Selective cloning of homoduplex nucleic acids

Abstract

The subject invention provides for a method of selectively cloning homoduplex nucleic acid molecules, in particular, by using a strain of host cells that contains a conditionally expressed and/or conditionally active mismatch-recognizing enzyme, e.g., a temperature sensitive variant of the gene encoding the endonuclease VII from phage T4. Using this host strain, the invention features a novel cloning method that selects for PCR products that are devoid of PCR-generated mutations.

What is claimed is:  
     
         1 . A host cell for selectively cloning homo duplex nucleic acid molecules, wherein the host cell is: 
 (a) competent;    (b) contains a gene encoding a resolvase that is conditionally expressed and/or conditionally active; and    (c) can be maintained under conditions under which the resolvase is not expressed or is repressed and propagated in inactive form.    
     
     
         2 . The host cell of  claim 1 , wherein said host cell is eukaryotic.  
     
     
         3 . The host cell of  claim 1 , wherein said host cell is prokaryotic.  
     
     
         4 . The host cell of  claim 1 , wherein said conditionally expressed resolvase is selected from the group consisting of: a bacteriophage resolvase, a prokaryotic resolvase, and a eukaryotic resolvase.  
     
     
         5 . The host cell of  claim 1 , wherein said conditionally expressed resolvase is bacteriophage T4 Endonuclease VII.  
     
     
         6 . The host cell of  claim 1 , wherein said conditionally expressed resolvase is a temperature sensitive mutant of bacteriophage T4 Endonuclease VII.  
     
     
         7 . The host cell of  claim 1 , wherein said conditionally expressed resolvase is a temperature sensitive mutant of bacteriophage Endonuclease VII encoded by SEQ ID NO:1.  
     
     
         8 . A method of selectively cloning homoduplex nucleic acid molecules, the method comprising: 
 (a) providing a host cell containing a gene encoding a resolvase that is conditionally expressed and/or conditionally active;    (b) transforming said host cell with a cloned nucleic acid molecule, thereby producing a transformed host cell; and    (c) maintaining the transformed host cell under conditions suitable for expression of the resolvase, wherein, if the host cell contains a heteroduplex cloned nucleic acid molecule, the heteroduplex cloned nucleic acid molecule is cleaved by the resolvase, and if the host cell contains a homoduplex cloned nucleic acid molecule, the homoduplex cloned nucleic acid molecule is not cleaved by the resolvase;    thereby selectively cloning homoduplex nucleic acid molecules.    
     
     
         9 . The method of  claim 8 , further comprising the step of, before (b), denaturing and renaturing the nucleic acid molecules.  
     
     
         10 . The method of  claim 8 , further comprising the step of, after (c), infecting said host cell with helper phage, thereby rescuing the homoduplex cloned nucleic acid molecule.  
     
     
         11 . The method of  claim 8 , further comprising the step of maintaining the host cell under conditions that prohibit the expression of the resolvase.  
     
     
         12 . The method of  claim 8 , wherein said host cell is eukaryotic.  
     
     
         13 . The method of  claim 8 , wherein said host cell is prokaryotic.  
     
     
         14 . The method of  claim 8 , wherein said cloned nucleic acid molecule is cloned via a phagemid cloning vector.  
     
     
         15 . The method of  claim 8 , wherein said conditionally expressed resolvase is selected from the group consisting of: a bacteriophage resolvase, a prokaryotic resolvase, and a eukaryotic resolvase.  
     
     
         16 . The method of  claim 8 , wherein said conditionally expressed resolvase is bacteriophage T4 Endonuclease VII.  
     
     
         17 . The method of  claim 8 , wherein said conditionally expressed resolvase is a temperature sensitive mutant of bacteriophage T4 Endonuclease VII.  
     
     
         18 . The method of  claim 8 , wherein said conditionally expressed resolvase is the temperature sensitive mutant of bacteriophage Endonuclease VII encoded by SEQ ID NO:1.  
     
     
         19 . A method of selectively cloning amplified nucleic acid molecules possessing a reduced number of heteroduplexes, the method comprising: 
 (a) providing a host cell containing a gene encoding a resolvase that is conditionally expressed and/or conditionally active;    (b) transforming said host cell with a cloned amplified nucleic acid molecule, thereby producing a transformed host cell; and    (c) maintaining the transformed host cell under conditions suitable for expression of the resolvase, wherein, if the host cell contains a heteroduplex cloned nucleic acid molecule, the heteroduplex cloned nucleic acid molecule is cleaved by the resolvase, and if the host cell contains a homoduplex cloned nucleic acid molecule, the homoduplex cloned nucleic acid molecule is not cleaved by the resolvase;    thereby selectively cloning amplified nucleic acid molecules possessing a reduced number of heteroduplexes.    
     
     
         20 . The method of  claim 19 , further comprising the step of, before (b), denaturing and renaturing the nucleic acid molecules.  
     
     
         21 . The method of  claim 19 , further comprising the step of, after (c), infecting said host cell with helper phage, thereby rescuing the homoduplex cloned nucleic acid molecules.  
     
     
         22 . The method of  claim 19 , further comprising the step of maintaining the host cell under conditions that prohibit the expression of the resolvase.  
     
     
         23 . The method of  claim 19 , wherein said host cell is eukaryotic.  
     
     
         24 . The method of  claim 19 , wherein said host cell is prokaryotic.  
     
     
         25 . The method of  claim 19 , wherein said cloned nucleic acid molecule is cloned via a phagemid cloning vector.  
     
     
         26 . The method of  claim 19 , wherein said conditionally expressed resolvase is selected from the group consisting of: a bacteriophage resolvase, a prokaryotic resolvase, and a eukaryotic resolvase.  
     
     
         27 . The method of  claim 19 , wherein said conditionally expressed resolvase is bacteriophage T4 Endonuclease VII.  
     
     
         28 . The method of  claim 19 , wherein said conditionally expressed resolvase is a temperature sensitive mutant of bacteriophage T4 Endonuclease VII.  
     
     
         29 . The method of  claim 19 , wherein said conditionally expressed resolvase is the temperature sensitive mutant of bacteriophage Endonuclease VII encoded by SEQ ID NO:1.  
     
     
         30 . A kit comprising a competent host cell containing a gene encoding a resolvase that is conditionally expressed and/or conditionally active, and packaging materials therefore.  
     
     
         31 . A kit comprising a competent host cell containing a gene encoding a conditionally expressed resolvase, wherein the host cell can be maintained under conditions under which the resolvase is expressed, and packaging materials therefore.  
     
     
         32 . A kit comprising a host cell containing an expression vector encoding the temperature sensitive mutant of bacteriophage T4 Endonuclease VII of SEQ ID NO:2, PCR reagents, helper phage and packaging materials therefore.  
     
     
         33 . A kit comprising an isolated DNA encoding the temperature sensitive mutant of bacteriophage T4 Endonuclease VII of SEQ ID NO:2 and packaging materials therefore.  
     
     
         34 . A kit comprising an expression vector encoding the temperature sensitive mutant of bacteriophage T4 Endonuclease VII of SEQ ID NO:2 and packaging materials therefore.  
     
     
         35 . A kit comprising a host cell containing an expression vector encoding the temperature sensitive mutant of bacteriophage T4 Endonuclease VII of SEQ ID NO:2 and packaging materials therefore.  
     
     
         36 . An isolated nucleic acid encoding a temperature sensitive mutant of bacteriophage T4 Endonuclease VII, wherein said isolated nucleic acid has the nucleic acid sequence of SEQ ID NO:1.  
     
     
         37 . The isolated nucleic acid of  claim 37 , wherein said isolated nucleic acid is cloned into an expression vector.  
     
     
         38 . An isolated protein of a temperature sensitive mutant of bacteriophage T4 Endonuclease VII, wherein said isolated protein has the amino acid sequence of SEQ ID NO:2.