CA2050276C

CA2050276C - Improved primer extension reactions

Info

Publication number: CA2050276C
Application number: CA002050276A
Authority: CA
Inventors: Stanley Tabor; Charles C. Richardson
Original assignee: Harvard College
Current assignee: Harvard College
Priority date: 1989-04-12
Filing date: 1990-04-10
Publication date: 2003-03-11
Anticipated expiration: 2010-04-10
Also published as: JP2997043B2; AU638246B2; CA2050276A1; AU5438290A; EP0467953A4; HUT61054A; KR920700294A; WO1990012111A1; JPH04506002A; HU903562D0; EP0467953A1; LTIP1519A

Abstract

A kit or solution for use in extension of an oligonucleotide primer having a first.single-stranded region on a template mole-cule having a second single-stranded region homologous to the first single-stranded region; comprising a first agent able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mix-ture, and a second agent able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

Description

IMPROVED PRIMER EXTENSION REACTIONS
Background of the Invention This invention was made with government support including a grant from Department of Energy Grant No. DE-SG02-88ER60688 and U.S. Public Health Service Grant No. A1-06045.
The U.S. government has certain rights to the invention.
This invention relates to methods for performing a primer extension reaction, such as a DNA sequencing reaction, or a polymerase chain reaction.
In a primer extension reaction an oligonucleotide primer having homology to a single-stranded template DNA, e.g., genomic DNA, is caused to anneal to the template DNA. The annealed mixture is then provided with a DNA polymerase in the presence of nucleoside triphosphates under conditions in which the DNA polymerase extends the primer to form a complementary DNA strand to the template DNA. In a DNA sequencing reaction, the primer is extended in the presence of a chain-terminating agent, e.g., a dideoxynucleoside triphosphate, to cause base-specific termination of the primer extension. Sanger et al., 74 Proc. Nat'1. Acad. Sci. 5463, 1977. In a polymerase chain reaction two primers are provided, each having homology to opposite strands of a double-stranded DNA molecule. After the primers are extended, they are separated from their templates, and additional primers caused to anneal to the templates and the extended primers. The additional primers are then extended.
The steps of separating, annealing, and extending are repeated in order to amplify the number of copies of template DNA. Saiki et al., 239 Science 487, 1988.
Summary of the Invention In a first aspect, the invention features a solution or kit for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region, the first and second regions being homologous. The solution or kit includes a first agent able to cause extension of the first single stranded region of the primer on the second single-stranded region of the template in a reaction mixture, and a second agent able to reduce the level of pyrophosphate in the reaction mixture below the level produced during extension in the absence of the second agent.
As a result, in accordance with one aspect of the invention, there is provided a solution or kit for use in a DNA
sequencing reaction, comprising a DNA polymerase, a chain-terminating agent, and an agent able to reduce the amount of pyrophosphate in a DNA polymerization reaction mixture.
By solution is meant any aqueous and/or buffered liquid containing the components described above. These components are present in the solution at concentrations sufficient to perform their desired function. For example, the second agent is present at a concentration sufficient to reduce the level of pyrophosphate in the solution. By kit is meant a container which holds one or more of the components of the solution separately. For example, the first and second agents are held in separate containers in solutions adapted to be mixed together.
By causing extension of the oligonucleotide primer is meant performing a reaction in which an oligonucleotide primer having a single-stranded region is annealed, or naturally occurs in the annealed state, with another nucleic acid molecule which acts as a template upon which the oligonucleotide primer can be - 3 - 205027b extended by addition of nucleoside triphosphate~ to form nucleic acid homologous to the template nucleic acid.
Generally, externsion entails providing a DNA polymerase or RNA polymerise to covalently add nucl:eot:des,to the primer.
A reaction mixture is any solution or solid phase suitable for performing an extension reaction.
Generally, it is a licuid buffer containing nucleoside or deoxynucleoside triphosphates and metal ions required for an extension reaction. The mixture may also contain any standard bufferirg~ agents and, for a DNA sequencing reaction, one or more dideoxy:~ucleos:de triphosphates, or an equivalent chain-terminating agent.
By reducing the level of pyrophosphate is meant that the amount of pyrophosphate .n the reaction mixture is reduced to an amount which has latle or no significant effect on the extension of the primer on she template. That is, the level of pyrophosphate is low enough to reduce pyrophosphorolysis to an insignificant level (less than 10~ the level of pyrophosphorolysis in the presence of 300 uM pyrophosphate). Preferably.
the level of pyrophosphate is reduced to below 25uM, even more preferably to below 5PM. This phase is meant to include use of an agent, such as a pyrophosphatase, which acts to prevent the build-up of pyrophosphate, as well as remove it from a solution.
Hy homologous is meant that the two single-stranded regions are able to form sufficient non-covalent bonds between their respective nucleotides to form a~stable double-stranded structure under conditions normally used for annealing nucleic acids, and for performing a primer extension reaction.

In preferred embodiments, the first agent is a DNA
polymerase, most preferably chosen from Klenow, Taq polymerase, a T7-type DNA polymerase (i.e., a polymerase similar to that in a phage in which the DNA polymerase requires host thioredoxin as a subunit, e.g., T7 DNA polymerase of the DNA polymerase of T3, ~I, III, H, W31, gh-1, Y, AA1122, or Sp6), T4 DNA
polymerase, T5 DNA polymerase, X29 DNA polymerase and reverse transcriptase; the second agent is an enzyme, most preferably a pyrophosphatase, for example, a pyrophosphatase resistant to heating at between 60°C and 95°C.
In a further aspect, the invention features an improved method for extending an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region, including providing a first agent able to cause extension of the primer on the template.
The improvement is provision of a second agent able to reduce the amount of pyrophosphate below the amount produced during extension in the absence of the second agent.
As a result, according to a further aspect of the present invention, there is provided an improved method for a DNA sequencing reaction, including providing a DNA polymerase, and a chain-terminating agent the improvement comprising:
providing an agent able to reduce the level of pyrophosphate below the amount produced during said extension in the absence of said agent.
In preferred embodiments, the method includes the steps of providing at least one or two oligonucleotide primers having single-stranded regions and at least one or two template molecules having single-stranded regions, and annealing the single-stranded regions of the primers and the templates to form an annealed mixture. The resulting annealed mixture is provided with the first and second agents to cause extension of the primers. The annealed mixture may also be provided with a dideoxynucleoside triphosphate. The method may further include 5 the step of separating the primers from the templates after their extension, and repeating the steps of providing primers, extending the primers, and separating the primers.
In a related aspect, the invention features a method for amplifying DNA, including performing a polymerase chain l0 reaction in the presence of an agent able to reduce the amount of pyrophosphate in the reaction below the amount produced during a polymerase chain reaction in the absence of the agent.
Preferably, the agent is a pyrophosphatase.
In another related aspect, the invention features a method for amplifying DNA comprising the step of performing a polymerase chain reaction with a DNA polymerase, in the presence of a agent able to reduce the amount of pyrophosphate in said reaction below the amount produced during said reaction in the absence of said agent.
In another related aspect, the invention features a method for amplifying DNA including providing a solution of X29 DNA polymerase, a DNA to be amplified, and an agent able to reduce the amount of pyrophosphate in the solution below that amount produced in the absence of the agent.
In another related aspect, the invention features a method for amplifying DNA comprising providing in a solution of DNA polymerase and a DNA to be amplified an agent able to reduce the amount of pyrophosphate in said solution below the amount produced in said solution in the absence of said agent.

5a Applicants have determined that pyrophosphorolysis, where an oligonucleotide chain is reduced in length, is detrimental to a primer extension reaction. The pyrophosphorolysis is caused by the availability of pyrophosphate. For example, a polymerase chain reaction, as described by Cetus (European Patent Application 0,258,017) and by Saiki et al., 239 Science 487, 1988, is inhibited by addition of pyrophosphate even at very low concentrations.
This pyrophosphorolysis can be prevented by providing an agent, for example, a pyrophosphatase, capable of removing pyrophosphate. Addition of pyrophosphatase to a polymerase chain reaction greatly enhances the progress of that reaction, and provides superior results compared to use of the method without a pyrophosphatase. Similarly addition of a pyrophosphatase to a DNA sequencing reaction provides more uniformity in 2o~o2~s _ 6 _ intensities of bands formed in a polyacrylamide gel used to identify products of the sequencing reaction. This unirormity is due to prevention of degradation of specific DNA products by pyrophosphorolysis.
Other features and advantages of the invention will be apparent from the following description of the preferred embodiment thereof, and from the claims.
Description of the Preferred Embodiments Any agent which is capable of inhibiting a pyrophosphorolysis reaction is useful in this invention. One way to inhibit pyrophosphorolysis .s to break down any pyrophosphate that is generated during a polymerase reaction, by adding the enzyme pyrophosphatase. Even trace addition of a pyrophosphatase (one thousanth the molar ratio of ANA
polymerase molecules in a solution) to a primer extension reaction completely stabilizes oligonucieot:de fragments produced in a polymerase reaction, by preventing pyrophosphorolysis. The agent should be added at a concentration sufficient to either catalyze the hydrolysis of pyrophosphate in the reaction mixture at a rate that will prevent accumulation of pyrophosphate to a level that will lead to ~5 pyrophosphorolysis, or prevent accumulation of pyrophosphate in any other manner. The amount of agent needed is readily determined by standard techniques.
There follows an example of the use of pyrophosphatase in a polymerase chain reaction. Tris example is not limiting to this invention; those skilled in the art will reccgnize that any primer extension reaction will be benefited by ~he addition of an agent as described above. Similarly, the use of pyrophosphatase in the examples below is not limiting to WO 90/12111 ~ ~ ~ ~ ~ ~ p~/US9p/01938 '" _ 7 this invention, other agents suitable for reducing the effect of excess pyrophosphate in a primer extension reaction are readily identified by those skilled in the art. The relative ccncentrations of primer, DNA
polymerase, and pyrophosphatase suitable in the . invention are readily determined by routine experimentation, and are well known to those in the art.
It is preferable that a pyrophosphatase used is this invention be resistant to heating at high temperatures, since high temperatures are used in a polymerase chain reac~:on, for example, _emgeratures between 95°C to 100°C, althoucr te~r~neratures between 65°C and 95°C are also cemmoniy used. T:~us, it is advantageous to provide a pyrophosphate resistant to heating at 65°C to 95°C. Such a pyrophosphatase can ~e readily obtained :rom any bacteriu.~~ that is naturally able to grow and flourish at high temperatures. e.g., Thermus acuaticus. Most bacteria have naturally-occurring pyrophosphatases, and those existing in natural environments at high te:npera~ures will therefore be suitable sources of this enzyme.
Use of a pyrophosphatase in a polymerase chain reaction as described below with Taq polymerase allows the reaction to run to completion--that is, to cause depletion of all the provided deoxynucleoside triphosphates. This allows diagnostic techniques which make use of a polymerase chain reaction to be automated. Assay for progress of -he reaction can entail measurement of the generation of phosphate or the generation of DNA from the deoxynucleoside triphosphates (for example, by acid precipitation?, both of which are simple and quick assays, instead of the necessity to run a gel to detect the product of the polymerase chain reaction.

-.,. . 8 Example 1: PCR Reaction with Pyrophophatase In this example DNA termed M13 Trx-F (the actual DNA
used is not critical in this invention) was amplified by provision of a forward and reverse primer using a polymerase chain reaction as follows: This method is generally described in Saiki et al., supra. Trx-F DNA at a concentration of 0.4 picomoles was mixed with 1 ~1 Tris (1M, pH 8.5), 10 ~1 magnesium chloride (15 mM), 6.7 ~1 of four deoxynucleoside triphosphates (3 mM), 10 ~1 of forward primer (10 picomole; from ALN), 20 ~., reverse primer (10 picomole, New England BioLabs), 2 ~1 gelatin (0.5%), and 55 ~1 distilled water. 0.5 ~,l of Taq polymerase (12 units, U.S. Biochemicals, Cleveland, Ohio) was then added and the solution heated to 94°C for one minute, 50°C for one minute, and 72°C, for two minutes and this cycle of heating repeated 40 times. Identical reactions were run in the absence or presence of pyrophosphate at various concentrations (12 ~M, 37 ~M, 333 ~M, and 1 mM) and in the presence of pyrophosphatase (yeast inorganic pyrophosphatase from Sigma, Catalog No. I-4503, used without purification, or used after purification on an FPLC Mono Q* column). Another source of pyrophosphatase is Worthington yeast inorganic pyrophosphatase without further purification.
Generally, 0.001 units of yeast inorganic pyrophosphate (4ng) are suitable in a reaction as described above. This amount may of course be considerably greater, and may be less. The range of concentrations is readily determined by routine experimentation. The concentration need only be enough to lower the level of pyrophosphate below about 5-50 ~M.
In the above reaction, pyrophosphate inhibited the polymerase chain reaction at levels of 25 ~M or *Trade-mark _ g _ greater. Pyrophosphatase reversed this inhibition and stimulated production of the polymerase chain reaction products by approximately two fold.
Example 2: Preparation of Heat Resistant Pvroohos~hatase This is an example of purification of an inorganic pyrophos~hatase from cells 4f Ther~us aawaticus. Cells of T. aQUaticus were obtainl f:om ;.'.:e American Type Culture Collection. 10 lute-rs of cells were grown at 70°C using the growth medium of-Chien et al. 127 J. Bacteriol. 1550 (1976). The cells were harvested (-20 gm), resuspended in 40 m1 of~ i0%
sucrose, 50 mM ':ris riCl , pH 7.5, 5 :nM EDTA: '_y'sed by three passages through a r=erch press: and cell debris removed by centrifugation at 30,000 rpm, for 60-min in a Hecicman 50Ti rotor. The supernatant was. treated with streptomycin sulfate ~o remove DNA. 4 m1 of a 40%
streptomycin solution was added to 40 rnl supernatant.
mixed for 30 min., and centrifuged for 30 min at 8.000 rpm. The resulting supernatant was then treated wits ammonium sulfate. No pyrophosphatase activity was precipitated at 60% ammonium sulfate, but all was precipitated by'70% ammonium sulfate: To 19 mI of supernatant 7.2 gm ammonium sulfate (60%) was added.
mixed for 30 min., and spun for 30 min. at 8.000 rpm.
To the supernatant 3-gm ammonium sulfate (70%) was added, mixed for 30 min., and spun far 3~ min. at 8,000 rpm. The pellet was resusperded in 20 ml 20 m~ ~Tr is-HC1 pH _7.5. 1 mM EDTA. 10% glycerol, 10 mM 2-mer~aotoethanol (Buffer A) and then dialyzed overnight against 2 liters of Suffer A. The dialysate was passed over a DEAE DE52 column (100 m1) ecuilibrated in Buf~er A, washed witz 300 ml of Buffer A + 50 mM NaCl, and-then run in a liter gradient of buffer A containing from 50 mM to 54'0 mM

- to - 2050276 NaCl. The pyrophophatase eluted at buffer A containing 125 mM NaCl. The eluate (60 mL) was dialyzed against 2 liters of 20 mM KP04 pH 7.4, 1 mM EDTA, 10 mM
2-mercaptoethanol, l0% glycerol (Buffer H) and loaded onto a phosphocellulose column (100 ml) equilibrated is buffer B. All of the pyrophosphatase activity flowed through the column. This flow-through was then dialyzed against 20 mM Tris HCl pH 7Ø 1 mM EDTA, 10% glycerol (Buffer C), and applied to an FPLC monoQ column in buffer C. A gradient, in Buffer C, containing 100 mM
NaCl to 250 mM NaCI was :un and the pyrophosphatase activity eluted at :80 ~.M NaCl. Fractions with pyrophosphazase activity were dialyzed against 20 :nM
KP04 pH 7.4, 0.1 mM EDTr, 50% glycerol, and stored at -20°C.
This pyrophosphatase activity was not affected by 40 cycles of a polymerase chain reaction, with eacz cycle containing a 95°C. 1 min. heating step. Further, the pyrophosphatase did not hydrolyze dNTPs, nor was it inhibited by dNTPs in the reaction mixture. The pyrophosphatase activity was assayed generally as described by Chen et al. 28 Anal. Chem. 1756 (1956), and Josse. 241 J. Biol. Chem. 1938 (1966).
Other Embodiments Other embodiments are within the following claims. For example, enzymes which use a protei~ primer rather than a DNA primer, e.g., X29 DNA polymerase which polymerizes double stranded DNA, can be used to amplify DNA without need for denaturing heating steps or reannealing steps. Blanco et al., DNA replication and mutagenesis, A.S.:~. Chapter 12, 1988. Inclusion of a pyrophosphatase, or its equivalent, in such an amplification reaction will enhance the yield of DNA
amplified in this system.

Claims

THE EMBODIMENTS OF THE INVENTION IN WHICH AN EXCLUSIVE
PROPERTY OR PRIVILEGE IS CLAIMED ARE DEFINED AS FOLLOWS:

1. A solution for use in a DNA sequencing reaction, comprising a DNA polymerase, a chain-terminating agent, and an agent able to reduce the amount of pyrophosphate in a DNA
polymerization reaction mixture.

2. The solution of claim 1 wherein the DNA polymerise is chosen from Taq polymerise, a T7-type DNA polymerise, T4 DNA
polymerise, .PHI.29 DNA polymerise, T5 DNA polymerise, and reverse transcriptase.

3. The solution of claim 2, wherein said T7-type DNA
polymerise is T7 DNA polymerise.

4. The solution of claim 1 or 2, wherein said agent is an enzyme.

5. The solution of claim 4, wherein said enzyme is a pyrophosphatase.

6. The solution of claim 5, wherein said pyrophosphatase retains sufficient activity to reduce the amount of pyrophosphate in said reaction mixture at a temperature between 60°C and 95°C.

7. The solution of claim 1, wherein said chain-terminating agent is a dideoxynucleoside triphosphate.

8. A kit for use in a DNA sequencing reaction, comprising a DNA polymerise, a chain-terminating agent, and an agent able to reduce the amount of pyrophosphate in a DNA polymerization reaction mixture.

9. The kit of claim 8, wherein the DNA polymerase is chosen from Taq polymerase, a T7-type DNA polymerase, T4 DNA
polymerase, X29 DNA polymerase, T5 DNA polymerase, and reverse transcriptase.

10. The kit of claim 9, wherein said T7-type DNA
polymerase is T7 DNA polymerase.

11. The kit of claim 8 or 20, wherein said agent is an enzyme.

12. The kit of claim 11, wherein said enzyme is a pyrophosphatase.

13. The kit of claim 12, wherein said pyrophosphatase retains sufficient activity to reduce the amount of pyrophosphate in said reaction mixture at a temperature between 60°C and 95°C.

14. The kit of claim 8, wherein said chain-terminating agent is a dideoxynucleoside triphosphate.

15. An improved method for a DNA sequencing reaction, including providing a DNA polymerase, and a chain-terminating agent the improvement comprising:
providing an agent able to reduce the level of pyrophosphate below the amount produced during said extension in the absence of said agent.

16. The method of claim 15, wherein the DNA polymerase is chosen from Taq polymerase, a T7-type DNA polymerase, T4 DNA
polymerase, X29 DNA polymerase, T5 DNA polymerase, and reverse transcriptase.

17. The method of claim 15, wherein said chain-terminating agent is a dideoxynucleoside triphosphate.

18. The method of claim 15 or 16, wherein said method further comprises the steps of providing two oligonucleotide primers having first single-stranded regions and two homologous template molecules having second single-stranded regions homologous to said first single-stranded regions, and annealing said primers to said template molecules to form an annealed mixture.

19. The method of claim 18, wherein said method further comprises the step of providing said annealed mixture with said DNA polymerase and said agent to cause extension of said primers.

20. The method of claim 18, wherein said method further comprises the step of separating said primers from said template molecules after said extension to provide single-stranded molecules.

21. The method of claim 20, further comprising repeating the steps of providing two primer ologonucleotides, extending said primers, and separating said primers.

22. A method for amplifying DNA comprising the step of performing a polymerase chain reaction with a DNA polymerase, in the presence of a agent able to reduce the amount of pyrophosphate in said reaction below the amount produced during said reaction in the absence of said agent.

23. The method for amplifying DNA according to claim 22, wherein the DNA polymerase is chosen from Taq polymerase, a T7 type DNA polymerase, T4 DNA polymerase, X29 DNA polymerase, T5 DNA polymerase, and reverse transcriptase.

24. The method of claim 22 or 23, wherein said agent is a pyrophosphatase.

25. The method of claim 22, wherein said method further comprises the step of providing said annealed mixture with a dideoxynucleoside triphosphate.

26. A method for amplifying DNA comprising providing in a solution of .PHI.DNA polymerase and a DNA to be amplified an agent able to reduce the amount of pyrophosphate in said solution below the amount produced in said solution in the absence of said agent.