Use of multiple recombination sites with unique specificity in recombinational cloning
First Claim
1. A method of cloning a nucleic acid molecule comprising:
- (a) providing a first nucleic acid segment flanked by a first and a second recombination site and a second nucleic acid segment flanked by a third and a fourth recombination site, wherein none of the recombination sites flanking the first and second nucleic acid segment is capable of recombining with any of the other sites flanking the first and second nucleic acid segment;
(b) providing a vector comprising a fifth, sixth, seventh and eighth recombination site, wherein each of the fifth, sixth, seventh and eighth recombination sites is capable of recombining with one of the first, second, third or fourth recombination site; and
(c) conducting a recombination reaction such that the two nucleic acid segments are recombined into the vector thereby cloning the first and the second nucleic acid segments.
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Abstract
The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites with unique specificity. The methods permit the simultaneous cloning of two or more different nucleic acid molecules. In some embodiments the molecules are fused together while in other embodiments the molecules are inserted into distinct sites in a vector. The invention also generally provides for linking or joining through recombination a number of molecules and/or compounds (e.g., chemical compounds, drugs, proteins or peptides, lipids, nucleic acids, carbohydrates, etc.) which may be the same or different. Such molecules and/or compounds or combinations of such molecules and/or compounds can also be bound through recombination to various structures or supports according to the invention.
192 Citations
65 Claims
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1. A method of cloning a nucleic acid molecule comprising:
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(a) providing a first nucleic acid segment flanked by a first and a second recombination site and a second nucleic acid segment flanked by a third and a fourth recombination site, wherein none of the recombination sites flanking the first and second nucleic acid segment is capable of recombining with any of the other sites flanking the first and second nucleic acid segment; (b) providing a vector comprising a fifth, sixth, seventh and eighth recombination site, wherein each of the fifth, sixth, seventh and eighth recombination sites is capable of recombining with one of the first, second, third or fourth recombination site; and (c) conducting a recombination reaction such that the two nucleic acid segments are recombined into the vector thereby cloning the first and the second nucleic acid segments.
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2. A method of cloning two or more nucleic acid segments, comprising:
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(a) providing two or more nucleic acid segments, each segment flanked by two recombination sites which do not recombine with each other; (b) providing a vector comprising a number of recombination sites equal to twice the number of nucleic acid segments, wherein each of the recombination sites is capable of recombining with one of the recombination sites flanking one of the nucleic acid segments; and (c) conducting a recombination reaction such that the nucleic acid segments are recombined into the vector thereby cloning the nucleic acid segments, wherein transcription of at least two of the nucleic acid segments results in the production of a single RNA. - View Dependent Claims (3, 4, 5, 6, 7)
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8. A method of cloning at least one nucleic acid molecule comprising:
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(a) providing a first, a second and a third nucleic acid segment, wherein the first nucleic acid segment is flanked by a first and a second recombination site, the second nucleic acid segment is flanked by a third and a fourth recombination site and the third nucleic acid segment is flanked by a fifth and a sixth recombination site, wherein the second recombination site is capable of recombining with the third recombination site and none of the first, fourth, fifth or sixth recombination sites is capable of recombining with any of the first through sixth recombination sites; (b) providing a vector comprising a seventh and an eighth recombination site flanking a first negative selectable marker and comprising a ninth and a tenth recombination site flanking a second negative selectable marker, wherein none of the seventh through tenth recombination sites can recombine with any of the seventh through tenth recombination sites; (c) conducting a first recombination reaction such that the second and the third recombination sites recombine; and (d) conducting a second recombination reaction such that the first and the fourth recombination sites recombine with the seventh and the eighth recombination sites and the fifth and the sixth recombination sites recombine with the ninth and the tenth recombination sites thereby cloning the first, second and third nucleic acid segments.
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9. A method of cloning at least one nucleic acid molecule comprising:
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(a) providing a first, a second and a third nucleic acid segment, wherein the first nucleic acid segment is flanked by a first and a second recombination site, the second nucleic acid segment is flanked by a third and a fourth recombination site and the third nucleic acid segment is flanked by a fifth and a sixth recombination site, wherein the second recombination site is capable of recombining with the third recombination site and the fourth recombination site is capable of recombining with the fifth recombination site; (b) providing a vector comprising a seventh and an eighth recombination site; and (c) conducting at least one recombination reaction such that the second and the third recombination sites recombine and the fourth and the fifth recombination sites recombine and the first and the sixth recombination sites recombine with the seventh and the eighth recombination sites respectively, thereby cloning the first, second and third nucleic acid segments. - View Dependent Claims (10)
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11. A method of cloning n nucleic acid fragments, wherein n is an integer greater than 2, comprising:
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(a) providing a 1st through an nth nucleic acid segment, each segment flanked by two recombination sites, wherein the recombination sites are selected such that one of the two recombination sites flanking the ith segment, ni, reacts with one of the recombination sites flanking the ni−
1th segment and the other recombination site flanking the ith segment reacts with one of the recombination sites flanking the ni+1th segment;(b) providing a vector comprising at least two recombination sites, wherein one of the two recombination sites on the vector reacts with one of the sites on the 1st nucleic acid segment and another site on the vector reacts with a recombination site on the nth nucleic acid segment; and (c) conducting at least one recombination reaction such that all of the nucleic acid fragments are recombined into the vector. - View Dependent Claims (12, 13, 14, 15)
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16. A method of joining two or more segments of nucleic acid, comprising:
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(a) providing two or more segments of nucleic acid, each segment comprising at least one recombination site capable of recombining with a recombination site present on the other segment; and (b) contacting the segments with one or more recombination proteins under conditions causing recombination between the recombination sites, thereby joining the segments, wherein the expression product is a ribozyme or an inhibitory RNA molecule.
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17. A method of joining n nucleic acid segments, wherein n is an integer greater than 2, comprising:
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(a) providing a 1st through an nth nucleic acid segment, each segment flanked by two recombination sites, wherein the recombination sites are selected such that one of the two recombination sites flanking the ith segment, ni, reacts with one of the recombination sites flanking the ni−
1th segment and the other recombination site flanking the ith segment reacts with one of the recombination sites flanking the ni+1th segment; and(b) contacting the segments with one or more recombination proteins under conditions causing the segments to join. - View Dependent Claims (18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45)
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46. A method of synthesizing a protein comprising:
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(a) providing a nucleic acid molecule comprising at least one recombination site and comprising a coding sequence containing at least one suppressible stop codon; (b) providing a vector comprising at least one recombination site and a coding sequence; (c) causing recombination in vitro such that the nucleic acid molecule is inserted into the vector to produce a modified vector with the two coding sequences connected in frame and separated by said stop codon; (d) transforming a host cell which expresses a suppressor tRNA with the modified vector; and (e) causing expression of the two coding sequences such that a fusion protein encoded by at least a portion of both of the coding sequences is produced. - View Dependent Claims (47, 48, 49, 50, 51, 52)
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53. A method for determining the gene expression profile in a cell or tissue comprising:
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(a) generating at least one population of cDNA molecules from RNA obtained from the cell or tissue, wherein cDNA molecules of the population comprise at least one recombination site capable of recombining with at least one recombination site present on cDNA molecules of the same or a different population; (b) contacting the nucleic acid molecules of (a) with one or more recombination proteins under conditions which cause the nucleic acid molecules to join; (c) determining the sequence of the joined nucleic acid molecules; and (d) comparing the sequence of said joined nucleic acid molecules to nucleic acid sequences cataloged in public databases to identify the gene expression profile. - View Dependent Claims (54, 55, 56, 57)
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58. A method of producing a population of hybrid nucleic acid molecules comprising:
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(a) mixing at least a first population of nucleic acid and molecules, wherein;
one or more nucleic acid molecules of said population comprises one or more recombination sites, with at least one target nucleic acid molecule comprising one or more recombination sites;(b) causing some or all of the nucleic acid molecules of the at least first population to recombine in vitro with all or some of the target nucleic molecules, thereby forming the population of hybrid nucleic acid molecules; and (c) selecting for the population of hybrid nucleic acid molecules and against the first population of nucleic acid molecules and against the target nucleic acid molecules.
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59. A method of cloning at least one nucleic acid molecule comprising:
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(a) providing a first population of nucleic acid molecules wherein all or a portion of such molecules are flanked by a first and a second recombination site; (b) providing at least one nucleic acid segment encoding a polypeptide selected from the group consisting of;
(i) the Fc portion of an immunoglobin;
(ii) β
-glucuronidase;
(iii) a fluorescent protein;
(iv) a purification tag;
(v) an epitope tag;
(vi) maltose binding protein;
(vii) a six histidine tag; and
(viii) glutathione S-transferase, flanked by a third and a fourth recombination site, wherein either the first or the second recombination site is capable of recombining with either the third or the fourth recombination site;(c) conducting a recombination reaction in vitro such that all or a portion of the nucleic acid molecules in the population is recombined with the segment to form a second population of nucleic acid molecules; and (d) cloning the second population of nucleic acid molecules.
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60. A method of producing a nucleic acid molecule comprising:
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(a) providing a first nucleic acid molecule comprising at least one recombination site and comprising a coding sequence containing at least one suppressible stop codon; (b) providing a second nucleic acid molecule comprising at least one recombination site and a coding sequence; and (c) causing recombination in vitro such that the first nucleic acid molecule is joined to the second nucleic acid molecule to produce a third nucleic acid molecule in which the two coding sequences are connected in frame and are separated by said stop codon. - View Dependent Claims (61, 62, 63, 64, 65)
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Specification