Abstract
The invention provides vectors and methods for directional cloning.
Claims
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A method for the directional subcloning of DNA fragments comprising:
a) providing a first vector comprising a first selectable marker gene and a DNA sequence of interest having an open reading frame, which DNA sequence of interest is flanked by at least two restriction enzyme sites, wherein one of the flanking restriction enzyme sites is a site for a first restriction enzyme which has infrequent restriction sites in cDNAs or open reading frames from at least one species and generates complementary single-strand DNA 3′ TA overhangs, wherein the other flanking restriction enzyme site is for a second restriction enzyme which has infrequent restriction sites in cDNAs or open reading frames from at least one species and generates blunt ends, wherein digestion of the first vector with the first restriction enzyme and the second restriction enzyme generates:
(i) a first linear DNA fragment which lacks the first selectable marker gene but comprises the DNA sequence of interest, and
(ii) a second linear DNA fragment comprising the first selectable marker gene;
b) providing a second vector comprising a second selectable marker gene which is distinguishable from the first selectable marker gene, and a DNA sequence encoding a lethal gene flanked by at least two restriction enzymes sites, wherein one of the flanking restriction enzyme sites in the second vector is for a third restriction enzyme which generates complementary single-strand DNA overhangs that are complementary to the single-strand DNA overhang generated by the first restriction enzyme in the first linear DNA fragment, wherein the other flanking restriction site in the second vector is for a fourth restriction enzyme which generates blunt ends, wherein digestion of the second vector with the third restriction enzyme and the fourth restriction enzyme generates:
(i) a third linear DNA fragment which lacks the lethal gene but comprises the second selectable marker and has ends which permit the oriented joining of the first linear DNA fragment to the third linear DNA fragment, and
(ii) a fourth linear DNA fragment comprising the lethal gene,
wherein sequences including a portion of the overhang generated by the third restriction enzyme include one or more codons that after oriented joining are in-frame with the open reading frame, thereby encoding a N-terminal fusion with the gene product encoded by the open reading frame, and/or wherein sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include one or more nucleotides (I) for a stop codon that after oriented joining are in-frame with the open reading frame or (II) for one or more codons that after oriented joining are in-frame with the open reading frame and thereby encode a C-terminal fusion with the gene product encoded by the open reading frame;
c) combining
(i) the first and second vectors,
(ii) the first vector, the third linear DNA fragment, and the fourth linear DNA fragment, or
(iii) the second vector, the first linear DNA fragment, and the second linear DNA fragment
in a suitable buffer with one or more restriction enzymes and DNA ligase under conditions effective to result in digestion and ligation to yield a mixture comprising a third vector comprising the first and third linear DNA molecules joined in an oriented manner.
- The method of claim 1 wherein the first and third restriction enzymes are not the same.
- The method of claim 1 wherein the second and fourth restriction enzymes are not the same.
- The method of claim 1 wherein the first restriction enzyme is SgfI.
- The method of claim 4 wherein the second restriction enzyme is PmeI.
- The method of claim 1 wherein the third restriction enzyme is PvuI or PacI.
- The method of claim 1 wherein the DNA sequence of interest comprises an open reading frame comprising one or more sites for the first or second restriction enzyme.
- The method of claim 7 wherein prior to digestion with the one or more restriction enzymes, the sites for the one or more restriction enzymes in the open reading frame are protected so as to prevent digestion.
- The method of claim 8 wherein the sites are protected by methylation.
- The method of claim 9 wherein prior to methylation the flanking sites for the first or second restriction enzyme are contacted with an oligonucleotide complementary to the flanking restriction enzyme site and RecA.
- The method of claim 1 wherein one of the restriction enzymes is DraI, NruI, PacI, PmeI, PvuI, SgfI, SrfI, or SwaI, or a restriction enzyme that has the same recognition site as DraI, NruI, PacI, PmeI, PvuI, SgfI, SrfI, or SwaI.
- The method of claim 1 wherein the second restriction enzyme is PmeI.
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A method for the directional subcloning of DNA fragments comprising:
a) providing a first vector comprising a first selectable marker gene and a DNA sequence of interest having an open reading frame, which DNA sequence of interest is flanked by at least two restriction enzyme sites, wherein one of the flanking restriction enzyme sites is a site for a first restriction enzyme that generates complementary single-strand DNA overhangs, wherein the other flanking restriction enzyme site is for a second restriction enzyme that generates blunt ends, wherein digestion of the first vector with the first restriction enzyme and the second restriction enzyme generates a first linear DNA fragment which lacks the first selectable marker gene but comprises the DNA sequence of interest and a second DNA fragment comprising the first selectable marker gene;
b) providing a second vector comprising a second selectable marker gene, which is distinguishable from the first selectable marker gene, and a DNA sequence encoding a lethal gene flanked by at least two restriction enzymes sites, wherein one of the flanking restriction enzyme sites in the second vector is for a third restriction enzyme which has infrequent restriction sites in cDNAs or open reading frames from at least one species and generates complementary single-strand 3′TA DNA overhangs that are complementary to the single-strand DNA overhang generated by the first restriction enzyme in the first linear DNA fragment, wherein the other flanking restriction site in the second vector is for a fourth restriction enzyme which has infrequent restriction sites in cDNAs or open reading frames from at least one species and generates blunt ends, and wherein digestion of the second vector with the third restriction enzyme and the fourth restriction enzyme generates:
(i) a third linear DNA fragment which lacks the lethal gene but comprises the second selectable marker and having ends which permit the oriented joining of the first linear DNA fragment to the third linear DNA fragment, and
(ii) a fourth linear DNA fragment comprising the lethal gene,
wherein (i) sequences including a portion of the overhang generated by the third restriction enzyme include one or more codons that after oriented joining are in-frame with the open reading frame, thereby encoding a N-terminal fusion with the gene product encoded by the open reading frame, and/or (ii) wherein sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include one or more nucleotides (a) for a stop codon that after oriented joining are in-frame with the open reading frame or (b) for one or more codons that after oriented joining are in-frame with the open reading frame and thereby encode a C-terminal fusion with the gene product encoded by the open reading frame; and
c) combining
(i) the first and second vectors,
(ii) the first vector, the third linear DNA fragment, and the fourth linear DNA fragment, or
(iii) the second vector, the first linear DNA fragment, and the second linear DNA fragment
in a suitable buffer with one or more restriction enzymes and DNA ligase under conditions effective to result in digestion and ligation to yield a mixture comprising a third vector comprising the first and third linear DNA molecules joined in an oriented manner.
- The method of claim 13 wherein the first and third restriction enzymes are not the same.
- The method of claim 13 wherein the second and fourth restriction enzymes are not the same.
- The method of claim 13 wherein the third restriction enzyme is SgfI.
- The method of claim 16 wherein the fourth restriction enzyme is PmeI.
- The method of claim 13 wherein the first restriction enzyme is PvuI or PacI.
- The method of claim 13 wherein the first restriction enzyme is SgfI and the second restriction enzyme is PmeI.
- The method of claim 1 or 13 wherein the sequences including a portion of the overhang generated by the third restriction enzyme include one or more codons that after oriented joining are in-frame with the open reading frame.
- The method of claim 20 wherein the sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include one or more nucleotides for the stop codon.
- The method of claim 20 wherein the sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include the one or more nucleotides for the one or more codons that after oriented joining are in-frame with the open reading frame.
- The method of claim 1 or 13 wherein the sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include the one or more nucleotides for the one or more codons that after oriented joining are in-frame with the open reading frame.
- The method of claim 23 wherein the open reading frame contains an in-frame initiation codon.
- The method of claim 1 or 13 wherein the open reading frame includes an in-frame initiation codon and an in-frame stop codon.
- The method of claim 1 or 13 wherein one of the vectors further comprises a site for AarI, AscI, BbrCI, CspI, FseI, NotI, SapI, SdaI, SfiI, or SplI, or a restriction enzyme that has the same recognition site as AarI, AscI, BbrCI, CspI, FseI, NotI, SapI, SdaI, SfiI, or SplI.
- The method of claim 1 or 13 wherein the second vector comprises a promoter which is 5′ to the recognition site for the third restriction enzyme and positioned so that an open reading frame, introduced by ligating the first linear DNA fragment with the third linear DNA fragment, is capable of being transcribed from the promoter.
- The method of claim 1 or 13 wherein the sequences including a portion of the overhang generated by the third restriction enzyme include one or more codons that after oriented joining are in-frame with the open reading frame and wherein the sequences forming a portion of and 3′ to the cleavage site generated by the fourth restriction enzyme include one or more nucleotides for one or more codons that after oriented joining are in-frame with the open reading frame, thereby encoding a N-terminal fusion and a C-terminal fusion with the gene product encoded by the open reading frame.
- The method of claim 20 wherein the third vector encodes a N-terminal fusion but not a C-terminal fusion.
- The method of claim 29 wherein the first or third restriction enzyme is SgfI.
- The method of claim 29 wherein the second restriction enzyme is PmeI.
- The method of claim 23 wherein the third vector encodes a C-terminal fusion but not a N-terminal fusion.
- The method of claim 32 wherein the first or third restriction enzyme is SgfI.
- The method of claim 32 wherein the second restriction enzyme is PmeI.
- The method of claim 28 wherein the first or third restriction enzyme is SgfI.
- The method of claim 28 wherein the second restriction enzyme is PmeI.
- The method of claim 1, wherein the lethal gene encodes a barnase.
- The method of claim 13, wherein the lethal gene encodes a barnase.
Owners (US)
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Promega Corporation
(Feb 03 2004)
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Applicants
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Slater Michael R
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Strauss Ethan Edward
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Wood Keith V
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Hartnett James Robert
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Promega Corp
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Inventors
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Slater Michael R
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Strauss Ethan Edward
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Wood Keith V
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Hartnett James Robert
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Document History
- Publication: Oct 23, 2012
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Application:
Oct 3, 2003
US 67896103 A
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Priority:
Oct 3, 2003
US 67896103 A