Methods of increasing the concentration of a nucleic acid

a nucleic acid and concentration technology, applied in the field of methods of increasing the concentration of nucleic acids, can solve the problems of difficult catalysis selection, serious shortcomings, and few attempts to improve the properties

Inactive Publication Date: 2008-07-10
HOLLINGER PHILLIP +2
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0024]In a preferred embodiment, the compartments consist of the encapsulated aqueous component of a water-in-oil emulsion. The water-in-oil emulsion is preferably produced by emulsifying an aqueous phase with an oil phase in the presence of a surfactant comprising 4.5% v / v Span 80, 0.4% v / v Tween 80 and 0.1% v / v Triton X100, or a surfactant comprising Span 80, Tween 80 and Triton X100 in substantially the same proportions. Preferably, the water:oil phase ratio is 1:2, which leads to adequate droplet size. Such emulsions have a higher thermal stability than more oil-rich emulsions.
[0032]In a ninth aspect of the present invention, there is provided a water-in-oil emulsion obtainable by emulsifying an aqueous phase with an oil phase in the presence of a surfactant comprising 4.5% v / v Span 80, 0.4% v / v Tween 80 and 0.1% v / v Triton X100, or a surfactant comprising Span 80, Tween 80 and Triton X100 in substantially the same proportions. Preferably, the water:oil phase ratio is 1:2. This ratio appears to permit diffusion of dNTPs (and presumably other small molecules) between compartments at higher temperatures, which is beneficial for some applications but not for others. Diffusion can be controlled by increasing water:oil phase ratio to 1:4.

Problems solved by technology

Selection for catalysis has proved harder.
While polymerases are a prerequisite for technologies that define molecular biology, i.e. site-directed mutagenesis, cDNA cloning and in particular Sanger sequencing and PCR, they often suffer from serious shortcomings due to the fact that they are made to perform tasks for which nature has not optimized them.
Few attempts appear to have been made to improve the properties of polymerases available from nature and to tailor them for specific applications by protein engineering.
However, the genetic complementation approach is limited in the properties that can be selected for.

Method used

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  • Methods of increasing the concentration of a nucleic acid
  • Methods of increasing the concentration of a nucleic acid
  • Methods of increasing the concentration of a nucleic acid

Examples

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example 1

Construction of Taq Polymerase Expression Plasmids

[0239]The Taq polymerase open reading frame is amplified by PCR from Thermus aquaticus genomic DNA using primers 1 & 2, cut with XbaI & SalI and ligated into pASK75 (Skerra A., 1994, Gene 151, 131) cut with XbaI & SalI. pASK75 is an expression vector which directs the synthesis of foreign proteins in E. coli under transcriptional control of the tetA promoter / operator.

[0240]Clones are screened for inserts using primers 3, 4 and assayed for expression of active Taq polymerase (Taq pol) (see below). The inactive Taq pol mutant D785H / E786V is constructed using Quickchange mutagenesis (Stratagene). The mutated residues are critical for activity (Doublie S. et al., 1998, Nature 391, 251; Kiefer J. R. et al., 1998, Nature 391, 304). Resulting clones are screened for mutation using PCR screening with primers 3, 5 and diagnostic digestion of the products with PmlI. Mutant clones are assayed for expression of active Taq pol (see below).

example 2

Protein Expression and Activity Assay

[0241]Transformed TG1 cells are grown in 2×TY 0.1 mg / ml ampicillin. For expression, overnight cultures are diluted 1 / 100 into fresh 2×TY medium and grown to OD600=0.5 at 37° C. Protein expression is induced by addition of anhydro tetracycline to a final concentration of 0.2 μg / ml. After 4 hours further incubation at 37° C., cells are spun down, washed once, and re-suspended in an equal volume of 1× SuperTaq polymerase buffer (50 mM KCl, 10 mM Tris-HCl (pH9.0), 0.1% Triton X-100, 1.5 mM MgCl2) (HT Biotechnology Ltd, Cambridge UK).

[0242]Washed cells are added directly to a PCR reaction mix (2 μl per 30 μl reaction volume) comprising template plasmid (20 ng), primers 4 and 5 (1 μM each), dNTPs (0.25 mM), 1× SuperTaq polymerase buffer, and overlaid with mineral oil. Reactions are incubated for 10 min at 94° C. to release Taq pol from the cells and then thermocycled with 30 cycles of the profile 94° C. (1 min), 55° C. (1 min), 72° C. (2 min).

example 3

Emulsification of Amplification Reactions

[0243]Emulsification of reactions is carried out as follows. 200 μl of PCR reaction mix (Taq expression plasmid (200 ng), primers 3 and 4 (1 μM each), dNTPs (0.25 mM), Taq polymerase (10 units) is added dropwise (12 drops / min) to the oil phase (mineral oil (Sigma)) in the presence of 4.5% (v / v) Span 80 (Fluka), 0.4% (v / v) Tween 80 (Sigma) and 0.05% (v / v) Triton X100 (Sigma) under constant stirring (1000 rpm) in 2 ml round bottom biofreeze vials (Costar, Cambridge Mass.). After complete addition of the aqueous phase, stirring is continued for a further 4 minutes. Emulsified mixtures are then transferred to 0.5 ml thin-walled PCR tubes (100 μl / tube) and PCR carried out using 25 cycles of the profile 94° C. (1 min), 60° C. (1 min), 72° C. (3 min) after an initial 5 min incubation at 94° C. Reaction mixtures are recovered by the addition of a double volume of ether, vortexing and centrifugation for 2 minutes prior to removal of the ether phase. A...

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Abstract

We describe a method of selecting an enzyme having replicase activity, the method comprising the steps of: (a) providing a pool of nucleic acids comprising members each encoding a replicase or a variant of the replicase; (b) subdividing the pool of nucleic acids into compartments, such that each compartment comprises a nucleic acid member of the pool together with the replicase or variant encoded by the nucleic acid member; (c) allowing nucleic acid replication to occur; and (d) detecting amplification of the nucleic acid member by the replicase. Methods for selecting agents capable of modulating replicase activity, and for selecting interacting polypeptides are also disclosed.

Description

[0001]This application is a divisional of U.S. utility application Ser. No. 10 / 387,387, filed Mar. 13, 2003, which is a continuation-in-part of international application PCT / GB01 / 04108, filed Sep. 13, 2001, which claims the priority of each of Great Britain application GB 0022458.4, filed Sep. 13, 2000, U.S. provisional application 60 / 283,771, filed Apr. 13, 2001 and U.S. provisional application 60 / 285,501, filed Apr. 20, 2001. Each of these priority documents is expressly incorporated herein in its entirety, including tables and drawings.FIELD OF THE INVENTION[0002]The present invention relates to methods for use in in vitro evolution of molecular libraries. In particular, the present invention relates to methods of selecting nucleic acids encoding gene products in which the nucleic acid and the activity of the encoded gene product are linked by compartmentalisation.BACKGROUND TO THE INVENTION[0003]Evolution requires the generation of genetic diversity (diversity in nucleic acid) f...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12P19/34G01N33/53C12N9/10C12N9/12C12N15/09C12N15/10C12N15/54C12Q1/02C12Q1/48C12Q1/68G01N33/15G01N33/566
CPCC07K2319/00C12N9/1252C12Q1/6867C12N15/1075C12N15/1058
Inventor HOLLINGER, PHILLIPGHADASSY, FARIDONG, JENNIFER LEE
Owner HOLLINGER PHILLIP
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