Compositions and methods of using a synthetic dnase i

Abstract

Compositions and method for making and using a synthetic bovine DNase I are disclosed. More particularly, the sbDNase I of the present invention is a versatile enzyme that cleaves DNA nonspecifically to release 5′-phosphorylated nucleotides. The sbDNase I molecules of the present invention find particular use in a wide range of molecular biology applications, including: degradation of contaminating DNA after RNA isolation; RNA clean-up prior to, or in conjunction with, RT-PCR after in vitro transcription; identification of protein binding sequences on DNA (DNase I footprinting); prevention of clumping when handling cultured cells; tissue dissociation and creation of fragmented DNA for in vitro recombination reactions.

1 - 95 . (canceled) 
     
     
         96 . An isolated and purified DNase I polypeptide having DNase activity that increases as the salt concentration increases above 10 mM and wherein the DNase I comprises one or more mutations selected from E13R, an N74K, an E13R and an N74K and sequences with 95% sequence homology thereto. 
     
     
         97 . The DNase I of  claim 96 , wherein the DNase I comprises a K.sub.m of less than about 600 nM in a DNase I buffer. 
     
     
         98 . The DNase I of  claim 96 , wherein the DNase I has a Km of about 100 nM in a solution comprising an ionic strength of greater than 25 mM. 
     
     
         99 . The DNase I of  claim 96 , wherein the DNase I degrades DNA in a buffer comprising an ionic strength of between about 25 mM to 300 mM. 
     
     
         100 . The DNase I of  claim 96 , wherein the DNase I prevents clumping of cultured cells in vitro. 
     
     
         101 . The DNase I of  claim 96 , wherein the DNase I dissociates tissue. 
     
     
         102 . The DNase I of  claim 96 , wherein the DNase I hydrolyzes DNA to create a fragmented library of DNA sequences for in vitro recombination reactions. 
     
     
         103 . The DNase I of  claim 96 , wherein the DNase I removes DNA from non-buffered solutions. 
     
     
         104 . The DNase I of  claim 96 , wherein the DNase I removes DNA and simultaneously with a reverse transcription reaction. 
     
     
         105 . The DNase I of  claim 96 , wherein the DNase I removes DNA from a proteinaceous sample prior to 2-D gel electrophoresis. 
     
     
         106 . The DNase I of  claim 96 , wherein the DNase I has activity in a buffer comprises an ionic strength greater than 50 mM or more and the synthetic DNase I has two-fold more activity that wild-type. 
     
     
         107 . The DNase I of  claim 96 , wherein the DNase I has activity in a buffer with a medium to high ionic strength. 
     
     
         108 . The DNase I of  claim 96 , wherein the DNase I has activity in a buffer with a low concentration of calcium. 
     
     
         109 . The DNase I of  claim 96 , wherein the DNase I has activity in a standard RT-PCR buffer. 
     
     
         110 . The DNase I of  claim 96 , wherein the activity of the DNase I is decreased in high salt concentrations by chelating calcium in the solution. 
     
     
         111 . The DNase I of  claim 96 , wherein the DNase I has activity in a solution selected from the group consisting of an RT buffer, a PCR buffer, a restriction enzyme buffer, or mixtures thereof and the synthetic DNase I maintains two-fold more activity that wild-type DNase I. 
     
     
         112 . The DNase I of  claim 96 , wherein the DNase I has activity in a solution comprising about 125 mM NaCl and about 0.5 mM CaCl 2 . 
     
     
         113 . An isolated and purified DNase I polypeptide having a DNase I activity greater than 50% wild-type in a buffer having an ionic strength greater than 25 mM and wherein the DNase I comprises one or more mutations selected from E13R, an N74K, an E13R and an N74K and sequences with 95% sequence homology thereto. 
     
     
         114 . A synthetic DNase I mutant in which the mutation is replacement of at least one of the amino acids of SEQ ID NO.: 2, SEQ ID NO.: 4 or SEQ ID NO.: 20, with an alternative naturally occurring L-amino acid, the replacement being selected from the group consisting of: (1) a substitution of any of isoleucine, valine, and leucine for any other of these amino acids; (2) a substitution of aspartic acid for glutamic acid or vice versa; (3) a substitution of glutamine for asparagine or vice versa; (4) a substitution of serine for threonine or vice versa; (5) a substitution of glycine for alanine or vice versa; (6) a substitution of alanine for valine or vice versa; (7) a substitution of methionine for any of leucine, isoleucine, or valine and vice versa; and (8) a substitution of lysine for arginine or vice versa, the mutant having DNase I activity in a solution comprising an ionic strength greater that 25 mM. 
     
     
         115 . A mutant synthetic bovine DNase I comprising an E13R, an N74K, or an E13R; N74K substitution and one or more replacements for alternative naturally occurring L-amino acids, the one or more replacements being selected from the group consisting of: (1) a substitution of any of isoleucine, valine, and leucine for any other of these amino acids; (2) a substitution of aspartic acid for glutamic acid or vice versa; (3) a substitution of glutamine for asparagine or vice versa; (4) a substitution of serine for threonine or vice versa; (5) a substitution of glycine for alanine or vice versa; (6) a substitution of alanine for valine or vice versa; (7) a substitution for methionine for any of leucine, isoleucine or valine, and vice versa; and (8) a substitution of lysine for arginine or vice versa, the mutant having DNase I activity in a solution comprising an ionic strength of greater than 25 mM.