -28- 3. By mutagenesis (site-specific, PCR, random, spontanteous, etc) of parental DNA sequences, which are recombined to generate a desired core sequence; and 4. By reverse transcription of an RNA encoding the desired core sequence.

The functionality of the mutant recombination sites can be demonstrated in ways that depend on the particular characteristic that is desired. For example, the lack of translation stop codons in a recombination site can be demonstrated by expressing the appropriate fusion proteins. Specificity of recombination between homologous partners can be demonstrated by introducing the appropriate molecules into in vitro reactions, and assaying for recombination products as described herein or known in the art. Other desired mutations in recombination sites might include the presence or absence of restriction sites, translation or traniscription start signals, protein binding sites, and other known fuinctionalities of nucleic acid base sequences. Genetic selection schemes for particular functional attributes in the recombination sites can be used according to known method steps. For example, the modification of sites to provide (from a pair of sites that do not interact) partners that do interact could be achieved by requiring deletion, via recombination between the sites, of a DNA sequence encoding a toxic substance. Similarly, selection for sites that remove translation stop sequences, the presence or absence of protein binding sites, etc., can be easily devised by those skilled in the art.

Accordingly, the present invention provides a nucleic acid molecule, comprising at least one DNA segment having at least two engineered recombination sites flanking a Selectable marker and/or a desired DNA segment, wherein at least one of said recombination sites comprises a core region having at least one engineered mutation that enhances recombination in vitro in the formation of a Cointegrate DNA or a Product DNA.

The nucleic acid molecule can have at least one mutation that confers at 3 least one enhancement of said recombination, said enhancement selected from the 1-group consisting of substantially favoring excisive integration; (ii) favoring i~ ecsive recombination; (ii) relieving the requirement for host factors; (iii) WO 96/40724 PCT/S96/10082 -29increasing the efficiency of said Cointegrate DNA or Product DNA formation; and (iv) increasing the specificity of said Cointegrate DNA or Product DNA formation.

The nucleic acid molecule preferably comprises at least one recombination site derived from attB, attP, attL or attR. More preferably the att site is selected from atti, att2, or att3, as described herein.

In a preferred embodiment, the core region comprises a DNA sequence selected from the group consisting of: RKYCWGCTITYKThTACNAASTSGB (m-att) (SEQ ID NO:); AGCCWGCTITYKTRTACNAACTSGB (m-attB) (SEQ ID NO:2); GITCAGC1TMCKTRTACNAACTSGB (m-attR) (SEQ ID NO:3); AGCCWGCTITCKTRTACNAAGTSGB (m-attL) (SEQ ID NO:4); 'GTCAGC1Tr KTRTACNAAG sGB(m-attPl) (SEQ ID or a corresponding or complementary DNA or RNA sequence, wherein R=A or G; K=G or TiU; Y=C or TU; W=A or N=A or C or G or T/U; S=Cor G; 20 and B=C or G or T/U, as presented in 37 C.F.R. §1-.822, which is entirely incorporated herein by reference, wherein the core region does not contain a stop codon in one or more reading frames.

The core region also preferably comprises a DNA sequence selected from the group consisting of: 25 AGCCTGC1T'ITIGTACAAACITGT (attB) )(SEQ ID NO:6); AGCCTGCiTCTGTACAAA CTTGT('attB2)(SEQ9NO:7); ACCCAGCTITCTGTACAAAC1TGT (attB3) (SEQ ID NO:8); 00% GTCAGCITTTTGTACAAACTTGT (attRl) (SEQ IDNO:9); GTCAGCTIMTCTGTACAAACITGT (attR2) (SEQID 3 GTTCAGCTTCTTGTACAAArTGG (attR3) (SEQ ID

RAL,

WO 96/40724 PCT/US96/10082 30 AGCCTGCITITITGTACAAAGTGG (attLl) (SEQ ID NO:12); AGCCTGCTTTCTTGTACAAAGTTGG (attL2) (SEQ ID NO:13); ACCCAGCTICTTGTACAAAGTTGG (attL3) (SEQ ID NO:14); GTICAGCITTITT GTACAAAGTTGG(attPl)(SEQ GTTCAGCTTTCTTGTACAAAGTTGG (attP2,P3) (SEQ ID NO: 16); or a corresponding or complementary DNA or RNA sequence.

The present invention thus also provides a method for making a nucleic acid molecule, comprising providing a nucleic acid molecule having at least one engineered recombination site comprising at least one DNA sequence having at least 80-99% homology (or any range or value therein) to at least one of SEQ ID NOS:1-16, or any suitable recombination site, or which hybridizes under stringent conditions thereto, as known in the art.

Clearly, there are various types and permutations of such well-known in vitro and in vivo selection methods, each of which are not described herein for S the sake of brevity. However, such variations and permutations are contemplated and considered to be the different embodiments of the present invention.

20 It is important to note that as-a result of the preferred embodiment being In vitro recombination reactions, non-biological molecules such as PCR products can be manipulated via the present recombinational cloning method. In one example, it is possible to clone linear molecules into circular vectors.

There are a number of applications for the present invention. These uses include, but are not limited to, changing vectors, apposing promoters with genes, constructing genes for fusion proteins, changing copy number, changing replicons, cloning into phages, and cloning, PCR products (with an attB site at one end and a loxP site at the other end), genomic DNAs, and cDNAs.

WO 96/40724 PCT/US96/10082 -31 The following examples are intended to further illustrate certain preferred embodiments of the invention and are not intended to be limiting in nature.

Examples The present recombinational cloning method accomplishes the exchange of nucleic acid segments to render something useful to the user, such as a change of cloning vectors. These segments must be flanked on both sides by recombination signals that are in the proper orientation with respect to one another. In the examples below the two parental nucleic acid molecules plasmids) are called the Insert Donor and the Vector Donor. The Insert Donor contains a segment that will become joined to a new vector contributed by the Vector Donor. The recombination intermediate(s) that contain(s) both starting molecules is called the Cointegrate(s). The second recombination event produces two daughter molecules, called the Product (the desired new clone) and the Byproduct.

15 Buffers Various known buffers can be used in the reactions of the present invention. For restriction enzymes, it is advisable to use the buffers recommended by the manufacturer. Alternative buffers can be readily found in the literature or can be devised by those of ordinary skill in the art.

Examples 1-3. One exemplary buffer for lambda integrase is comprised of 50 mM Tris-HCl, at pH 7.5-7.8, 70 mM KCI, 5 mM spermidine,5 mM EDTA, and 0.25 mg/ml bovine serum albumin, and optionally, 10 %o glycerol.

One preferred buffer for PI Cre recombinase is comprised of 50 mM Tris-HCl at pH 7.5, 33 mM NaC1, 5 mM spermidine, and 0.5 mg/ml bovine serum albumin.

The buffer for other site-specific recombinases which are similar to F/ 4 lambda Int and P1 Cre are either known in the art or can be determined WO 96/40724 PCT/US96/10082 -32empirically by the skilled artisans, particularly in light of the above-described buffers.

Example 1: Recombinational Cloning Using Cre and Cre Int Two pairs ofplasmids were constructed to do the in vitro recombinational cloning method in two different ways. One pair, pEZC705 and pEZC726 (Figure 2A), was constructed with loxP and att sites, to be used with Cre and X integrase. The other pair, pEZC602 and pEZC629 (Figure 3A), contained the loxP (wild type) site for Cre, and a second mutant lox site, loxP 511, which differs from loxP in one base (out of 34 total). The minimum requirement for recombinational cloning of the present invention is two recombination sites in each plasmid, in general X and Y, and X and Y. Recombinational cloning takes place if either or both types of site can recombine to form a Cointegrate X and and if either or both (but necessarily a site different from the type forming the Cointegrate) can recombine to excise the Product and Byproduct plasmids from the Cointegrate Y and It is important that the recombination sites on the same plasmid do not recombine. It was found that the present recombinational cloning could be done with Cre alone.

Cre-Only Two plasmids were constructed to demonstrate this conception (see Figure 3A). pEZC629 was the Vector Donor plasmid. It contained a constitutive drug marker (chloramphenicol resistance), an origin of replication, loxP and loxP 511 sites, a conditional drug marker (kanamycin resistance whose expression is controlled by the operator/promoter of the tetracycline resistance operon of transposon TnlO), and a constitutively expressed gene for the tet 25 repressor protein, tetR. E. coli cells containing pEZC629 were resistant to chloramphenicol at 30 tg/ml, but sensitive to kanamycin at 100 pg/ml. pEZC602 was the Insert Donor plasmid, which contained a different drug marker WO 96/40724 PCTIUS96/10082 -33- (axnpicillin resistance), an origin, and loxP and laxp SI, sites flanking a multiple cloning site.

This experiment was comprised of two parts as follows: Part About 75 ng each of pEZC6O2 and pEZC629 were mixed in a total volume of 30 gl of Cre buffer (50 mM Tris-HCl pH- 7.5, 33 mM NaCi, mM spermidine-HCI, 500 txg/m1d bovine serum albumin). Two 10 gl aliquots were transferred to new tubes. One tube received 0.5 gil of Ore protein (approx.

4 units per jil; partially purified according to Abremski and Hoess, J BioL Chem.

259:1509 (1984)). Both tubes were incubated at 37*C for 30 minutes, then 700C for 10 minutes. Aliquots of each reaction were diluted and transformed into Following -expression, aliquots were plated on 30 ilig/ml chloramphenicol; 100 gni1 amrpicillin plus 200 pg/mI metbicilli or 100 g/mi kanamycin. Resus:- See Table 1. The reaction without Ore gave 1.11 x ampiciflin resistant colonies (from the Insert Donor plasmid pEZC6O2); 7.8xI 0 chloramphenicol resistant colonies (from the Vector Donor plasmid pEZC629); and 140 kanamycin resistant colonies (background). The reaction with added Cre gave 7.5xl0 5 ampicillin resistant colonies (from the Insert Donor plasmid pEZO6O2); 6.Il 0' cliloramphenicol resistant colonies (from the Vector Donor plasmid pEZC629); and 760 kanamycin resistant colonies (mixture of background colonies and colonies from the recombinational cloning Product plasmid). Analysis:- Because the number of colonies on the kanarnycin plates was much higher in the presence of Ore, nmany or most of them were predicted to contain the desired Product plasmid.

Table 1 o 25 Enzyme Ampicillin Chloramphenicol Kanamycin Efficiency None 1.lXlO' 7.8x10' 140 140t7.8xio0 5 =O.02% Cre 7.Sx1O1 6.1x10' 760 76016.1x1010O.12% Part Twenty four colonies from the Ore" kanamycin plates were IVRL, picked and inoculated into medium containng 100 pg/mIA kanamycin. Minipreps 3 were done, and the miniprep DNAs, uncut or cut with SinaI or Hindu!l, were WO 96/40724 PCT/US96/10082 -34electrophoresed. Results: 19 of the 24 minipreps showed supercoiled plasmid of the size predicted for the Product plasmid. All 19 showed the predicted Smal and HindIII restriction fragments. Analysis: The Cre only scheme was demonstrated. Specifically, it was determined to have yielded about 70% (19 of 24) Product clones. The efficiency was about 0.1% (760 kanamycin resistant clones resulted from 6.1x10 s chloramphenicol resistant colonies).

Cre Plus Integrase The plasmids used to demonstrate this method are exactly analogous to those used above, except that pEZC726, the Vector Donor plasmid, contained an attP site in place of loxP 511, and pEZC705, the Insert Donor plasmid, contained an attB site in place of loxP 511 (Figure 2A).

This experiment was comprised of three parts as follows: Part I: About 500 ng of pEZC705 (the Insert Donor plasmid) was cut with Scal, which linearized the plasmid within the ampicillin resistance gene.

(This was done because the A integrase reaction has been historically done with the attB plasmid in a linear state Nash, personal communication). However, it was found later that the integrase reaction proceeds well with both plasmids .supercoiled.) Then, the linear plasmid was ethanol precipitated and dissolved in 20 pl of I integrase buffer (50 mM Tris-HCl, about pH 7.8,70 mM KCI, 5 mM spermidine-HCl, 0.5 mM EDTA, 250 ttg/ml bovine serum albumin). Also, about 500 ng of the Vector Donor plasmid pEZC726 was ethanol precipitated and *to dissolved in 20 Il I integrase buffer. Just before use, A integrase (2 gl, 393 pg/ml) was thawed and diluted by adding 18 l cold I integrase buffer.

One l IHF (integration host factor, 2.4 mg/ml, an accessory protein) was diluted into 150 tl cold I integrase buffer. Aliquots (2 Vl) of each DNA were mixed with integrase buffer, with or without 1 pl each X integrase and IHF, in a total of 10 pl. The mixture was incubated at 25"C for 45 minutes, then at 70C for minutes. Half of each reaction was applied to an agarose gel. Results: In the SR1AL, presence of integrase and IHF, about 5% of the total DNA was converted to a \linear Cointegrate form. Analysis: Activity of integrase and IHF was confirmed.

WO 96/40724 PCT/US96/100S2 35 PartHl: Three microliters of each reaction -with or without integrase and WH) were diluted into 27 p±l of Cre buffer (above), then each reaction was split into two 10 pl aliquots (four altogether). To two of these reactions, 0.5 p1 of Gre protein (above) were added, and Ail reactions were incubated at 3-TC for 30 minutes, then at 70-C for 10 minutes. TE buffer (90 p1; TB: 10 mM Tris-HC1, pH 7.5, 1 ruM EDTA) was added to each reaction, and I ILI each was transformed into E. coli DH5em. The transformation mixtures were plated on 100 igg/ml anipicillin plus 200 p±g/ml methicillin; 30 pg/mI chloramphenicol; or 100 pg/mI kanamycin. Results: See Table 2.

Table 2 1 Enzynie Amnpicillin Chloramphenicol Kanamycin Efficiency None 990 20000 4 4 2xl0' 0.020/ Cre only 280 3640 0 0 htegrase' 1040 27000 9 9/ 2.7x10' =0.03% only Integrase* 110 1110 76 76 /.Lx1O' 6.9% Cre I_ I_ Integrase reactions also contained IHf.

Analyis: The Cre protein impaired transformation. When adjusted for this effect, the number of kanmycin resistant colonies, compared to the control reactions, increased more than 100 fold when both Cre and Integrase were used.

This suggests a specificity of greater thani 99%.

Part 111: 38 colonies were picked from the Integrase plus Cre plates, miniprep DNAs were made and cut with Hindul to give diagnqstt'kiiapping information. Result: All 38 had precisely the expected fragment sizes.

Ainalysis: The Cre plus A integrase method was observed to have much higher specificity than Gre-alone. Conclusion: The Gre plus X integrase method was demonstrated. Efficiency and specificity were much higher than for Cre only.

WO 96/40724 PCT/US96/10082 -36- Example 2: Using in vitro Recombinational Cloning to Subclone the Chloramphenicol Acetyl Transferase Gene into a Vector for Expression in Eukaryotic Cells (Figure 4A) An Insert Donor plasmid, pEZC843, was constructed, comprising the chloramphenicol acetyl transferase gene of E. coli, cloned between loxP and attB sites such that the loxP site was positioned at the 5'-end of the gene (Figure 4B).

A Vector Donor plasmid, pEZC1003, was constructed, which contained the cytomegalovirus eukaryotic promoter apposed to a loxP site (Figure 4C). One microliter aliquots of each supercoiled plasmid (about 50 ng crude miniprep DNA) were combined in a ten microliter reaction containing equal parts of lambda integrase buffer (50 mM Tris-HC1, pH 7.8, 70 mM KC1, 5 mM spermidine, 0.5 mM EDTA, 0.25 mg/ml bovine serum albumin) and Cre recombinase buffer (50 mM Tris-HCl, pH 7.5, 33 mM NaCI, 5 mM spermidine, mg/ml bovine serum albumin), two units of Cre recombinase, 16 ng integration host factor, and 32 ng lambda integrase. After incubation at 30'C for minutes and 75°C for 10 minutes, one microliter was transformed into competent E. coli strain DH5a (Life Technologies, Inc.). Aliquots of transformations were spread on agar plates containing 200 tg/ml kanamycin and incubated at 37°C overight An otherwise identical control reaction contained 20 the Vector Donor plasmid only. The plate receiving 10k of the control reaction transformation gave one colony, the plate receiving 10% of the recombinational cloning reaction gave 144 colonies. These numbers suggested that greater than 99% of the recombinational cloning colonies contained the desired product plasmid. Miniprep DNA made from six recombinational cloning colonies gave 25 the predicted size plasmid (5026 base pairs), CMVProd. Restriction digestion with NcoI gave the fragments predicted for the chloramphenicol acetyl transferase cloned downstream of the CMV promoter for all six plasmids.

.0"0 WO 96/40724 PCT/US96/10082 -37- Example 3: Subcloned DNA Segments Flanked by attB Sites Without Stop Codons Part I: Background The above examples are suitable for transcriptional fusions, in which transcription crosses recombination sites. However, both attR and loxP sites contain multiple stop codons on both strands, so translational fusions can be difficult, where the coding sequence must cross the recombination sites, (only one reading frame is available on each strand of loxP sites) or impossible (in attR or attL).

A principal reason for subcloning is to fuse protein domains. For example, fusion of the glutathione S-transferase (GST) domain to a protein of interest allows the fusion protein to be purified by affinity chromatography on glutathione agarose (Pharmacia, Inc., 1995 catalog). If the protein of interest is fused to runs of consecutive histidines (for example His6), the fusion protein can be purified by affinity chromatography on chelating resins containing metal ions (Qiagen, Inc.). It is often desirable to compare amino terminal and carboxy terminal fusions for activity, solubility, stability, and the like.

The attB sites of the bacteriophage X integration system were examined as an alternative to loxP sites, because they are small (25 bp) and have some sequence flexibility (Nash, HA. et al., Proc. NatL Acad Sd. USA 84:4049-4053 (1987). It was not previously suggested that multiple mutations to remove all stop codes would result in useful recombination sites for recombinational subcloning.

Using standard nomenclature for site specific recombination nlambda bacteriophage (Weisber, in Lambda III, Hendrix, et al., eds., Cold Spring Harbor WO 96/40724 PCT/US96/10082 -38- Laboratory, Cold Spring Harbor, NY (1989)), the nucleotide regions that participate in the recombination reaction in an E. coli host cell are represented as follows: attP attB Int, IHF It Xis, Int, IHF attR attL where: O represents the 15 bp core DNA sequence found in both the phage and E. coli genomes; B and B' represent approximately 5 bases adjacent to the core in the E. coli genome; and PI, HI, P2, X, H2, C, C, P'1, P2, and P'3 represent known DNA sequences encoding protein binding domains in the bacteriophage 15 genome.

The reaction is reversible in the presence of the protein Xis (excisionase); recombination between attL and attR precisely excise the X genome from its integrated state, regenerating the circular I genome containing attP and the linear E. coli genome containing attB.

20 Part II: Construction and Testing ofPlasmids Containing Mutant att Sites SMutant attL and attR sites were constructed. Importantly, Landy et al.

(Ann. Rev. Biochem. 58:913 (1989)) observed that deletion of the PI and HI domains of attP facilitated the excision reaction and eliminated the integration reaction, thereby making the excision reaction irreversible. Therefore, as mutations were introduced in attR, the PI and HI domains were also deleted.

attR sites in the present example lack the P1 and HI regions and have the Ndel site removed (base 27630 changed from C to and contain sequences WO 96/40724 PCT/US96fl 0082 -39corresponding to bacteriophage I coordinates 27619-27738 (GenBank release 92.0, bg:LAMCG, "Complete Sequence of Bacteriophage Lambda").

The sequence of attB produced by recombination of wild type attL and attR sites is: B 0 B' attlwt: 5' AGCCT G TTTATACMA CTMA 3' (SEQ. ID NO: 3 1) 3' TCGGA CGAAAAAjATQTT GACT The stop codons are italicized and underlined. Note that sequences of att,attRt, and attP can be derived from the attB sequence and the boundaries of bacteriophage I contained within attL and attR (coordinates 27619 to 27818).

When mutant attRl and attLI sites were recombined the sequence attB 1 was produced (mutations in bold, large font): B 0 BI *attfll: 5' AGCCT GCTTTTrTOTAcAAA cTr. 3 (SEQ. ID NO: 6) 3' TcQ cGAAAC AoTir.T GmcA s' Note that the four stop codons arc gone.

When an additional mutation was introduced in the attRI and attLI sequences (bold), attR2 and attL2 sites resulted. Recombination of attR2 and attL2 produced the attB2 site: B 0 B' *attB2: 5' AGCCT GCrrCTrGTACAAA CTTGT 3' (SEQ. ID NO: 7) TCGGA CGAA1AGAACATGCr GIAA s Tt he recombination activities of the above attL and attR sites were-assayed .r as follows. The attB site of plasmid pEZC7O5 (Figuare 2B3) was replaced with WO 96/40724 WO 9640724PCT/US96/1 0082 attLwt, attLi, or attL2. The attP site of plasinid pEZC726 (Figure 2C) was replaced with attRwt (lacking regions I1 and HI), attRI, or attR2. Thus, the resulting plasmids could recombine via their loxP sites, mediated by Cre, and via their attR and attL sites, mediated by hIt, Xis, and IHE Pairs of plasmids: were mixed and reacted with Gre, hIt, Xis, and 11W, transformed. into E. coli competent cells, and plated on agar containing kanamycin. The results are presented in Table 3: Table 3 .20 Vector donor att site Gene donor att site fi of kanamycin resistant colonies* attRwt(pEZCI3Ol) None 1 (background) attdwt (EZC 1313) 147 attLi (pEZC13 17) 47 attL2 (pEZCl321) 0 attRl (pEZCI3O5) None 1 (background) atd-wt (pEZCl1313) 4 attLi (pEZC1317)- 128 attL2 (pEZCl321) 0 attR2 (pEZC13O9) None 9 (background) attLwt (pEZCI1313) 0 attL2 (pEZWl3l7) 0 (pEZC1321) 209 1% of each transformation was spread on a kanamycin plate.) The above data show that whereas the wild type alt and atti sites recombine to a small extent, the atti and att2 sites do not recombine detectably with each other.

Part IH. Recombination was demonstraed when the core region of both attB sites flanking the DNA segment of interest did not contain stop codons. The physical state of the participating plasmids; was discovered to influence recombination efficiency.

The appropriate alt sites were moved into pEZC7O5 and pEZC726 to make the plasmids pEZC14O5 (Figure 5Gi) (attRl and attR2) and pEZCI5O2 (Figure 511) (attL I and attL2). The desired DNA segment in tis experiment was Scopy of the chloramphenicol resistance gene cloned between the two attL sites WO 96/40724 PCTIUS9610082 -41of pEZC1502. Pairs of plasmids were recombined in vitro using Int, Xis, and IHF (no Cre because no loxP sites were present). The yield of desired kanamycin resistant colonies was determined when both parental plasmids were circular, or when one plasmid was circular and the other linear as presented in Table 4: Table 4

S.

20 *oo Vector donor' Gene donor' Kanamycin resistant colonies 2 Circular pEZC 1405 None Circular pEZC1405 Circular pEZC1502 2680 Linear pEZC1405 None Linear pEZC1405 Circular pEZC1502 172000 Circular pEZC1405 Linear pEZC1502 73000 DNAs were purified with Qiagen columns, concentrations determined by A260, and linearized with Xba I (pEZC1405) or AlwN I (pEZC1502). Each reaction contained 100 ng of the indicated DNA. All reactions (10 pl total) contained 3 pl of enzyme mix (Xis, Int, and HF). After incubation (45 minutes at 25°, 10 minutes at one pl was used to transform E. coli DHSa cells.

2 Number of colonies expected if the entire transformation reaction (1 ml) had been plated. Either 100 pl or 1 pl of the transformations were actually plated.

Analysis: Recombinational cloning using mutant attR and attL sites was confirmed. The desired DNA segment is subcloned between attB sites that do not contain any stop codons in either strand. The enhanced yield of Product DNA (when one parent was linear) was unexpected because of earlier observations that the excision reaction was more efficient when both participating molecules were supercoiled and proteins were limiting (Nunes-Duby et al., Cell 50:779-788 (1987).

Example 4: Demonstration of Recombinational Cloning Withounverted Repeats Part I: Rationale The above Example 3 showed that plasmids containing inverted repeats of the appropriate recombination sites (for example, attL1 and attL2 in plasmid pEZC1502) (Figure 5H) could recombine to give the desired DNA segment WO 96/40724 PCT/US96/10082 -42 flanked by attB sites without stop codons, also in inverted orientation. A concern was the in vivo and in vitro influence of the inverted repeats. For example, transcription of a desired DNA segment flanked by attB sites in inverted orientation could yield a single stranded RNA molecule that might form a. hairpin structure, thereby inhibiting translation.

Inverted orientation of similar recomnbination site's can be avoided by placing the sites in direct repeat arrangement att sites. If parental plasmids each have a wid tp tLand wild type attR site, in direct repeat the hIt, Xis, and Wli proteins will simply remove the DNA segment flanked by those sites in an intramolecular reaction. However, the mutant sites described in the above Example 3 suggested that it might be possible to inhibit the intramolecular reaction while allowing the intermolecular recombination to proceed as desired.

Part H. Structure of Plasmid Without Invyerted Repeatfor Recombinational Cloning The attR2 sequence in plasinid pEZC 1405 (Figure 5G) was replaced with attL2, in the opposite orientation, to make pEZC 1603 (Figure 6A). The attL2 sequence of pEZClSO2 (Figure 5H) was replaced with attR2 in the opposite orientation, to make pEZCl1706 (Figure 6B). E-ach of these plasmids gontained mutations in the core region that make intramolecular reactions between atti and att2 cores very inefficient (see Example 3, above).

Plasmids pEZCI4O5, pEZClSO2, pEZCl6O3 and pEZCl7O6 were purified on Qiagen columns (Qiagen, Inc.). Aliquots of plasmids pEZCI4OS and pEZC16O3 were linearized with Xba 1. Aliquots of plasmids pEZC 1502 and pEZCl1706 were linearized with AlwN 1. One hundred ng of plasmids were mixed in buffer (equal volumes of 50 mM Tris LIC1 pH 7.5, 25 mM Tris HCl pH 70 mMv KCI, 5 mM spennidine, 0.5 maM EDTA, 2 5 0Itg/ml BSA, glycerol) containing Int (43.5 ng), Xis (4.3 ng) and ll{F (8.1 ng) in a final volume of 10 pd. Reactions were incubated for 45 mninutes at 25 T, 10 minutes at 65 *C, and 1 p1 was transformned into E. coli DH5.a. After expression, aliquots were spread on agar plates containing 200 pig/mi kanamycin and incubated at 37 0

C.

WO 96/40724 PCT/US96110082 -43 Results, expressed as the number of colonies per 1 gil of recombination reaction are presented in Table Table Vector Donor Gene Donor Colonies Predicted product Circular 1405 -100 Circular 1405 Circular 1502 3740 3640/3740 97% Linear 1405 Linear 1405 Circular 1502 172,000 171,910/172,000 =99.9 0 /o Circular 1405 Linear 1502 73,000 72,900173,000 =99.9% Circular 1603 Circular 1603 Circular 1706 410 330/4 10 Linear 1603 270 Linear 1603 Circular 1706 7000 673017000 96% Circular 1603 Linear 1706 10,800 10,530/10,800 =97% Analpsis. In all configurations, circular or linear, the pEZC14O5 x PEWC 1502 pair (with att sites in inverted repeat configuration) was mare efficient than pEZC16O3 x pEZC1706 pair (with att sites mutated to avoid hairpin formation). The pEZC16O3 x pEZC17O6 pair gave higher backgrounds and lower efficiencies than the pEZC 1405 x pEZC1 502 pair. While less efficient, or more of the colonies from the pEZCI6O3 x pEZCl7O6 reactions were expected to contain the desired plasmid product Making one partner linear stimulated the reactions in all cases.- Part III: Confirmation of Product Plasmids Structure Six colonies each from the linear pEZC14OS (Figure 5G) x circular pEZCI502 (Figure 5H), circular pEZCl4O5 x linear pEZCI5O2, linear pEZCI6O3 (Figure 6A) x circular pEZCl7O6 (Figure 6B), and circular U) pEZC 1603 x linear pEZC1706 reactions were picked into rich medium and

S

S

S

WO 96/40724 PCT/US96/10082 -44miniprep DNAs were prepared. Diagnostic cuts with Ssp I gave the predicted restriction fragments for all 24 colonies.

Analysis. Recombination reactions between plasmids with mutant attL and attR sites on the same molecules gave the desired plasmid products with a high degree of specificity.

Example 5: Recombinational Cloning with a Toxic Gene Part I: Background Restriction enzyme Dpn I recognizes the sequence GATC and cuts that sequence only if the A is methylated by the dam methylase. Most commonly used E. coli strains are dam*. Expression of Dpn I in dam' strains of E coli is lethal because the chromosome of the cell is chopped into many pieces.

However, in dam- cells expression of Dpn I is innocuous because the chromosome is immune to Dpn I cutting.

In the general recombinational cloning scheme, in which the vector donor 0 15 contains two segments C and D separated by recombination sites, selection for the desired product depends upon selection for the presence of segment D, and the absence of segment C. In the original Example segment D contained a drug resistance gene (Km) that was negatively controlled by a repressor gene found on segment C. When C was present, cells containing D were not resistant to 20 kanamycin because the resistance gene was turned off.

The Dpn I gene is an example of a toxic gene that can replace the repressor gene of the above embodiment If segment C expresses the Dpn I gene product, transforming plasmid CD into a dam' host kills the cell. If segment D is transferred to a new plasmid, for example by recombinational cloning, then 25 selecting for the drug marker will be successful because the toxic gene is no longer present.

WO 96/40724 PCTIUS96/10082 Part II: Construction of a Vector Donor Using Dpn I as a Toxic Gene The gene encoding Dpn I endonuclease was amplified by PCR using primers S'CCA CCA CAA ACG CGT CCA TGG AAT TAC ACT TTA ATT TAG3' (SEQ. ID NO: 17) and 5'CCA CCA CAA GTC GAC GCA TGC CGA CAG CCT TCC AAA TGT3' (SEQ. ID NO:18) and a plasmid containing the Dpn I gene (derived from plasmids obtained from Sanford A. Lacks, Brookhaven National Laboratory, Upton, New York; also available from American Type Culture Collection as ATCC 67494) as the template.

Additional mutations were introduced into the B and B' regions of attL and attR, respectively, by amplifying existing attL and attR domains with primers containing the desired base changes. Recombination of the mutant attL3 (made with oligo Xis 15) and attR3 (made with oligo Xisl 12) yielded attB3 with the following sequence (differences from attBI in bold): B O B' ACCCA GCTTTCTTGTACAAA GTGGT (SEQ. ID NO:8) TGGGT CGAAAGAACATGTTT CACCA The attL3 sequence was cloned in place of attL2.of an existing Gene Donor plasmid to give the plasmid pEZC2901 (Figure 7A). The attR3 sequence was cloned in place of attR2 in an existing Vector Donor plasmid to give plasmid pEZC2913 (Figure 7B) Dpn I gene was cloned into plasmid pEZC2913 to replace the tet repressor gene. The resulting Vector Donor plasmid was named pEZC3101 (Figure 7C). When pEZC3101 was transformed into the dam" strain SCS 110 (Stratagene), hundreds of colonies resulted. When the same pmid was transformed into the dam+ strain DH5ax, only one colony was produced, even though the DH5a cells were about 20 fold more competent than the SCS 110 cells. When a related plasmid that did not contain the Dpn I gene was Uq S transformed into the same two cell lines, 28 colonies were produced from the SCS 110 cells, while 448 colonies resulted from the DH5a cells. This is evidence WO 96/40724 PCT/US96/10082 46that the Dpn I gene is being expressed on plasmid pEZC3 101 (Figure 7C), and that it is killing the dam*~ MHa cells but not the dam- SCSI 10 cells.

Part M.I Demonstration of Recombinauional Cloning Using Dpn I Selection A pair of plasnids was used to demonstrate recombinational cloning with selection for product dependent upon the toxic gene Dpn L. Plasmid pEZC3 101 (Figure 7C) was linearized with Mlu I and reacted with circular plasmid pEZC29O 1 (Figure 7A). A second pair of plasmids using selection based on control of drug resistance by a repressor gene was used as a control: plasmid pEZC18O2 (Figure 7D)) was linearized with Xba I and reacted with circular plasmid pEZC15O2 (Figure 511). Eight microliter reactions containing the same buffer and proteins XGs, Int, and 11ff as in previous examples were incubated for minutes at 25 OC, then 10 minutes at 75CC, and I M1 aliquots were transformed into DH5ca dam+i) competent cells, as presented in Table 6.

Table 6 Reaction Vector donor Basis of selecton Gene donor Colonies I pEZC31O/Mu Dpa Itoxicity 3 3 2 pE5ZC31IIMu Dpn I[toxicity Circlar PEZC2901 4000 3 pEZC18O2IXba Tet repressr 0 4 PEZC18O2/Xba Ter rpresor Circular pEZC15O2 112100 Miniprep DNAs were prepared from four colonies from reaction and cut with restriction enzyme Ssp 1. All gave the predicted firagments.

Analysis:, Subeloning using selection with a toxic gene was demonstrated. Plasmids of the predicted structure were produced.

a..

WO 96/40724 PCTIUS96/10082 -47 Example 6: Clning of Genes with Uracil DNA Glycosylase and Subcloning of the Genes with Recombinahional Cloning to Make Fusion Proteins Part Converting an Existing Expression Vector to a Vector Donor for Recombinational Cloning A cassette useful for converting existing vectors into functional Vector Donors was made as follows. Plasinid pEZC3 101 (Figure 7C) was digested with Apa I and Kpn 1, treated with T4 DNA polymerase and dNT~s to render the ends blunt, further digested with Sma 1, Hpa 1, and AIwN I to render the undesirable DNAfr~gents sall, andthe 2.6 kb casecontaining the attRI CmR-Dpn I attR-3 domains was gel purified. the concentration of the purified cassette was estimated to be about 75 ng DNA4ILI.

Plasmid pGEX-2TK, (Figure 8A) (Pliarmwaia) allows fusions between the protein glutathione S transferase and any second coding sequence that can be inserted in its multiple cloning site. pGEX-2TK DNA was digested with Sma 1 and treated with alkaline phosphatase. About 75 zig of the above purified DNA cassette was ligated with about 100 ng of the pGEX-2TK vector for 2.5 hours in 5: aSpl ligation, then 1 pl was transformed into competent BRL 3056 cells (a damw derivative of DHIOB; dam7 stains commercially available include DM1 from Life Technologies, Inc., and SOS 110 from Stratagene). Aliquots of the transformation mixture were plated on LB agar containing 100 tghml amnpicillin (resistance gene present on pGEX-2TK) and 30 t&gtm1 chloramphenicol (resistance gene present on the DNA cassette). Colonies were picked and miniprep DNAs were made. The orientation of the cassette in pGEX.2TK was determined by diagnostic cuts with EcoR 1. A plasmid with tlr-desired 25 orientation was named pEZC35OI (Figure 8B).

WO 96/40724 PMUS96110082 -48- Part Cloning Reporter Genes Into an Recombinational Cloning Gene Donor Plasmnid in Three Reading Frames Uracil DNA glycosylase (UDG) cloning is a method for cloning PCR amplification products into cloning vectors patent No. 5,334,51-5, entirely incorporated herein by reference). Briefly, PCR amplification of the desired DNA segment is performed with primers that contain uracil bases in place of thymidine bases in their 5'ends. When such POR products are incubated with the enzyme UDO, the uracil bases are specifically removed. The loss of these bases weakens base pairing in the ends of the POR product DNA, and when incubated at a suitable temperature 3700), the ends of such products are largely single stranded. If such incubations are done in the presence of linear cloning vectors containing protruding 3' tails that are complementary to the 3' ends of the PCR products, base pairing efficiently anneals the PCR products to the cloning vector.

When the annealed product is introduced into E. coli cells by transformation, in vivo processes efficiently convert it into a recombinant plasmid.

UDG cloning vectors that enable cloning of any PCR product in all three reading frmes were prepared from pEZC32OI (Figure 8K) as follows. Eight *oligonucleotides were obtained from Life Technologies, Inc. (all written 5,-3Y: rfl top (GOCC GAT TAC GAT ATO CCA ACG ACC GAA AAC CTG TAT Trl CAG GOT) (SEQ. 11D NO: 19), Ml bottom (CAG GIT TFC GOT CGT TGO GAT ATC GTA ATC)(SEQ. MD NO:20), r12 top (GOCCA GAT TAO GAT ATC CCA ACG ACC GAA AAC CTG TAT TIT CAG GOT)(SEQ. ID *0.00:NO:21), K12 bottom (CAG GIT TlC GOT CGT TGG GAT ATC GTA ATC T)(SEQ. ID NO:22), r13 top (GOCCAA GAT TAC GAT ATC OCA AG ACC GAA AAC CTG TAT TilT CAG GGT)(SEQ. ID N0:23), Mf bottom OTIT ITC GOT CGT TO GAT ATC OTA ATC TT(SEQ. ID NQ:24), carboxy top (ACC GTT TAO GTG GAC)(SEQ. ID NO:25) and carboxy bottom (TOGA GTO CAC GTA AAC GGT TCC CAC TITA TrA)(SEQ. ID NO:26). The rfl, 2, and 3 top strands and' the carboxy bottom strand were phosphorylated on their 5' ends with T4 polynucleotide kinase, and then the J;,ALI 1, conmplementay strands of each pair were hybridized. Plasmid pEZC32OI fi3) P ,1 WO 96/40724 PCT/US96/10082 -49- (Figure 8K) was cut with Not I and Sal I, and aliquots of cut plasmid were mixed with the carboxy-oligo duplex (Sal I end) and either the rfl, rf2, or rf3 duplexes (Not I ends) (10 pg cut plasmid (about 5 pmol) mixed with 250 pmol carboxy oligo duplex, split into three 20 tl volumes, added 5 pl (250 pmol) of rfl, rf2, or rf3 duplex and 2 pl 2 units T4 DNA ligase to each reaction). After 90 minutes of ligation at room temperature, each reaction was applied to a preparative agarose gel and the 2.1 kb vector bands were eluted and dissolved in 50 1il of TE.

Part I: PCR ofCAT andphoA Genes Primers were obtained from Life Technologies, Inc., to amplify the chloramphenicol acetyl transferase (CAT) gene from plasmid pACYC 84, and phoA, the alkaline phosphatase gene from E. coli. The primers had 12-base extensions containing uracil bases, so that treatment of PCR products with uracil DNA glycosylase (UDG) would weaken base pairing at each end of the DNAs and allow the 3' strands to anneal with the protruding 3' ends ofthe rfl, 2, and 3 vectors.described above. The sequences of the primers (all written 5' 3') were: CAT left, UAU UUU CAG GGU ATG GAG AAA AAA ATC ACT GGA TAT ACC (SEQ. ID NO:27); CAT right, UCC CAC UUA UUA CGC CCC GCC CTG CCA CTC ATC (SEQ. ID NO:28); phoA left,UAU UUU CAG GGU SATG CCT GTT CTG GAA AAC CGG (SEQ. ID NO:29); and phoA right, UCC CAC UUA UUA TIT CAG CCC CAG GGC GGC TIT C (SEQ. ID The primers were then used for PCR reactions using known method steps (see, U.S. patent No. 5,334,515, entirely incorporated herein by reference), and the polymerase chain reaction amplification products obtained with theseprimers comprised the CAT or phoA genes with the initiating ATGs but w ithout any transcriptional signals. In addition, the uracil-containing sequences on the amino termini encoded the cleavage site for TEV protease (Life Technologies, Inc.), and those on the carboxy terminal encoded consecutive TAA nonsense codons.

Unpurified PCR products (about 30 ng) were mixed with the gel purified, linear rfl, rf2, or rf3 cloning vectors (about 50 ng) in a 10 pl reaction containing IX REact 4 buffer (LT) and 1 unit UDG (LTI). After 30 minutes at 37 0 C, 1 pl WO 96/40724 PCTIUS96/10092 aliquots of each reaction were transformed into competent E. coli DH5a cells (LTI) and plated on agar containing 50 jig/ml kanamycin. Colonies were picked and analysis of miniprep DNA showed that the CAT gene had been cloned in reading fr-ame 1 (pEZC36OI)(Figure. SC), reading frame 2 (pEZC36O9)(Figure 8D) and reading frame 3 (pEZC3617)(Figure 8E), and that the phoA gene hadbeen cloned in reading frame I (pEZC36O6)(Figure 8F), reading fr-ame 2 (pEZC36l3)(Figure 8G) and reading frame 3 (pEZC362 1)(Figure 814.

Padt IV: Subclon ing of CA T or phoA from UD G Clon ing Vectors into a GST Fusion Vector Plasmids encoding fusions between GST and either CAT or phoA in all three reading fr-ames were constructed by recombinational cloning as follows.

Miniprep DNA of GST vector donor pEZC35Ol (Figure SB3) (derived from Phannacia, plasinid pGEX-2TK as described above) was linearized with Cla I.

About 5 ng of vector donor were mixed with about 10 ng each of the appropriate circular gene donor vectors contaning CAT or phoA in 8 gi reactions containing buffer and recombination proteins Int, Xis, and IHE (above). After incubation, 1 jil of each reaction was transformed into E. coli stain DHi5c and plated on ampicillin, as presented in Table 7.

Table 7 **000* 0 0000 0000 0 25 0 0 000 0 0000 DNA Colonies (10% of each transformation) Linear vector donor (pEZC35OI/Cla) 0 Vector donor CAT rfl 110 Vector donor CAT rf2 71 Vector donor CAT rf3 14.8 Vector donor phoA rfl 121 Vector donor t phoA rf2 128 Vector donor phoA rf3 31 WO 96/40724 PCT/US96/10082 -51- Part V: Expression of Fusion Proteins Two colonies from each transformation were picked into 2 ml of rich medium (CircleGrow, BiolOl0 Inc.) in 17 x 100 nmm plastic tubes (Falcon 2059, Becton Dickinson) containing 100 pg/ml ampicillin and shaken vigorously for about 4 hours at 37°C, at which time the cultures were visibly turbid. One ml of each culture was transferred to a new tube containing 10 pi of 10% IPTG to induce expression of GST. After 2 hours additional incubation, all cultures had about the same turbidity; the A600 of one culture was 1.5. Cells from 0.35 ml each culture were harvested and treated with sample buffer (containing SDS and P-mercaptoethanol) and aliquots equivalent to about 0.15 A600 units of cells were applied to a Novex 4-20% gradient polyacrylamide gel. Following electrophoresis the gel was stained with Coomassie blue.

Results: Enhanced expression of single protein bands was seen for all 12 cultures. The observed sizes of these proteins correlated well with the sizes predicted for GST being fused (through attB recombination sites without stop codons) to CAT or phoA in three reading frames: CAT rfl 269 amino acids; CATr2=303 amino acids; CAT rf3= 478 amino acids; phoA rfl 282 amino acids; phoA rt2 280 amino acids; and phoA rf3 705 amino acids.

:":"Analysis: Both CAT and phoA genes were subcloned into a GST fusion oo..

vector in all three reading frames, and expression of the six fusion proteins was Sodemonstrated.

While the foregoing invention has been described in some detail for 0 purposes of clarity and understanding, it will be appreciated by one skilled in the art from a reading of this disclosure that various changes in form and deail can 25 be made without departing from the true scope of the invention and appended "*-:-claims. All patents and publications cited herein are entirely incorporated herein by reference.

PCT/US 96/10082 18 Rec'd PCTPTO JAN 1997 -51.1- SEQUENCE LISTING GENERAL INFORMATION: APPLICANT: Life Technologies, Inc.

8717 Grovemont Circle Gaithersburg, MD 20884-9980 United States of America APPLICANT/INVENTORS: Hartley, James L.

Brasch, Michael A.

(ii) TITLE OF INVENTION: Recombinational Cloning Using Engineered Recombination Sites (iii) NUMBER OF SEQUENCES: 31 (iv) CORRESPONDENCE ADDRESS: ADDRESSEE: STERNE, KESSLER, GOLDSTEIN FOX, P.L.L.C STREET: 1100 New York Ave., N. W. Suite 600 CITY: Washington STATE: DC COUNTRY: USA ZIP: 20005-3934 COMPUTER READABLE FORM: MEDIUM TYPE: Floppy disk COMPUTER: IBM PC compatible OPERATING SYSTEM: PC-DOS/MS-DOS SOFTWARE: PatentIn Release Version #1.30 (vi) CURRENT APPLICATION DATA: APPLICATION NUMBER: PCT/US96/10082 FILING DATE: 07-JUN-1996

CLASSIFICATION:

(ix) TELECOMMUNICATION INFORMATION: TELEPHONE: 202-371-2600 TELEFAX: 202-371-2540 INFORMATION FOR SEQ ID NO:1: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both MOLECULE TYPE: cDNA AMENDED

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U 9 6/ 1 0 08Z 106 Rec'd Gtiis' FTO1997 -51.2- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: RKYCWGCTTT YKTRTACNAA STSGB INFORMATION FOR SEQ ID NO:2: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: AGCCWGCTTT YKTRTACNAA CTSGB INFORMATION FOR SEQ ID NO:3: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA SEQUENCE DESCRIPTION: SEQ ID NO:3: GTTCAGCTTT CKTRTACNAA CTSGB INFORMATION FOR SEQ ID NO:4: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: GTTGCTTT CKTRTACNAA GTSGB

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SPCTUS 96/10082 -51.3- 7jJec 3O INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: CDNA (xi) SEQUENCE DESCRIPTION: SEQ ID GTTCAGCTTT YKTRTACNAA GTSGB INFORMATION FOR SEQ ID NO:6: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: AGCCTGCTTT TTTGTACAAA CTTGT S INFORMATION FOR SEQ ID NO:7: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: CDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: AGCCTGCTTT CTTGTACAAA CTTGT INFORMATION FOR SEQ ID NO:8: 0 SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs AMENDED SHEET pgT/us q(-io 082 -514.1% Reed PGTIP1 u0k JAN4 1997 TYPE: nucleic acid IC) STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) 'SEQUENCE DESCRIPTION: SEQ ID NO: 8: ACCCAGCTTT CTTGTACAAA CTTGT INFORMATION FOR SEQ ID NO:9: Wi SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID 140:9: GTTCAGCTTT TrTGTACAAA CTTGT INFORMATION FOR SEQ ID NO:.O:' Ci SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid CC) STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID 140:10: GTTCAGCTTT CTTGTACAAA CTTGT INFORMATION FOR SEQ ID NO:11: SEQUENCE

CHARACTERISTICS:

LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both lp'A CD) TOPOLOGY: both AMENDED SHEET pCTIUS qcnoQS' -51.5- 106Re'dPCTTO ji 1997 (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: GTTCAGCTTT CTTGTACAAA GTTGG INFORMATION FOR SEQ ID NO:12: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: AGCCTGCTTT TTTGTACAAA GTTGG INFORMATION FOR SEQ ID NO:13: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: *AGCCTGCTTT CTTGTACAAA GTTGG INFORMATION FOR SEQ ID.NO:14: 9 SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA END SHEET AMENDED

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PCT/US 96/10082 106 Rec'd PCTPTOC OJA '997 -51.6- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: ACCCAGCTTT CTTGTACAAA GTTGG INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID GTTCAGCTTT TTTGTACAAA GTTGG INFORMATION FOR SEQ ID NO:16: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: GTTCAGCTTT CTTGTACAAA GTTGG INFORMATION FOR SEQ ID NO:17: SEQUENCE CHARACTERISTICS: LENGTH: 39 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: -fA ACCACAAA CGCGTCCATG GAATTACACT TTAATTTAG 39 AMENDED

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-pcT/us 9611OO8 2 -51.7- 106 Red'd PCT TO C.6JAk,- 1997 INFORMATION FOR SEQ ID NO:18: SEQUENCE CHARACTERISTICS: LENGTH: 39 base pairs TYPE; nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: CCACCACAAG TCGACGCATG CCGACAGCCT TCCAAATGT 39 INFORMATION FOR SEQ ID N0:19: SEQUENCE CHARACTERISTICS: LENGTH: 46 base pairs TYPE: nucleic acid STRANflEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA Cxi) SEQUENCE DESCRIPTION: SEQ ID NO:19: GGCCGATTAC GATATCCCAA CGACCGAAAA CCTGTATTTT CAGGGT 46 INFORMATION FOR SEQ ID Wi SEQUENCE CHARACTERISTICS: LENGTH: 30 base pairs TYPE: nucleic acid STRAN4DEDNESS: both TOPOLOGY: both (iMOLECULE TYPE: CDNA (xi) SEQUENCE DESCRIPTION: SEQ ID N0:20: CAGGTTTTCG GTCGTTGGGA TATCGTAATC INFORMATION FOR SEQ ID NO:21: L Ci) SEQUENCE CHARACTERISTICS: LENGTH: 47 base pairs ~T?~NT UAMENDED SHEET PGTUS 96/1008Z) TYPE: nucleic acid -18 lcd~TDc j~ 19 rc) STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21- GGCCAGATTA CGATATCCCA ACGACCGAAA ACCTGTATTT TCAGGGT 47 INFORMATION FOR SEQ ID NO:22: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 31 base pairs TYPE: nucleic acid STRANDEDNESS: both CD) TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: *CAGGTTTTCG GTCGTTGGGA TATCGTAATC T 31 INFORMATION FOR SEQ ID NO:23: Ci) SEQUENCE CHARACTERISTICS: CA) LENGTH: 48 base pairs TYPE: nucleic acid STRANDEDNESS: both 0 CD) TOPOLOGY: both (ii) MOLECULE TYPE: cDNA Cxi) SEQUENCE DESCRIPTION: SEQ ID N0:23: :GGCCAAGATT ACGATATCCC AACGACCGA.A AACCTGTATT TTCAGGGT 48 INFORMATION FOR SEQ ID NO:24: Wi SEQUENCE CHARACTERISTICS: CA) LENGTH: 32 base pairs TYPE: nucl.eic acid STRANDEDNESS: both TOPOLOGY: both AMENDED

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199 (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: CAGGTTTTCG GTCGTTGGGA TATCGTAATC TT 32 INFORMATION FOR SEQ -ID SEQUENCE CHARACTERISTICS: LENGTH: 15 base pairs TYPE: nucleic acid STRANDfEDNESS: both TOPOLOGY- both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID ACCGTTTACG TGGAC 1 INFORMATION FOR SEQ ID 110:26: SEQUENCE CHARACTERISTICS: LENGTH: 31 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both UJ 3 -WtCtLE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26- TCGAGTCCAC GTAAACGGT CCCACTTATT A 31 INFORMATION FOR SEQ ID NO: 27: SEQUENCE CHARACTERISTICS: LENGTH: 39 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA AMENDED SHEET pCT'US 96fi 00 8 2 ,ReeCWP O u JAN 1997 -51.10- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: UAUUUUCAGG GUATGGAGAA AAAAATCACT GGATATACC 39 INFORMATION FOR SEQ ID NO:28: SEQUENCE CHARACTERISTICS: LENGTH: 33 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28: UCCCACUUAU UACGCCCCGC CCTGCCACTC ATC 33 INFORMATION FOR SEQ ID NO:29: SEQUENCE CHARACTERISTICS: LENGTH: 33 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both see* (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29: UAUUUUCAGG GUATGCCTGT TCTGGAAAAC CGG 33 ,o INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 34 base pairs TYPE: nucleic acid STRANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID JS C CCACUUAU UATTTCAGCC CCAGGGCGGC TTTC 34 POTIUS 96110082 INFORMATION FOR SEQ ID NO:31: Wi SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STR.ANDEDNESS: both TOPOLOGY: both (ii) MOLECULE TYPE: cDNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:31: AGCCTGCTTT TTTATACTAA CTTGA AMENDED SHEET 51.12- Where the terms "comprise", "comprises", "comprised" or "comprising" are used in this specification, they are to be interpreted as specifying the presence of the stated features, integers, steps or components referred to, but not to preclude the presence or addition of one or more other feature, integer, step, component or group thereof.

This is a divisional application of Australian Patent No. 724922 and the disclosures thereof are incorporated herein by way of reference.

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Claims (28)

1. 2. A Vector Donor DNA molecule according to claim 1, wherein the Selectable marker is at least one DNA segment selected from the group consisting of: a DNA segment that encodes a product that provides resistance against otherwise toxic compounds; (ii) a DNA segment that encodes a product that is otherwise lacking in the recipient cell; (iii) a DNA segment that encodes a product that suppresses the activity of a gene product; (iv) a DNA segment that encodes a product that can be readily identified; S 20 a DNA segment that encodes a product that is detrimental to cell survival and/or function; ooooo (vi) a DNA segment that inhibits the activity of any of the DNA segments of above; (vii) a DNA segment that binds a product that modifies a substrate; (viii) a DNA segment that provides for isolation of a desired molecule; and (ix) a DNA segment that encodes a specific nucleotide sequence which can be otherwise non-functional; and 20O1/01.mgdiv spec.52 WO 96/40724 PCT/US96/10082 53 a DNA segment that, when absent, directly or indirectly confers sensitivity to particular compounds.
2. 3. A Vector Donor DNA according to claim 2, wherein said Selectable marker is at least one selected from the group consisting of an antibiotic resistance gene, a tRNA gene, an auxotrophic marker, a toxic gene, a phenotypic marker, an antisense oligonucleotide; a restriction endonuclease; a restriction endonuclease cleavage site, an enzyme cleavage site, a protein binding site; and a sequence complementary PCR primer.
3. 4. A Vector Donor DNA molecule according to claim 1, wherein said Selectable marker comprises at least one inactive fragment of a Selectable marker, wherein the inactive fragment is capable of reconstituting a functional Selectable marker when recombined across said first or second recombination site with a further DNA segment comprising another inactive fragment of the Selectable marker. 15 5. An Insert Donor DNA molecule, comprising a desired DNA "segment flanked by a first recombination site and a second recombination site, wherein the first and second recombination sites are engineered and do not recombine with each other.
4. 6. An Insert Donor DNA molecule according to claim 5, wherein 20 said desired DNA segment codes for at least one selected from the group :consisting of a cloning site, a restriction site, a promoter, an operon, an origin of replication, a functional DNA, an antisense RNA, a PCR fragment, a protein or 0. 0 a protein fragment.
5. 7. A kit comprising a container being compartmentalized to receive in close confinement therein at one compartment, wherein a first compartment contains a Vector Donor DNA molecule comprising a first DNA segment and a second DNA segment, said first or second DNA segment containing at least one WO 96/40724 PCT/US96/10082 54 Selectable marker, wherein the first and second segments are flanked either by, in a circular Vector Donor, a first and a second recombination site, or (ii) in a linear Vector Donor, a first recombination site, wherein each pair of flanking recombination sites are engineered and do not recombine with each other.
6. 8. A kit according to claim 7, further comprising a second compartment containing an Insert Donor DNA molecule comprising a desired DNA segment flanked by a first recombination site and a second recombination site, wherein the first and second recombination sites are engineered and do not recombine with each other.
7. 9. A kit according to claim 7, further comprising an additional compartment containing at least one recombination protein capable of recombining a DNA segment comprising at least one of said recombination sites. A nucleic acid molecule, comprising at least one DNA segment having at least two recombination sites flanking a Selectable marker or a desired ::15 DNA segment, wherein at least one of said recombination sites comprises a core region having at least one engineered mutation that enhances recombination in vitro in the formation of a Co integrate DNA or a Product DNA.
8. 11. A nucleic acid molecule according to claim 10, wherein said mutation confers at least one enhancement of said recombination, said enhancement selected from the group consisting of substantially favoring excisive recombination; (ii) favoring integrative recombination; (iii) relieving the requirement for host factors; (iv) increasing the efficiency of said Cointegrate .*DNA or Product DNA formration;(v) increasing the specificity of said Cointegrate DNA or Product DNA formation; and contributes desirable attributes to the Product DNA. WO 96/40724 PCT/US96/10082
9. 12. A nucleic acid molecule according to claim 10, wherein said recombination site is derived from at least one recombination site selected from the group consisting of attB, attP, attL and attR.
10. 13. A nucleic acid molecule according to claim 12, wherein said att site is selected from the groups consisting of attl, att2 and att3.
11. 14. A nucleic acid according to claim 10, wherein said core region comprises a DNA sequence selected from the group consisting of: RKYCWGCTITYKTRTACNAASTSGB (m-att) (SEQ ID NO:1); AGCCWGCTITYKTRTACNAACTSGB (m-attB) (SEQ ID NO:2); GTTCAGCTITCKTRTACNAACTSGB (m-attR) (SEQ ID NO:3); AGCCWGCTITTCKTRTACNAAGTSGB (m-attL) (SEQ ID NO:4); GTTCAGCTTTYKTRTACNAAGTSGB(m-attPl) (SEQ ID and a corresponding or complementary DNA or RNA sequence, wherein R=A or G; K=G or TIU; Y=C or T/U; W=A or T/U; N=A or C or G or T/U; S=Cor G; and B=C or G or T/U.
12. 15. A nucleic acid according to claim 14, wherein said core region comprises a DNA sequence selected from the group consisting of: AGCCTGC1TITIT GTACAAACTTGT (attB I)(SEQ ID NO:6); AGCCTGCTITCTTGTACAAACTTGT(attB2) (SEQ ID NO:7); ACCCAGCTITCTTGTACAAACTGT (attB3) (SEQ ID NO:8); GTTCAGCTFITITGTACAAACTTGT (attRI1) (SEQ ID NO:9); GTFCAGCTTTCTGTACAAACTTGT (attR2) (SEQED NO: GTTCAGCTTTCTTGTACAAAGTTGG (attR3) (SEQ ID NO: 11); WO 96/40724 PCT/US96/10082 56 AGCCTGCTTTTTTGTACAAAGTTGG (attLl) (SEQ ID NO:12); AGCCTGCTTTCTTGTACAAAGTTGG (attL2) (SEQ ID NO:13); ACCCAGCTTTCTTGTACAAAGTTGG (attL3) (SEQ ID NO:14); GTTCAGCTITnTGTACAAAGTTGG(attP1) (SEQ ID NO: GTTCAGCTTCTTGTACAAAGTT-GG (attP2,P3) (SEQ ID NO:16); and a corresponding or complementary DNA or RNA sequence.
13. 16. A method for making a nucleic acid molecule, comprising providing a nucleic acid molecule having at least one engineered recombination site comprising at least one DNA sequence having at least homology to at least one of SEQ ID NOS:1-16. 15
14. 17. A nucleic acid molecule provided by a method according to claim 16.
15. 18. A composition, comprising a nucleic acid molecule according to claim
16. 19. A kit, comprising a container being compartmentalized to receive 20 in close confinement therein at least one compartment, wherein a first compartment contains a composition according to claim 18.
17. 20. A kit according to claim 19, further comprising a second compartment having at least one recombination protein that recognizes said recombination site. WO 96/40724 PCT/US96/1 0082 57
18. 21. A kit comprising a container being compartmentalized to receive in close confiement therein at least one recombination protein in isolated form, useful for a method according to claim 22.
19. 22. A method of making a Cointegrate DNA molecule, comprising combining in vitro: an Insert Donor DNA molecule, comprising a desired DNA segment flanked by a first recombination site and a second recombination site, wherein the farst and second recombination sites do not recombine with each other; (ii) a Vector Donor DNA molecule containing a third recombination site and a fourth recombination site, wherein the third and fourth recombination sites do not recombine with each other; and (iii) at least one site specific recombination protein capable of recombining said first and third recombinational sites said :second and fourth recombinationbij sites; thereby allowing recombination to occur, so as to produce a Cointegrate DNA molecule comprising said first and third or said second and fourth recombination sites.
20. 23. A method according to claim 22, wherein a Product DNA molecule is produced from said Cointegrate DNA by recombining at least one of said first and third, or (ii) said second and fourth, recombination sites, said Product DNA comprising said desired DNA segment. :24. A method according to claim 23, wherein said method also produces a Byproduct DNA molecule. A method according to claim 23, further comprising selecting for the Product DNA molecule. WO 96/40724 PCT/US96/10082 -58-
21. 26. A method as claimed in claim 22, wherein the Vector Donor DNA molecule comprises a vector segment flanked by said third and the fourth recombination sites.
22. 27. A method as claimed in claim 22, wherein the Vector Donor DNA molecule further comprises a toxic gene and a Selectable marker, wherein the toxic gene and the Selectable marker are on different DNA segments, the DNA segments being separated either by in a circular DNA molecule, two recombination sites, or (ii) in a linear DNA molecule, one recombination site.
23. 28. A method as claimed in claim 22, wherein the Vector Donor DNA molecule further comprises a repression cassette and a Selectable marker, repressed by the repressor of the repression cassette, and wherein the Selectable marker and the repression cassette are on different DNA segments, the DNA segments being separated either by, in a circular DNA molecule, two recombination sites, or (ii) in a linear DNA molecule, one recombination site. 15
24. 29. A method as claimed in claim 22, wherein at least one of the Insert S: Donor DNA molecule and the Vector Donor DNA molecule is a circular DNA molecule. A method as claimed in claim 22, wherein at least one of the Insert Donor DNA molecule and the Vector Donor DNA molecule is a linear DNA 20 molecule.
25. 31. A method as claimed in claim 22, wherein the selecting step is carried out in vitro or in vivo.
26. 32. A method as claimed in claim 22, wherein said recombination protein comprises at least a first recombination protein and a second recombination protein, said second recombination protein being different from said first recombination protein. -59
27. 33. A method as claimed in claim 22, wherein said recombination protein is Int.
28. 34. A method as claimed in claim 22, wherein the at least one recombination protein is selected from Int and IHF and (ii) Int, Xis and IHF. DATED this 5 th day of January 2001 INVITROGEN CORPORATION By their patent attorneys CALLINAN LAWRIE 2101/O1.mgdiv spec,59